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Sample records for pa-08-098 functional links

  1. Linking plant and ecosystem functional biogeography

    PubMed Central

    Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D.; Kattge, Jens; Baldocchi, Dennis D.

    2014-01-01

    Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere–atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches. PMID:25225392

  2. Sperm competition: linking form to function

    PubMed Central

    2008-01-01

    Background Using information from physics, biomechanics and evolutionary biology, we explore the implications of physical constraints on sperm performance, and review empirical evidence for links between sperm length and sperm competition (where two or more males compete to fertilise a female's eggs). A common theme in the literature on sperm competition is that selection for increased sperm performance in polyandrous species will favour the evolution of longer, and therefore faster swimming, sperm. This argument is based on the common assumption that sperm swimming velocity is directly related to sperm length, due to the increased thrust produced by longer flagella. Results We critically evaluate the evidence for links between sperm morphology and swimming speed, and draw on cross-disciplinary studies to show that the assumption that velocity is directly related to sperm length will rarely be satisfied in the microscopic world in which sperm operate. Conclusion We show that increased sperm length is unlikely to be driven by selection for increased swimming speed, and that the relative lengths of a sperm's constituent parts, rather than their absolute lengths, are likely to be the target of selection. All else being equal, we suggest that a simple measure of the ratio of head to tail length should be used to assess the possible link between morphology and speed. However, this is most likely to be the case for external fertilizers in which females have relatively limited opportunity to influence a sperm's motility. PMID:19032741

  3. Linking Long Noncoding RNA Localization and Function.

    PubMed

    Chen, Ling-Ling

    2016-09-01

    Recent studies have revealed the regulatory potential of many long noncoding RNAs (lncRNAs). Most lncRNAs, like mRNAs, are transcribed by RNA polymerase II and are capped, polyadenylated, and spliced. However, the subcellular fates of lncRNAs are distinct and the mechanisms of action are diverse. Investigating the mechanisms that determine the subcellular fate of lncRNAs has the potential to provide new insights into their biogenesis and specialized functions. PMID:27499234

  4. Drosophila mechanotransduction--linking proteins and functions.

    PubMed

    Albert, Jörg T; Nadrowski, Björn; Göpfert, Martin C

    2007-01-01

    The sensation of touch, gravity, and sound all rely on dedicated ion channels that transduce mechanical stimulus forces into electrical signals. The functional workings and molecular identities of these mechanotransducer channels are little understood. Recent work shows that the mechanotransducers for fly and vertebrate hearing share equivalent gating mechanisms, whereby this mechanism can be probed non-invasively in the mechanics of the Drosophila ear. Here, we describe how this mechanics can be used to evaluate the roles of identified proteins in the process of mechanosensation and, specifically, their contributions to mechanotransduction. PMID:18820433

  5. Introduction: Links between Social Interaction and Executive Function

    ERIC Educational Resources Information Center

    Lewis, Charlie; Carpendale, Jeremy I. M.

    2009-01-01

    The term executive function is used increasingly within developmental psychology and is often taken to refer to unfolding brain processes. We trace the origins of research on executive function to show that the link with social interaction has a long history. We suggest that a recent frenzy of research exploring methods for studying individual…

  6. Stochastic choice of basis functions in adaptive function approximation and the functional-link net.

    PubMed

    Igelnik, B; Pao, Y H

    1995-01-01

    A theoretical justification for the random vector version of the functional-link (RVFL) net is presented in this paper, based on a general approach to adaptive function approximation. The approach consists of formulating a limit-integral representation of the function to be approximated and subsequently evaluating that integral with the Monte-Carlo method. Two main results are: (1) the RVFL is a universal approximator for continuous functions on bounded finite dimensional sets, and (2) the RVFL is an efficient universal approximator with the rate of approximation error convergence to zero of order O(C/ radicaln), where n is number of basis functions and with C independent of n. Similar results are also obtained for neural nets with hidden nodes implemented as products of univariate functions or radial basis functions. Some possible ways of enhancing the accuracy of multivariate function approximations are discussed.

  7. Linking changes in community composition and function under climate change.

    PubMed

    Mokany, Karel; Thomson, Joshua J; Lynch, Jasmyn J; Jordan, Gregory J; Ferrier, Simon

    2015-12-01

    Climate change is expected to directly alter the composition of communities and the functioning of ecosystems across the globe. Improving our understanding of links between biodiversity and ecosystem functioning across large spatial scales and rapid global change is a major priority to help identify management responses that will retain diverse, functioning systems. Here we address this challenge by linking projected changes in plant community composition and functional attributes (height, leaf area, seed mass) under climate change across Tasmania, Australia. Using correlative community-level modeling, we found that projected changes in plant community composition were not consistently related to projected changes in community mean trait values. In contrast, we identified specific mechanisms through which alternative combinations of projected functional and compositional change across Tasmania could be realized, including loss/replacement of functionally similar species (lowland grasslands/grassy woodlands) and loss of a small number of functionally unique species (lowland forests). Importantly, we demonstrate how these linked projections of change in community composition and functional attributes can be utilized to inform specific management actions that may assist in maintaining diverse, functioning ecosystems under climate change.

  8. The scientific process--its links, functions and problems.

    PubMed

    Kinne, O

    1988-06-01

    The scientific process comprises production, quality control, dissemination, and consumption of knowledge. Its links are represented by author, editor and referees, publisher, and user. The basic units of the scientific process are research articles, the basic substrate learned journals. The formalized scientific process provides the foundation for orderly worldwide public communication among scientists and for establishing priority in scientific findings and ideas. The functions and problems of the author-editor, editor-publisher and publisher-user connections are outlined and discussed, and suggestions are offered for reducing potentially detrimental effects of diverging link interests. PMID:3205308

  9. Orthogonal least squares based complex-valued functional link network.

    PubMed

    Amin, Md Faijul; Savitha, Ramasamy; Amin, Muhammad Ilias; Murase, Kazuyuki

    2012-08-01

    Functional link networks are single-layered neural networks that impose nonlinearity in the input layer using nonlinear functions of the original input variables. In this paper, we present a fully complex-valued functional link network (CFLN) with multivariate polynomials as the nonlinear functions. Unlike multilayer neural networks, the CFLN is free from local minima problem, and it offers very fast learning of parameters because of its linear structure. Polynomial based CFLN does not require an activation function which is a major concern in the complex-valued neural networks. However, it is important to select a smaller subset of polynomial terms (monomials) for faster and better performance since the number of all possible monomials may be quite large. Here, we use the orthogonal least squares (OLS) method in a constructive fashion (starting from lower degree to higher) for the selection of a parsimonious subset of monomials. It is argued here that computing CFLN in purely complex domain is advantageous than in double-dimensional real domain, in terms of number of connection parameters, faster design, and possibly generalization performance. Simulation results on a function approximation, wind prediction with real-world data, and a nonlinear channel equalization problem exhibit that the OLS based CFLN yields very simple structure having favorable performance.

  10. Orthogonal least squares based complex-valued functional link network.

    PubMed

    Amin, Md Faijul; Savitha, Ramasamy; Amin, Muhammad Ilias; Murase, Kazuyuki

    2012-08-01

    Functional link networks are single-layered neural networks that impose nonlinearity in the input layer using nonlinear functions of the original input variables. In this paper, we present a fully complex-valued functional link network (CFLN) with multivariate polynomials as the nonlinear functions. Unlike multilayer neural networks, the CFLN is free from local minima problem, and it offers very fast learning of parameters because of its linear structure. Polynomial based CFLN does not require an activation function which is a major concern in the complex-valued neural networks. However, it is important to select a smaller subset of polynomial terms (monomials) for faster and better performance since the number of all possible monomials may be quite large. Here, we use the orthogonal least squares (OLS) method in a constructive fashion (starting from lower degree to higher) for the selection of a parsimonious subset of monomials. It is argued here that computing CFLN in purely complex domain is advantageous than in double-dimensional real domain, in terms of number of connection parameters, faster design, and possibly generalization performance. Simulation results on a function approximation, wind prediction with real-world data, and a nonlinear channel equalization problem exhibit that the OLS based CFLN yields very simple structure having favorable performance. PMID:22386786

  11. Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function

    PubMed Central

    Schwarz, Emanuel; Izmailov, Rauf; Liò, Pietro; Meyer-Lindenberg, Andreas

    2016-01-01

    Schizophrenia is a severe and highly heritable psychiatric disorder affecting approximately 1% of the population. Genome-wide association studies have identified 108 independent genetic loci with genome-wide significance but their functional importance has yet to be elucidated. Here, we develop a novel strategy based on network analysis of protein–protein interactions (PPI) to infer biological function associated with variants most strongly linked to illness risk. We show that the schizophrenia loci are strongly linked to synaptic transmission (P FWE < .001) and ion transmembrane transport (P FWE = .03), but not to ontological categories previously found to be shared across psychiatric illnesses. We demonstrate that brain expression of risk-linked genes within the identified processes is strongly modulated during birth and identify a set of synaptic genes consistently changed across multiple brain regions of adult schizophrenia patients. These results suggest synaptic function as a developmentally determined schizophrenia process supported by the illness’s most associated genetic variants and their PPI networks. The implicated genes may be valuable targets for mechanistic experiments and future drug development approaches. PMID:27056717

  12. Integrative data-mining tools to link gene and function.

    PubMed

    El Yacoubi, Basma; de Crécy-Lagard, Valérie

    2014-01-01

    Information derived from genomic and post-genomic data can be efficiently used to link gene and function. Several web-based platforms have been developed to mine these types of data by integrating different tools. This method paper is designed to allow the user to navigate these platforms in order to make functional predictions. The main focus is on phylogenetic distribution and physical clustering tools, but other tools such as pathway reconstruction, gene fusions, and analysis of high-throughput experimental data are also surveyed.

  13. Linking biodiversity to ecosystem function: Implications for conservation ecology

    USGS Publications Warehouse

    Schwartz, M.W.; Brigham, C.A.; Hoeksema, J.D.; Lyons, K.G.; Mills, M.H.; van Mantgem, P.

    2000-01-01

    We evaluate the empirical and theoretical support for the hypothesis that a large proportion of native species richness is required to maximize ecosystem stability and sustain function. This assessment is important for conservation strategies because sustenance of ecosystem functions has been used as an argument for the conservation of species. If ecosystem functions are sustained at relatively low species richness, then arguing for the conservation of ecosystem function, no matter how important in its own right, does not strongly argue for the conservation of species. Additionally, for this to be a strong conservation argument the link between species diversity and ecosystem functions of value to the human community must be clear. We review the empirical literature to quantify the support for two hypotheses: (1) species richness is positively correlated with ecosystem function, and (2) ecosystem functions do not saturate at low species richness relative to the observed or experimental diversity. Few empirical studies demonstrate improved function at high levels of species richness. Second, we analyze recent theoretical models in order to estimate the level of species richness required to maintain ecosystem function. Again we find that, within a single trophic level, most mathematical models predict saturation of ecosystem function at a low proportion of local species richness. We also analyze a theoretical model linking species number to ecosystem stability. This model predicts that species richness beyond the first few species does not typically increase ecosystem stability. One reason that high species richness may not contribute significantly to function or stability is that most communities are characterized by strong dominance such that a few species provide the vast majority of the community biomass. Rapid turnover of species may rescue the concept that diversity leads to maximum function and stability. The role of turnover in ecosystem function and

  14. Linking community size structure and ecosystem functioning using metabolic theory

    PubMed Central

    Yvon-Durocher, Gabriel; Allen, Andrew P.

    2012-01-01

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change. PMID:23007088

  15. From Elements to Metabolism: Linking Organismal Stoichiometry to Ecosystem Function

    NASA Astrophysics Data System (ADS)

    Cohen, M. J.; Nifong, R. L.

    2014-12-01

    Metabolism is an integrative metric of ecosystem function and energetics, synthesizing the relative contributions of multiple inputs, processes, and interactions. Stoichiometry is a framework based on elemental ratios for understanding how organisms interact within ecosystems. Linking the two has the potential to yield fresh insight about how ecosystems utilize elements and energy. We sought to quantify the link between the stoichiometry of ecosystem metabolism, specifically the C:N:P ratios of integrated autotrophic assimilation, and the stoichiometric tissue ratios observed in the dominant autotrophs. Using high frequency in situ nutrient sensors we estimated the assimilatory fluxes of C, N, and P in multiple spring-fed rivers of varying autotrophic species composition. We measured autotroph cover in each spring river, collected composite vegetation samples, and evaluated tissue stoichiometry; as expected, we observed large differences in C:N and N:P between algal and vascular plant taxa. We observed associations between measured tissue stoichiometry and elemental ratios at the ecosystem scale, suggesting that aggregated assimilatory fluxes may be useful for partitioning primary production and linking organismal nutrient content to the stoichiometry of ecosystem metabolism.

  16. Mitochondrial function in the brain links anxiety with social subordination

    PubMed Central

    Hollis, Fiona; van der Kooij, Michael A.; Zanoletti, Olivia; Lozano, Laura; Cantó, Carles; Sandi, Carmen

    2015-01-01

    Dominance hierarchies are integral aspects of social groups, yet whether personality traits may predispose individuals to a particular rank remains unclear. Here we show that trait anxiety directly influences social dominance in male outbred rats and identify an important mediating role for mitochondrial function in the nucleus accumbens. High-anxious animals that are prone to become subordinate during a social encounter with a low-anxious rat exhibit reduced mitochondrial complex I and II proteins and respiratory capacity as well as decreased ATP and increased ROS production in the nucleus accumbens. A causal link for these findings is indicated by pharmacological approaches. In a dyadic contest between anxiety-matched animals, microinfusion of specific mitochondrial complex I or II inhibitors into the nucleus accumbens reduced social rank, mimicking the low probability to become dominant observed in high-anxious animals. Conversely, intraaccumbal infusion of nicotinamide, an amide form of vitamin B3 known to enhance brain energy metabolism, prevented the development of a subordinate status in high-anxious individuals. We conclude that mitochondrial function in the nucleus accumbens is crucial for social hierarchy establishment and is critically involved in the low social competitiveness associated with high anxiety. Our findings highlight a key role for brain energy metabolism in social behavior and point to mitochondrial function in the nucleus accumbens as a potential marker and avenue of treatment for anxiety-related social disorders. PMID:26621716

  17. Linking biological soil crust diversity to ecological functions

    NASA Astrophysics Data System (ADS)

    Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

    2016-04-01

    Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

  18. Mitochondrial function in the brain links anxiety with social subordination.

    PubMed

    Hollis, Fiona; van der Kooij, Michael A; Zanoletti, Olivia; Lozano, Laura; Cantó, Carles; Sandi, Carmen

    2015-12-15

    Dominance hierarchies are integral aspects of social groups, yet whether personality traits may predispose individuals to a particular rank remains unclear. Here we show that trait anxiety directly influences social dominance in male outbred rats and identify an important mediating role for mitochondrial function in the nucleus accumbens. High-anxious animals that are prone to become subordinate during a social encounter with a low-anxious rat exhibit reduced mitochondrial complex I and II proteins and respiratory capacity as well as decreased ATP and increased ROS production in the nucleus accumbens. A causal link for these findings is indicated by pharmacological approaches. In a dyadic contest between anxiety-matched animals, microinfusion of specific mitochondrial complex I or II inhibitors into the nucleus accumbens reduced social rank, mimicking the low probability to become dominant observed in high-anxious animals. Conversely, intraaccumbal infusion of nicotinamide, an amide form of vitamin B3 known to enhance brain energy metabolism, prevented the development of a subordinate status in high-anxious individuals. We conclude that mitochondrial function in the nucleus accumbens is crucial for social hierarchy establishment and is critically involved in the low social competitiveness associated with high anxiety. Our findings highlight a key role for brain energy metabolism in social behavior and point to mitochondrial function in the nucleus accumbens as a potential marker and avenue of treatment for anxiety-related social disorders.

  19. Mitochondrial function in the brain links anxiety with social subordination.

    PubMed

    Hollis, Fiona; van der Kooij, Michael A; Zanoletti, Olivia; Lozano, Laura; Cantó, Carles; Sandi, Carmen

    2015-12-15

    Dominance hierarchies are integral aspects of social groups, yet whether personality traits may predispose individuals to a particular rank remains unclear. Here we show that trait anxiety directly influences social dominance in male outbred rats and identify an important mediating role for mitochondrial function in the nucleus accumbens. High-anxious animals that are prone to become subordinate during a social encounter with a low-anxious rat exhibit reduced mitochondrial complex I and II proteins and respiratory capacity as well as decreased ATP and increased ROS production in the nucleus accumbens. A causal link for these findings is indicated by pharmacological approaches. In a dyadic contest between anxiety-matched animals, microinfusion of specific mitochondrial complex I or II inhibitors into the nucleus accumbens reduced social rank, mimicking the low probability to become dominant observed in high-anxious animals. Conversely, intraaccumbal infusion of nicotinamide, an amide form of vitamin B3 known to enhance brain energy metabolism, prevented the development of a subordinate status in high-anxious individuals. We conclude that mitochondrial function in the nucleus accumbens is crucial for social hierarchy establishment and is critically involved in the low social competitiveness associated with high anxiety. Our findings highlight a key role for brain energy metabolism in social behavior and point to mitochondrial function in the nucleus accumbens as a potential marker and avenue of treatment for anxiety-related social disorders. PMID:26621716

  20. Linking geophysics and soil function modelling - two examples

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Dietrich, P.; Behrens, T.; Schmidt, K.; Fank, J.; Kroulik, M.

    2011-12-01

    iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission within the RTD activities of the FP7 Thematic Priority Environment. The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the methodological procedure on two different examples. Example A focuses on the turnover conditions for soil organic matter (SOM) since many soil functions in a direct or indirect way depend on SOM and SOM depletion is amongst the worst soil threats. Example B deals with the dynamics of soil water and the direct influence on crop biomass production. The applied CANDY model (Franko et al. 1995) was developed to describe dynamics of soil organic matter and mineral nitrogen as well as soil water and temperature. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences (Krüger et al. 2011). The methodological procedure of example A illustrates a model application for a field site in the Czech Republic using generated soil maps from combined geophysical data. Modelling requires a complete set of soil parameters. Combining measured soil properties and data of geophysical measurements (electrical conductivity and gamma spectrometry) is the basis for digital soil mapping which provided data about clay, silt and sand as well as SOC content. With these data pedotransfer functions produce detailed soil input data (e.g. bulk and particle density, field capacity, wilting point, saturated conductivity) for the rooted soil profile. CANDY calculated different indicators for SOM and gave hints about

  1. Linking soil functions to carbon fluxes and stocks

    NASA Astrophysics Data System (ADS)

    Olesen, Jørgen E.

    2014-05-01

    Farming practices causing declining returns and inputs of carbon (C) to soils pose threats to sustainable soil functioning by reducing availability of organic matter for soil microbial activities and by affecting soil structure, and soil C stocks that contribute to regulating greenhouse gas emissions. Declines in soil C also affect availability and storage capacity of a range of essential plant nutrients thus affecting needs for external inputs. Soil degradation is considered a serious problem in Europe and a large part of the degradation is caused by agricultural activity with intensive cultivation in arable and mixed farming system contributing to several soil threats. About 45% of European soils are estimated to have low SOM content, principally in southern Europe, but also in areas of France, UK and Germany. The European SOC stocks follow a clear north to south gradient with cooler temperatures favouring higher stocks. However, SOC stocks strongly depend on soil and land management, and there is thus a potential to both increase and lose SOC, although the potential to increase SOC strongly depends on incentives and structures for implementing improved management. Understanding the role of soil C may be better conceptualised by using a soil C flow and stocks concept to assess the impact of C management on crop productivity, soil organic C stocks and other ecosystem services. This concept distinguishes C flows and stocks, which may be hypothesized to have distinctly different effects on biological, chemical and physical soil functions. By separating the roles of carbon flows from the role of carbon stocks, it may become possible to better identify critical levels not only of soil carbon stocks, but also critical levels of carbon inputs, which directly relate to needs for crop and soil management measures. Such critical soil carbon stocks may be linked to soil mineralogy through complexed organic carbon on clay and silt surfaces. Critical levels of soil carbon

  2. Linking geophysics and soil function modelling - biomass production

    NASA Astrophysics Data System (ADS)

    Krüger, J.; Franko, U.; Werban, U.; Fank, J.

    2012-04-01

    The iSOIL project aims at reliable mapping of soil properties and soil functions with various methods including geophysical, spectroscopic and monitoring techniques. The general procedure contains three steps (i) geophysical monitoring, (ii) generation of soil property maps and (iii) process modelling. The objective of this work is to demonstrate the mentioned procedure with a focus on process modelling. It deals with the dynamics of soil water and the direct influence on crop biomass production. The new module PLUS extends CANDY to simulate crop biomass production based on environmental influences. A soil function modelling with an adapted model parameterisation based on data of ground penetration radar (GPR) and conductivity (EM38) was realized. This study shows an approach to handle heterogeneity of soil properties with geophysical data used for biomass production modelling. The Austrian field site Wagna is characterised by highly heterogenic soil with fluvioglacial gravel sediments. The variation of thickness of topsoil above a sandy subsoil with gravels strongly influences the soil water balance. EM38, mounted on a mobile platform, enables to rapidly scan large areas whereas GPR requires a greater logistical effort. However, GPR can detect exact soil horizon depth between topsoil and subsoil, the combination of both results in a detailed large scale soil map. The combined plot-specific GPR and field site EM38 measurements extends the soil input data and improves the model performance of CANDY PLUS for plant biomass production (Krüger et al. 2011). The example demonstrates how geophysics provides a surplus of data for agroecosystem modelling which identifies and contributes alternative options for agricultural management decisions. iSOIL - "Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping" is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission

  3. Optimizing Linked Perceptual Class Formation and Transfer of Function

    ERIC Educational Resources Information Center

    Fields, Lanny; Garruto, Michelle

    2009-01-01

    A linked perceptual class consists of two distinct perceptual classes, A' and B', the members of which have become related to each other. For example, a linked perceptual class might be composed of many pictures of a woman (one perceptual class) and the sounds of that woman's voice (the other perceptual class). In this case, any sound of the…

  4. Testing the link between functional diversity and ecosystem functioning in a Minnesota grassland experiment.

    PubMed

    Clark, Christopher M; Flynn, Dan F B; Butterfield, Bradley J; Reich, Peter B

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao's Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness) that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture) within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD) that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao's Q, FDis, FDiv). More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system.

  5. Linking and Psychological Functioning in a Chinese Sample: The Multiple Mediation of Response to Positive Affect

    ERIC Educational Resources Information Center

    Yang, Hongfei; Li, Juan

    2016-01-01

    The present study examined the associations between linking, response to positive affect, and psychological functioning in Chinese college students. The results of conducting multiple mediation analyses indicated that emotion- and self-focused positive rumination mediated the relationship between linking and psychological functioning, whereas…

  6. Soil-borne microbiome: linking diversity to function.

    PubMed

    Mendes, Lucas W; Tsai, Siu M; Navarrete, Acácio A; de Hollander, Mattias; van Veen, Johannes A; Kuramae, Eiko E

    2015-07-01

    Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.

  7. Developmental imaging genetics: linking dopamine function to adolescent behavior.

    PubMed

    Padmanabhan, Aarthi; Luna, Beatriz

    2014-08-01

    Adolescence is a period of development characterized by numerous neurobiological changes that significantly influence behavior and brain function. Adolescence is of particular interest due to the alarming statistics indicating that mortality rates increase two to three-fold during this time compared to childhood, due largely to a peak in risk-taking behaviors resulting from increased impulsivity and sensation seeking. Furthermore, there exists large unexplained variability in these behaviors that are in part mediated by biological factors. Recent advances in molecular genetics and functional neuroimaging have provided a unique and exciting opportunity to non-invasively study the influence of genetic factors on brain function in humans. While genes do not code for specific behaviors, they do determine the structure and function of proteins that are essential to the neuronal processes that underlie behavior. Therefore, studying the interaction of genotype with measures of brain function over development could shed light on critical time points when biologically mediated individual differences in complex behaviors emerge. Here we review animal and human literature examining the neurobiological basis of adolescent development related to dopamine neurotransmission. Dopamine is of critical importance because of (1) its role in cognitive and affective behaviors, (2) its role in the pathogenesis of major psychopathology, and (3) the protracted development of dopamine signaling pathways over adolescence. We will then focus on current research examining the role of dopamine-related genes on brain function. We propose the use of imaging genetics to examine the influence of genetically mediated dopamine variability on brain function during adolescence, keeping in mind the limitations of this approach. PMID:24139694

  8. Developmental imaging genetics: linking dopamine function to adolescent behavior

    PubMed Central

    Padmanabhan, Aarthi; Luna, Beatriz

    2014-01-01

    Adolescence is a period of development characterized by numerous neurobiological changes that significantly influence behavior and brain function. Adolescence is of particular interest due to the alarming statistics indicating that mortality rates increase two to three-fold during this time compared to childhood, due largely to a peak in risk-taking behaviors resulting from increased impulsivity and sensation seeking. Furthermore, there exists large unexplained variability in these behaviors that are in part mediated by biological factors. Recent advances in molecular genetics and functional neuroimaging have provided a unique and exciting opportunity to noninvasively study the influence of genetic factors on brain function in humans. While genes do not code for specific behaviors, they do determine the structure and function of proteins that are essential to the neuronal processes that underlie behavior. Therefore, studying the interaction of genotype with measures of brain function over development could shed light on critical time points when biologically mediated individual differences in complex behaviors emerge. Here we review animal and human literature examining the neurobiological basis of adolescent development related to dopamine neurotransmission. Dopamine is of critical importance because of (1) its role in cognitive and affective behaviors, (2) its role in the pathogenesis of major psychopathology, and (3) the protracted development of dopamine signaling pathways over adolescence. We will then focus on current research examining the role of dopamine-related genes on brain function. We propose the use of imaging genetics to examine the influence of genetically mediated dopamine variability on brain function during adolescence, keeping in mind the limitations of this approach. PMID:24139694

  9. Linking stoichiometric homoeostasis with ecosystem structure, functioning and stability.

    PubMed

    Yu, Qiang; Chen, Quansheng; Elser, James J; He, Nianpeng; Wu, Honghui; Zhang, Guangming; Wu, Jianguo; Bai, Yongfei; Han, Xingguo

    2010-11-01

    Ecosystem structure, functioning and stability have been a focus of ecological and environmental sciences during the past two decades. The mechanisms underlying their relationship, however, are not well understood. Based on comprehensive studies in Inner Mongolia grassland, here we show that species-level stoichiometric homoeostasis was consistently positively correlated with dominance and stability on both 2-year and 27-year temporal scales and across a 1200-km spatial transect. At the community level, stoichiometric homoeostasis was also positively correlated with ecosystem function and stability in most cases. Thus, homoeostatic species tend to have high and stable biomass; and ecosystems dominated by more homoeostatic species have higher productivity and greater stability. By modulating organism responses to key environmental drivers, stoichiometric homoeostasis appears to be a major mechanism responsible for the structure, functioning and stability of grassland ecosystems.

  10. The origin and function of mirror neurons: the missing link.

    PubMed

    Lingnau, Angelika; Caramazza, Alfonso

    2014-04-01

    We argue, by analogy to the neural organization of the object recognition system, that demonstration of modulation of mirror neurons by associative learning does not imply absence of genetic adaptation. Innate connectivity defines the types of processes mirror neurons can participate in while allowing for extensive local plasticity. However, the proper function of these neurons remains to be worked out.

  11. Morphology and behaviour: functional links in development and evolution

    PubMed Central

    Bertossa, Rinaldo C.

    2011-01-01

    Development and evolution of animal behaviour and morphology are frequently addressed independently, as reflected in the dichotomy of disciplines dedicated to their study distinguishing object of study (morphology versus behaviour) and perspective (ultimate versus proximate). Although traits are known to develop and evolve semi-independently, they are matched together in development and evolution to produce a unique functional phenotype. Here I highlight similarities shared by both traits, such as the decisive role played by the environment for their ontogeny. Considering the widespread developmental and functional entanglement between both traits, many cases of adaptive evolution are better understood when proximate and ultimate explanations are integrated. A field integrating these perspectives is evolutionary developmental biology (evo-devo), which studies the developmental basis of phenotypic diversity. Ultimate aspects in evo-devo studies—which have mostly focused on morphological traits—could become more apparent when behaviour, ‘the integrator of form and function’, is integrated into the same framework of analysis. Integrating a trait such as behaviour at a different level in the biological hierarchy will help to better understand not only how behavioural diversity is produced, but also how levels are connected to produce functional phenotypes and how these evolve. A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed. PMID:21690124

  12. Controlled degradation of hydrogels using multi-functional cross-linking molecules.

    PubMed

    Lee, Kuen Yong; Bouhadir, Kamal H; Mooney, David J

    2004-06-01

    Hydrogels, chemically cross-linked or physically entangled, have found a number of applications as novel delivery vehicles of drugs and cells. However, the narrow ranges of degradation rates and mechanical strength currently available from many hydrogels limits their applications. We have hypothesized that utilization of multi-functional cross-linking molecules to form hydrogels could provide a wider range and tighter control over the degradation rates and mechanical stiffness of gels than bi-functional cross-linking molecules. To address the possibility, we isolated alpha-L-guluronate residues of sodium alginate, and oxidized them to prepare poly(aldehyde guluronate) (PAG). Hydrogels were formed with either poly(acrylamide-co-hydrazide) (PAH) as a multi-functional cross-linking molecule or adipic acid dihydrazide (AAD) as a bi-functional cross-linking molecule. The initial properties and degradation behavior of both PAG gel types were monitored. PAG/PAH hydrogels showed higher mechanical stiffness before degradation and degraded more slowly than PAG/AAD gels, at the same concentration of cross-linking functional groups. The enhanced mechanical stiffness and prolonged degradation behavior could be attributed to the multiple attachment points of PAH in the gel at the same concentration of functional groups. This approach to regulating gel properties with multifunctional cross-linking molecules could be broadly used in hydrogels. PMID:14751730

  13. Modeling behavior: the quest to link mechanisms to function.

    PubMed

    Janus, C; Dubnau, J

    2003-02-01

    T. Dobzhansky (1973) has been credited with saying: 'nothing in biology makes sense, except in the light of evolution'. The evolutionary conservation of gene function, as well as remarkable conservation of elemental behavioral mechanisms, guarantees that much of what we learn in one organism will inform our understanding of behavior in all animals, including humans. This insight has permitted behavior-geneticists to choose organisms based on experimental tractability for a given scientific question. IBANGS as a society has clearly embraced this Dobzhanskian worldview. As a result, the intellectual synergy of cross-species behavior-genetic analysis was palpable at the IBANGS meeting in Tours, France.

  14. Effects on Scale Linking of Different Definitions of Criterion Functions for the IRT Characteristic Curve Methods

    ERIC Educational Resources Information Center

    Kim, Seonghoon; Kolen, Michael J.

    2007-01-01

    Under item response theory, the characteristic curve methods (Haebara and Stocking-Lord methods) are used to link two ability scales from separate calibrations. The linking methods use their respective criterion functions that can be defined differently according to the symmetry- and distribution-related schemes. The symmetry-related scheme…

  15. Linked Sex Differences in Cognition and Functional Connectivity in Youth.

    PubMed

    Satterthwaite, Theodore D; Wolf, Daniel H; Roalf, David R; Ruparel, Kosha; Erus, Guray; Vandekar, Simon; Gennatas, Efstathios D; Elliott, Mark A; Smith, Alex; Hakonarson, Hakon; Verma, Ragini; Davatzikos, Christos; Gur, Raquel E; Gur, Ruben C

    2015-09-01

    Sex differences in human cognition are marked, but little is known regarding their neural origins. Here, in a sample of 674 human participants ages 9-22, we demonstrate that sex differences in cognitive profiles are related to multivariate patterns of resting-state functional connectivity MRI (rsfc-MRI). Males outperformed females on motor and spatial cognitive tasks; females were faster in tasks of emotion identification and nonverbal reasoning. Sex differences were also prominent in the rsfc-MRI data at multiple scales of analysis, with males displaying more between-module connectivity, while females demonstrated more within-module connectivity. Multivariate pattern analysis using support vector machines classified subject sex on the basis of their cognitive profile with 63% accuracy (P < 0.001), but was more accurate using functional connectivity data (71% accuracy; P < 0.001). Moreover, the degree to which a given participant's cognitive profile was "male" or "female" was significantly related to the masculinity or femininity of their pattern of brain connectivity (P = 2.3 × 10(-7)). This relationship was present even when considering males and female separately. Taken together, these results demonstrate for the first time that sex differences in patterns of cognition are in part represented on a neural level through divergent patterns of brain connectivity.

  16. Multipolar functions of BCL-2 proteins link energetics to apoptosis

    PubMed Central

    Hardwick, J. Marie; Chen, Ying-bei; Jonas, Elizabeth A.

    2012-01-01

    Classical apoptotic cell death is now sufficiently well understood to be interrogated with mathematical modeling and to be skillfully manipulated with targeted drugs for clinical benefit. However, a biological black hole has emerged with the realization that apoptosis regulators are functionally multipolar. BCL-2 family proteins appear to have much greater effects on cells than can be explained by their known roles in apoptosis. While these effects may be observable simply because the cell is not dead, the general assumption is that BCL-2 proteins have yet undiscovered biochemical activities. Conversely, these yet uncharacterized day-jobs may underlie their profound effects on cell survival, challenging current assumptions about classical apoptosis. Even their sub-mitochondrial localizations remain controversial. Here we attempt to integrate seemingly conflicting information with the prospect that BCL-2 proteins themselves may be the critical crosstalk between life and death. PMID:22560661

  17. Linking vegetation structure, function and physiology through spectroscopic remote sensing

    NASA Astrophysics Data System (ADS)

    Serbin, S.; Singh, A.; Couture, J. J.; Shiklomanov, A. N.; Rogers, A.; Desai, A. R.; Kruger, E. L.; Townsend, P. A.

    2015-12-01

    Terrestrial ecosystem process models require detailed information on ecosystem states and canopy properties to properly simulate the fluxes of carbon (C), water and energy from the land to the atmosphere and assess the vulnerability of ecosystems to perturbations. Current models fail to adequately capture the magnitude, spatial variation, and seasonality of terrestrial C uptake and storage, leading to significant uncertainties in the size and fate of the terrestrial C sink. By and large, these parameter and process uncertainties arise from inadequate spatial and temporal representation of plant traits, vegetation structure, and functioning. With increases in computational power and changes to model architecture and approaches, it is now possible for models to leverage detailed, data rich and spatially explicit descriptions of ecosystems to inform parameter distributions and trait tradeoffs. In this regard, spectroscopy and imaging spectroscopy data have been shown to be invaluable observational datasets to capture broad-scale spatial and, eventually, temporal dynamics in important vegetation properties. We illustrate the linkage of plant traits and spectral observations to supply key data constraints for model parameterization. These constraints can come either in the form of the raw spectroscopic data (reflectance, absorbtance) or physiological traits derived from spectroscopy. In this presentation we highlight our ongoing work to build ecological scaling relationships between critical vegetation characteristics and optical properties across diverse and complex canopies, including temperate broadleaf and conifer forests, Mediterranean vegetation, Arctic systems, and agriculture. We focus on work at the leaf, stand, and landscape scales, illustrating the importance of capturing the underlying variability in a range of parameters (including vertical variation within canopies) to enable more efficient scaling of traits related to functional diversity of ecosystems.

  18. Glutamatergic Neurotransmission Links Sensitivity to Volatile Anesthetics with Mitochondrial Function.

    PubMed

    Zimin, Pavel I; Woods, Christian B; Quintana, Albert; Ramirez, Jan-Marino; Morgan, Philip G; Sedensky, Margaret M

    2016-08-22

    An enigma of modern medicine has persisted for over 150 years. The mechanisms by which volatile anesthetics (VAs) produce their effects (loss of consciousness, analgesia, amnesia, and immobility) remain an unsolved mystery. Many attractive putative molecular targets have failed to produce a significant effect when genetically tested in whole-animal models [1-3]. However, mitochondrial defects increase VA sensitivity in diverse organisms from nematodes to humans [4-6]. Ndufs4 knockout (KO) mice lack a subunit of mitochondrial complex I and are strikingly hypersensitive to VAs yet resistant to the intravenous anesthetic ketamine [7]. The change in VA sensitivity is the largest reported for a mammal. Limiting NDUFS4 loss to a subset of glutamatergic neurons recapitulates the VA hypersensitivity of Ndufs4(KO) mice, while loss in GABAergic or cholinergic neurons does not. Baseline electrophysiologic function of CA1 pyramidal neurons does not differ between Ndufs4(KO) and control mice. Isoflurane concentrations that anesthetize only Ndufs4(KO) mice (0.6%) decreased the frequency of spontaneous excitatory postsynaptic currents (sEPSCs) only in Ndufs4(KO) CA1 neurons, while concentrations effective in control mice (1.2%) decreased sEPSC frequencies in both control and Ndufs4(KO) CA1 pyramidal cells. Spontaneous inhibitory postsynaptic currents (sIPSCs) were not differentially affected between genotypes. The effects of isoflurane were similar on evoked field excitatory postsynaptic potentials (fEPSPs) and paired pulse facilitation (PPF) in KO and control hippocampal slices. We propose that CA1 presynaptic excitatory neurotransmission is hypersensitive to isoflurane in Ndufs4(KO) mice due to the inhibition of pre-existing reduced complex I function, reaching a critical reduction that can no longer meet metabolic demands. PMID:27498564

  19. Growth Points in Linking Representations of Function: A Research-Based Framework

    ERIC Educational Resources Information Center

    Ronda, Erlina

    2015-01-01

    This paper describes five growth points in linking representations of function developed from a study of secondary school learners. Framed within the cognitivist perspective and process-object conception of function, the growth points were identified and described based on linear and quadratic function tasks learners can do and their strategies…

  20. Practical Application of a Synthetic Linking Function on Small-Sample Equating

    ERIC Educational Resources Information Center

    Kim, Sooyeon; von Davier, Alina A.; Haberman, Shelby

    2011-01-01

    The synthetic function is a weighted average of the identity (the linking function for forms that are known to be completely parallel) and a traditional equating method. The purpose of the present study was to investigate the benefits of the synthetic function on small-sample equating using various real data sets gathered from different…

  1. New scavenger resin for the reversible linking and monoprotection of functionalized aromatic aldehydes.

    PubMed

    Zhu, Mingzhao; Ruijter, Eelco; Wessjohann, Ludger A

    2004-10-28

    [reaction: see text] Polymer-supported benzylhydrazines were synthesized using poly(ethylene glycol) acrylamide (PEGA) resin. They can be used to scavenge electrophiles reactive with hydrazine. Especially aromatic aldehydes can be captured selectively, monoprotected, and reversibly linked in the presence of other functional groups, including electrophilic ones. Various reactions can be performed on these protectively linked aldehydes, which afterward can be released either with full restoration of the aldehyde function or, alternatively, with simultaneous conversion.

  2. Flexible Link Functions in Nonparametric Binary Regression with Gaussian Process Priors

    PubMed Central

    Li, Dan; Lin, Lizhen; Dey, Dipak K.

    2015-01-01

    Summary In many scientific fields, it is a common practice to collect a sequence of 0-1 binary responses from a subject across time, space, or a collection of covariates. Researchers are interested in finding out how the expected binary outcome is related to covariates, and aim at better prediction in the future 0-1 outcomes. Gaussian processes have been widely used to model nonlinear systems; in particular to model the latent structure in a binary regression model allowing nonlinear functional relationship between covariates and the expectation of binary outcomes. A critical issue in modeling binary response data is the appropriate choice of link functions. Commonly adopted link functions such as probit or logit links have fixed skewness and lack the flexibility to allow the data to determine the degree of the skewness. To address this limitation, we propose a flexible binary regression model which combines a generalized extreme value link function with a Gaussian process prior on the latent structure. Bayesian computation is employed in model estimation. Posterior consistency of the resulting posterior distribution is demonstrated. The flexibility and gains of the proposed model are illustrated through detailed simulation studies and two real data examples. Empirical results show that the proposed model outperforms a set of alternative models, which only have either a Gaussian process prior on the latent regression function or a Dirichlet prior on the link function. PMID:26686333

  3. Flexible link functions in nonparametric binary regression with Gaussian process priors.

    PubMed

    Li, Dan; Wang, Xia; Lin, Lizhen; Dey, Dipak K

    2016-09-01

    In many scientific fields, it is a common practice to collect a sequence of 0-1 binary responses from a subject across time, space, or a collection of covariates. Researchers are interested in finding out how the expected binary outcome is related to covariates, and aim at better prediction in the future 0-1 outcomes. Gaussian processes have been widely used to model nonlinear systems; in particular to model the latent structure in a binary regression model allowing nonlinear functional relationship between covariates and the expectation of binary outcomes. A critical issue in modeling binary response data is the appropriate choice of link functions. Commonly adopted link functions such as probit or logit links have fixed skewness and lack the flexibility to allow the data to determine the degree of the skewness. To address this limitation, we propose a flexible binary regression model which combines a generalized extreme value link function with a Gaussian process prior on the latent structure. Bayesian computation is employed in model estimation. Posterior consistency of the resulting posterior distribution is demonstrated. The flexibility and gains of the proposed model are illustrated through detailed simulation studies and two real data examples. Empirical results show that the proposed model outperforms a set of alternative models, which only have either a Gaussian process prior on the latent regression function or a Dirichlet prior on the link function. PMID:26686333

  4. Socioeconomic Risk Moderates the Link between Household Chaos and Maternal Executive Function

    PubMed Central

    Deater-Deckard, Kirby; Chen, Nan; Wang, Zhe; Bell, Martha Ann

    2012-01-01

    We examined the link between household chaos (i.e., noise, clutter, disarray, lack of routines) and maternal executive function (i.e., effortful regulation of attention and memory), and whether it varied as a function of socioeconomic risk (i.e., single parenthood, lower mother and father educational attainment, housing situation, and father unemployment). We hypothesized that: 1) higher levels of household chaos would be linked with poorer maternal executive function, even when controlling for other measures of cognitive functioning (e.g., verbal ability), and 2) this link would be strongest in the most socioeconomically distressed or lowest-socioeconomic status households. The diverse sample included 153 mothers from urban and rural areas who completed a questionnaire and a battery of cognitive executive function tasks and a verbal ability task in the laboratory. Results were mixed for hypothesis 1, and consistent with hypothesis 2. Two-thirds of the variance overlapped between household chaos and maternal executive function, but only in families with high levels of socioeconomic risk. This pattern was not found for chaos and maternal verbal ability, suggesting that the potentially deleterious effects of household chaos may be specific to maternal executive function. The findings implicate household chaos as a powerful statistical predictor of maternal executive function in socioeconomically distressed contexts. PMID:22563703

  5. Cross-Linked Conjugated Polymer Fibrils: Robust Nanowires from Functional Polythiophene Diblock Copolymers

    SciTech Connect

    Hammer, Brenton A. G.; Bokel, Felicia A.; Hayward, Ryan C.; Emrick, Todd

    2011-09-27

    A series of poly(3-hexyl thiophene) (P3HT)-based diblock copolymers were prepared and examined in solution for their assembly into fibrils, and post-assembly cross-linking into robust nanowire structures. P3HT-b-poly(3-methanol thiophene) (P3MT), and P3HT-b-poly(3-aminopropyloxymethyl thiophene) (P3AmT) diblock copolymers were synthesized using Grignard metathesis (GRIM) polymerization. Fibrils formed from solution assembly of these copolymers are thus decorated with hydroxyl and amine functionality, and cross-linking is achieved by reaction of diisocyanates with the hydroxyl and amine groups. A variety of cross-linked structures, characterized by transmission electron microscopy (TEM), were produced by this method, including dense fibrillar sheets, fibril bundles, or predominately individual fibrils, depending on the chosen reaction conditions. In solution, the cross-linked fibrils maintained their characteristic vibronic structure in solvents that would normally disrupt (dissolve) the structures.

  6. Direct Patterning of Organic Functional Polymers through Conventional Photolithography and Noninvasive Cross-Link Agents.

    PubMed

    Squillaci, Marco A; Qiu, Feng; Aliprandi, Alessandro; Zhang, Fan; Feng, Xinliang; Samorì, Paolo

    2016-07-01

    A new technique for direct patterning of functional organic polymers using commercial photolithography setups with a minimal loss of the materials' performances is reported. This result is achieved through novel cross-link agents made by boron- and fluorine-containing heterocycles that can react between themselves upon UV- and white-light exposure.

  7. Remission of Depression in Parents: Links to Healthy Functioning in Their Children

    ERIC Educational Resources Information Center

    Garber, Judy; Ciesla, Jeff A.; McCauley, Elizabeth; Diamond, Guy; Schloredt, Kelly A.

    2011-01-01

    This study examined whether improvement in parents' depression was linked with changes in their children's depressive symptoms and functioning. Participants were 223 parents and children ranging in age from 7 to 17 years old (M = 12.13, SD = 2.31); 126 parents were in treatment for depression and 97 parents were nondepressed. Children were…

  8. Exploring Population Sensitivity of Linking Functions across Three Law School Admission Test Administrations

    ERIC Educational Resources Information Center

    Liu, Mei; Holland, Paul W.

    2008-01-01

    The simplified version of the Dorans and Holland (2000) measure of population invariance, the root mean square difference (RMSD), is used to explore the degree of dependence of linking functions on the Law School Admission Test (LSAT) subpopulations defined by examinees' gender, ethnic background, geographic region, law school application status,…

  9. Geochip: A high throughput genomic tool for linking community structure to functions

    SciTech Connect

    Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe; Zhou, Jizhong

    2009-01-30

    GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis.

  10. Functional analysis of N-linking oligosaccharyl transferase enzymes encoded by deep-sea vent proteobacteria.

    PubMed

    Mills, Dominic C; Jervis, Adrian J; Abouelhadid, Sherif; Yates, Laura E; Cuccui, Jon; Linton, Dennis; Wren, Brendan W

    2016-04-01

    Bacterial N-linking oligosaccharyl transferases (OTase enzymes) transfer lipid-linked glycans to selected proteins in the periplasm and were first described in the intestinal pathogen Campylobacter jejuni, a member of the ε-proteobacteria-subdivision of bacteria. More recently, orthologues from other ε-proteobacterial Campylobacter and Helicobacter species and a δ-proteobacterium, Desulfovibrio desulfuricans, have been described, suggesting that these two subdivisions of bacteria may be a source of further N-linked protein glycosylation systems. Whole-genome sequencing of both ε- and δ-proteobacteria from deep-sea vent habitats, a rich source of species from these subdivisions, revealed putative ORFs encoding OTase enzymes and associated adjacent glycosyltransferases similar to the C. jejuni N-linked glycosylation locus. We expressed putative OTase ORFs from the deep-sea vent species Nitratiruptor tergarcus, Sulfurovum lithotrophicum and Deferribacter desulfuricans in Escherichia coli and showed that they were able to functionally complement the C. jejuni OTase, CjPglB. The enzymes were shown to possess relaxed glycan specificity, transferring diverse glycan structures and demonstrated different glycosylation sequon specificities. Additionally, a permissive D. desulfuricans acceptor protein was identified, and we provide evidence that the N-linked glycan synthesized by N. tergarcus and S. lithotrophicum contains an acetylated sugar at the reducing end. This work demonstrates that deep-sea vent bacteria encode functional N-glycosylation machineries and are a potential source of biotechnologically important OTase enzymes. PMID:26610891

  11. Functional analysis of N-linking oligosaccharyl transferase enzymes encoded by deep-sea vent proteobacteria

    PubMed Central

    Mills, Dominic C.; Jervis, Adrian J.; Abouelhadid, Sherif; Yates, Laura E.; Cuccui, Jon; Linton, Dennis; Wren, Brendan W.

    2016-01-01

    Bacterial N-linking oligosaccharyl transferases (OTase enzymes) transfer lipid-linked glycans to selected proteins in the periplasm and were first described in the intestinal pathogen Campylobacter jejuni, a member of the ε-proteobacteria-subdivision of bacteria. More recently, orthologues from other ε-proteobacterial Campylobacter and Helicobacter species and a δ-proteobacterium, Desulfovibrio desulfuricans, have been described, suggesting that these two subdivisions of bacteria may be a source of further N-linked protein glycosylation systems. Whole-genome sequencing of both ε- and δ-proteobacteria from deep-sea vent habitats, a rich source of species from these subdivisions, revealed putative ORFs encoding OTase enzymes and associated adjacent glycosyltransferases similar to the C. jejuni N-linked glycosylation locus. We expressed putative OTase ORFs from the deep-sea vent species Nitratiruptor tergarcus, Sulfurovum lithotrophicum and Deferribacter desulfuricans in Escherichia coli and showed they were able to functionally complement the C. jejuni OTase, CjPglB . The enzymes were shown to possess relaxed glycan specificity, transferring diverse glycan structures and demonstrated different glycosylation sequon specificities. Additionally a permissive D. desulfuricans acceptor protein was identified, and we provide evidence that the N-linked glycan synthesised by N. tergarcus and S. lithotrophicum contains an acetylated sugar at the reducing end. This work demonstrates that deep-sea vent bacteria encode functional N-glycosylation machineries and are a potential source of biotechnologically important OTase enzymes. PMID:26610891

  12. Summary goodness-of-fit statistics for binary generalized linear models with noncanonical link functions.

    PubMed

    Canary, Jana D; Blizzard, Leigh; Barry, Ronald P; Hosmer, David W; Quinn, Stephen J

    2016-05-01

    Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness-of-fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (TG), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer-Lemeshow (HL) and Pigeon-Heyse (J(2) ) statistics can be applied directly. In a simulation study, TG, HL, and J(2) were used to evaluate the fit of probit, log-log, complementary log-log, and log models, all calculated with a common grouping method. The TG statistic consistently maintained Type I error rates, while those of HL and J(2) were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, TG had more power than HL or J(2) . PMID:26584470

  13. Summary goodness-of-fit statistics for binary generalized linear models with noncanonical link functions.

    PubMed

    Canary, Jana D; Blizzard, Leigh; Barry, Ronald P; Hosmer, David W; Quinn, Stephen J

    2016-05-01

    Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness-of-fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (TG), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer-Lemeshow (HL) and Pigeon-Heyse (J(2) ) statistics can be applied directly. In a simulation study, TG, HL, and J(2) were used to evaluate the fit of probit, log-log, complementary log-log, and log models, all calculated with a common grouping method. The TG statistic consistently maintained Type I error rates, while those of HL and J(2) were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, TG had more power than HL or J(2) .

  14. Trophic links between functional groups of arable plants and beetles are stable at a national scale.

    PubMed

    Brooks, David R; Storkey, Jonathan; Clark, Suzanne J; Firbank, Les G; Petit, Sandrine; Woiwod, Ian P

    2012-01-01

    1. There is an urgent need to accurately model how environmental change affects the wide-scale functioning of ecosystems, but advances are hindered by a lack of knowledge of how trophic levels are linked across space. It is unclear which theoretical approach to take to improve modelling of such interactions, but evidence is gathering that linking species responses to their functional traits can increase understanding of ecosystem dynamics. Currently, there are no quantitative studies testing how this approach might improve models of multiple, trophically interacting species, at wide spatial scales. 2. Arable weeds play a foundational role in linking food webs, providing resources for many taxa, including carabid beetles that feed on their seeds and weed-associated invertebrate prey. Here, we model associations between weeds and carabids across farmland in Great Britain (GB), to test the hypothesis that wide-scale trophic links between these groups are structured by their species functional traits. 3. A network of c. 250 arable fields, covering four crops and most lowland areas of GB, was sampled for weed, carabid and invertebrate taxa over 3 years. Data sets of these groups were closely matched in time and space, and each contained numerous species with a range of eco-physiological traits. The consistency of trophic linkages between multiple taxa sharing functional traits was tested within multivariate and log-linear models. 4. Robust links were established between the functional traits of taxa and their trophic interactions. Autumn-germinating, small-seeded weeds were associated with smaller, spring-breeding carabids, more specialised in seed feeding, whereas spring-germinating, large-seeded weeds were associated with a range of larger, autumn-breeding omnivorous carabids. These relationships were strong and dynamic, being independent of changes in invertebrate food resources and consistent across sample dates, crops and regions of GB. 5. We conclude that, in at

  15. Estimating marginal and incremental effects on health outcomes using flexible link and variance function models.

    PubMed

    Basu, Anirban; Rathouz, Paul J

    2005-01-01

    We propose an extension to the estimating equations in generalized linear models to estimate parameters in the link function and variance structure simultaneously with regression coefficients. Rather than focusing on the regression coefficients, the purpose of these models is inference about the mean of the outcome as a function of a set of covariates, and various functionals of the mean function used to measure the effects of the covariates. A commonly used functional in econometrics, referred to as the marginal effect, is the partial derivative of the mean function with respect to any covariate, averaged over the empirical distribution of covariates in the model. We define an analogous parameter for discrete covariates. The proposed estimation method not only helps to identify an appropriate link function and to suggest an underlying distribution for a specific application but also serves as a robust estimator when no specific distribution for the outcome measure can be identified. Using Monte Carlo simulations, we show that the resulting parameter estimators are consistent. The method is illustrated with an analysis of inpatient expenditure data from a study of hospitalists.

  16. Single proteins that serve linked functions in intracellular and extracellular microenvironments

    SciTech Connect

    Radisky, Derek C.; Stallings-Mann, Melody; Hirai, Yohei; Bissell, Mina J.

    2009-06-03

    Maintenance of organ homeostasis and control of appropriate response to environmental alterations requires intimate coordination of cellular function and tissue organization. An important component of this coordination may be provided by proteins that can serve distinct, but linked, functions on both sides of the plasma membrane. Here we present a novel hypothesis in which non-classical secretion can provide a mechanism through which single proteins can integrate complex tissue functions. Single genes can exert a complex, dynamic influence through a number of different processes that act to multiply the function of the gene product(s). Alternative splicing can create many different transcripts that encode proteins of diverse, even antagonistic, function from a single gene. Posttranslational modifications can alter the stability, activity, localization, and even basic function of proteins. A protein can exist in different subcellular localizations. More recently, it has become clear that single proteins can function both inside and outside the cell. These proteins often lack defined secretory signal sequences, and transit the plasma membrane by mechanisms separate from the classical ER/Golgi secretory process. When examples of such proteins are examined individually, the multifunctionality and lack of a signal sequence are puzzling - why should a protein with a well known function in one context function in such a distinct fashion in another? We propose that one reason for a single protein to perform intracellular and extracellular roles is to coordinate organization and maintenance of a global tissue function. Here, we describe in detail three specific examples of proteins that act in this fashion, outlining their specific functions in the extracellular space and in the intracellular space, and we discuss how these functions may be linked. We present epimorphin/syntaxin-2, which may coordinate morphogenesis of secretory organs (as epimorphin) with control of

  17. Distributed intrusion monitoring system with fiber link backup and on-line fault diagnosis functions

    NASA Astrophysics Data System (ADS)

    Xu, Jiwei; Wu, Huijuan; Xiao, Shunkun

    2014-12-01

    A novel multi-channel distributed optical fiber intrusion monitoring system with smart fiber link backup and on-line fault diagnosis functions was proposed. A 1× N optical switch was intelligently controlled by a peripheral interface controller (PIC) to expand the fiber link from one channel to several ones to lower the cost of the long or ultra-long distance intrusion monitoring system and also to strengthen the intelligent monitoring link backup function. At the same time, a sliding window auto-correlation method was presented to identify and locate the broken or fault point of the cable. The experimental results showed that the proposed multi-channel system performed well especially whenever any a broken cable was detected. It could locate the broken or fault point by itself accurately and switch to its backup sensing link immediately to ensure the security system to operate stably without a minute idling. And it was successfully applied in a field test for security monitoring of the 220-km-length national borderline in China.

  18. Thermoreversible physical gels of poly(dimethylsiloxane) without cross-links or functionalization.

    PubMed

    Dahan, Elianne; Sundararajan, Pudupadi R

    2013-07-01

    The preparation of gels of poly(dimethylsiloxane) (PDMS) reported in the literature so far involves catalysts and chemical cross-links (chemical gels) or functionalization with organogelators. We report that thermoreversible physical gels of PDMS, without cross-links or functionalization, can be made with propylamine or hexylamine as a solvent. The gels consist of spherical domains as small as 20 nm. We show that these spherical domains are part of a network. Differential scanning calorimetry (DSC), optical microscopy, and rheology show that the gel is thermoreversible. With the DSC experiments, we have devised a procedure to achieve thermoreversibility with very similar gel-sol transition endotherms in the first and second heating cycles. PMID:23799797

  19. CRISPR/Cas9 Promotes Functional Study of Testis Specific X-Linked Gene In Vivo

    PubMed Central

    Jiang, Xue; Chen, Yuxi; Zhang, Zhen; Zhang, Xiya; Liang, Puping; Zhan, Shaoquan; Cao, Shanbo; Songyang, Zhou; Huang, Junjiu

    2015-01-01

    Mammalian spermatogenesis is a highly regulated multistage process of sperm generation. It is hard to uncover the real function of a testis specific gene in vitro since the in vitro model is not yet mature. With the development of the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9) system, we can now rapidly generate knockout mouse models of testis specific genes to study the process of spermatogenesis in vivo. SYCP3-like X-linked 2 (SLX2) is a germ cell specific component, which contains a Cor1 domain and belongs to the XLR (X-linked, lymphocyte regulated) family. Previous studies suggested that SLX2 might play an important role in mouse spermatogenesis based on its subcellular localization and interacting proteins. However, the function of SLX2 in vivo is still elusive. Here, to investigate the functions of SLX2 in spermatogenesis, we disrupted the Slx2 gene by using the CRISPR/Cas9 system. Since Slx2 is a testis specific X-linked gene, we obtained knockout male mice in the first generation and accelerated the study process. Compared with wild-type mice, Slx2 knockout mice have normal testis and epididymis. Histological observation of testes sections showed that Slx2 knockout affected none of the three main stages of spermatogenesis: mitosis, meiosis and spermiogenesis. In addition, we further confirmed that disruption of Slx2 did not affect the number of spermatogonial stem cells, meiosis progression or XY body formation by immunofluorescence analysis. As spermatogenesis was normal in Slx2 knockout mice, these mice were fertile. Taken together, we showed that Slx2 itself is not an essential gene for mouse spermatogenesis and CRISPR/Cas9 technique could speed up the functional study of testis specific X-linked gene in vivo. PMID:26599493

  20. Linking structure and function in food webs: maximization of different ecological functions generates distinct food web structures.

    PubMed

    Yen, Jian D L; Cabral, Reniel B; Cantor, Mauricio; Hatton, Ian; Kortsch, Susanne; Patrício, Joana; Yamamichi, Masato

    2016-03-01

    Trophic interactions are central to ecosystem functioning, but the link between food web structure and ecosystem functioning remains obscure. Regularities (i.e. consistent patterns) in food web structure suggest the possibility of regularities in ecosystem functioning, which might be used to relate structure to function. We introduce a novel, genetic algorithm approach to simulate food webs with maximized throughput (a proxy for ecosystem functioning) and compare the structure of these simulated food webs to real empirical food webs using common metrics of food web structure. We repeat this analysis using robustness to secondary extinctions (a proxy for ecosystem resilience) instead of throughput to determine the relative contributions of ecosystem functioning and ecosystem resilience to food web structure. Simulated food webs that maximized robustness were similar to real food webs when connectance (i.e. levels of interaction across the food web) was high, but this result did not extend to food webs with low connectance. Simulated food webs that maximized throughput or a combination of throughput and robustness were not similar to any real food webs. Simulated maximum-throughput food webs differed markedly from maximum-robustness food webs, which suggests that maximizing different ecological functions can generate distinct food web structures. Based on our results, food web structure would appear to have a stronger relationship with ecosystem resilience than with ecosystem throughput. Our genetic algorithm approach is general and is well suited to large, realistically complex food webs. Genetic algorithms can incorporate constraints on structure and can generate outputs that can be compared directly to empirical data. Our method can be used to explore a range of maximization or minimization hypotheses, providing new perspectives on the links between structure and function in ecological systems.

  1. Fluorescent structural DNA nanoballs functionalized with phosphate-linked nucleotide triphosphates.

    PubMed

    Anderson, Jon P; Reynolds, Bambi L; Baum, Kristin; Williams, John G

    2010-03-10

    Highly labeled DNA nanoballs functionalized with phosphate-linked nucleotide triphosphates (dNTPs) were developed as a source of dNTPs for DNA polymerase. The particles were prepared by strand-displacement polymerization from a self-complementary circular template. Imaged by atomic force microscopy, these functionalized particles appear as condensed fuzzy balls with diameters between 50 and 150 nm. They emit a bright fluorescent signal, detected in 2 ms exposures with a signal-to-noise ratio of 25 when imaged using a TIR fluorescence microscope. PMID:20158249

  2. Fluorescent Structural DNA Nanoballs Functionalized With Phosphate-Linked Nucleotide Triphosphates

    PubMed Central

    Anderson, Jon P.; Reynolds, Bambi L.; Baum, Kristin; Williams, John G.

    2010-01-01

    Highly labeled DNA nanoballs functionalized with phosphate-linked nucleotide triphosphates (dNTPs) were developed as a source of dNTPs for DNA polymerase. The particles were prepared by strand-displacement polymerization from a self-complementary circular template. Imaged by atomic force microscopy, these functionalized particles appear as condensed fuzzy balls with diameters between 50–150 nm. They emit a bright fluorescent signal, detected in 2 msec exposures with a signal-to-noise of 25 when imaged using a TIR fluorescence microscope. PMID:20158249

  3. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

    PubMed

    Spencer, Sarah J; Tamminen, Manu V; Preheim, Sarah P; Guo, Mira T; Briggs, Adrian W; Brito, Ilana L; A Weitz, David; Pitkänen, Leena K; Vigneault, Francois; Juhani Virta, Marko P; Alm, Eric J

    2016-02-01

    Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells. PMID:26394010

  4. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

    PubMed Central

    Spencer, Sarah J; Tamminen, Manu V; Preheim, Sarah P; Guo, Mira T; Briggs, Adrian W; Brito, Ilana L; A Weitz, David; Pitkänen, Leena K; Vigneault, Francois; Virta, Marko PJuhani; Alm, Eric J

    2016-01-01

    Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells. PMID:26394010

  5. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

    PubMed

    Spencer, Sarah J; Tamminen, Manu V; Preheim, Sarah P; Guo, Mira T; Briggs, Adrian W; Brito, Ilana L; A Weitz, David; Pitkänen, Leena K; Vigneault, Francois; Juhani Virta, Marko P; Alm, Eric J

    2016-02-01

    Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.

  6. Gauging and Tuning Cross-Linking Kinetics of Catechol-PEG Adhesives via Catecholamine Functionalization.

    PubMed

    Paez, Julieta I; Ustahüseyin, Oya; Serrano, Cristina; Ton, Xuan-Anh; Shafiq, Zahid; Auernhammer, Günter K; d'Ischia, Marco; del Campo, Aránzazu

    2015-12-14

    The curing time of an adhesive material is determined by the polymerization and cross-linking kinetics of the adhesive formulation and needs to be optimized for the particular application. Here, we explore the possibility of tuning the polymerization kinetics and final mechanical properties of tissue-adhesive PEG gels formed by polymerization of end-functionalized star-PEGs with catecholamines with varying substituents. We show strong differences in cross-linking time and cohesiveness of the final gels among the catecholamine-PEG variants. Installation of an electron-withdrawing but π-electron donating chloro substituent on the catechol ring resulted in faster and more efficient cross-linking, while opposite effects were observed with the strongly electron-withdrawing nitro group. Chain substitution slowed down the kinetics and hindered cross-linking due either to chain breakdown (β-OH group, in norepinephrine) or intramolecular cyclization (α-carboxyl group, in DOPA). Interesting perspectives derive from use of mixtures of catecholamine-PEG precursors offering further opportunities for fine-tuning of the curing parameters. These are interesting properties for the application of catecholamine-PEG gels as tissue glues or biomaterials for cell encapsulation. PMID:26583428

  7. Phylogenetic and functional potential links pH and N2O emissions in pasture soils

    PubMed Central

    Samad, M. d. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

    2016-01-01

    Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2. PMID:27782174

  8. ChIP bias as a function of cross-linking time.

    PubMed

    Baranello, Laura; Kouzine, Fedor; Sanford, Suzanne; Levens, David

    2016-05-01

    The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins in vivo. Formaldehyde cross-linking of DNA and proteins is a critical step required to trap their interactions inside the cells before immunoprecipitation and analysis. Yet insufficient attention has been given to variables that might give rise to artifacts in this procedure, such as the duration of cross-linking. We analyzed the dependence of the ChIP signal on the duration of formaldehyde cross-linking time for two proteins: DNA topoisomerase 1 (Top1) that is functionally associated with the double helix in vivo, especially with active chromatin, and green fluorescent protein (GFP) that has no known bona fide interactions with DNA. With short time of formaldehyde fixation, only Top1 immunoprecipation efficiently recovered DNA from active promoters, whereas prolonged fixation augmented non-specific recovery of GFP dramatizing the need to optimize ChIP protocols to minimize the time of cross-linking, especially for abundant nuclear proteins. Thus, ChIP is a powerful approach to study the localization of protein on the genome when care is taken to manage potential artifacts. PMID:26685864

  9. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties.

    PubMed

    Powell, Jeff R; Welsh, Allana; Hallin, Sara

    2015-07-01

    Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAIC(c) = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAIC(c) = 12.02], and the abundance of one denitrifier genotype [ΔAIC(c) = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). This approach provides a valuable tool for explicitly linking microbial communities to ecosystem functioning. By making this link, we have demonstrated that including aspects of microbial community structure and diversity in biogeochemical models can improve predictions of nutrient cycling in ecosystems and enhance our understanding of ecosystem functionality.

  10. Crucial role of detailed function, task, timeline, link and human vulnerability analyses in HRA

    SciTech Connect

    Ryan, T.G.; Haney, L.N.; Ostrom, L.T.

    1992-10-01

    This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.

  11. What are the Links Between Maternal Social Status, Hippocampal Function, and HPA Axis Function in Children?

    PubMed Central

    Sheridan, Margaret A.; How, Joan; Araujo, Melanie; Schamberg, Michelle A.; Nelson, Charles A.

    2013-01-01

    The association of parental social status with multiple health and achievement indicators in adulthood has driven researchers to attempt to identify mechanisms by which social experience in childhood could shift developmental trajectories. Some accounts for observed linkages between parental social status in childhood and health have hypothesized that early stress exposure could result in chronic disruptions in hypothalamic-pituitary-adrenal (HPA) axis activation, and that this activation could lead to long term changes. A robust literature in adult animals has demonstrated that chronic HPA axis activation leads to changes in hippocampal structure and function. In the current study, consistent with studies in animals, we observe an association between both maternal self-rated social status and hippocampal activation in children and between maternal self-rated social status and salivary cortisol in children. PMID:24033572

  12. Epigenetic Function of Activation-Induced Cytidine Deaminase and Its Link to Lymphomagenesis

    PubMed Central

    Dominguez, Pilar M.; Shaknovich, Rita

    2014-01-01

    Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination of immunoglobulin (Ig) genes during B cell maturation and immune response. Expression of AID is tightly regulated due to its mutagenic and recombinogenic potential, which is known to target not only Ig genes, but also non-Ig genes, contributing to lymphomagenesis. In recent years, a new epigenetic function of AID and its link to DNA demethylation came to light in several developmental systems. In this review, we summarize existing evidence linking deamination of unmodified and modified cytidine by AID to base-excision repair and mismatch repair machinery resulting in passive or active removal of DNA methylation mark, with the focus on B cell biology. We also discuss potential contribution of AID-dependent DNA hypomethylation to lymphomagenesis. PMID:25566255

  13. Links between adolescent sympathetic and parasympathetic nervous system functioning and interpersonal behavior over time.

    PubMed

    Diamond, Lisa M; Cribbet, Matthew R

    2013-06-01

    Extensive research has investigated links between individual differences in youths' autonomic nervous system (ANS) functioning and psychological outcomes related to emotion regulation, yet little of this research has examined developmental change. The study tested whether individual differences in youths' tonic and stress-induced ANS functioning, assessed at age 14, and changes in ANS functioning from age 14 to 16 predicted corresponding changes in youths' behavioral warmth, as displayed during videotaped mother-child conflict interactions conducted at age 14 and 16. Increased behavioral warmth was predicted by increased baseline respiratory sinus arrhythmia (RSA), increased SCL stress reactivity, decreased RSA stress reactivity (i.e., greater vagal suppression), and decreased baseline SCL. There was also an interaction between RSA stress reactivity at age 14 and changes in maternal warmth from age 14 to 16, such that increased maternal warmth was only associated with increased adolescent warmth for adolescents with lower RSA stress reactivity at age 14.

  14. Longitudinal links between childhood peer victimization, internalizing and externalizing problems, and academic functioning: developmental cascades.

    PubMed

    Vaillancourt, Tracy; Brittain, Heather L; McDougall, Patricia; Duku, Eric

    2013-11-01

    Developmental cascade models linking childhood peer victimization, internalizing and externalizing problems, and academic functioning were examined in a sample of 695 children assessed in Grade 3 (academic only) and Grades 5, 6, 7, and 8. Results revealed several complex patterns of associations in which poorer functioning in one domain influenced poorer outcomes in other areas. For example, a symptom driven pathway was consistently found with internalizing problems predicting future peer victimization. Support for an academic incompetence model was also found-- lower GPA in Grade 5, 6, and 7 was associated with more externalizing issues in the following year, and poor writing performance in Grade 3 predicted lower grades in Grade 5, which in turn predicted more externalizing problems in Grade 6. Results highlight the need to examine bidirectional influences and multifarious transactions that exist between peer victimization, mental health, and academic functioning over time. PMID:23907699

  15. Non-dipolar gauge links for transverse-momentum-dependent pion wave functions

    NASA Astrophysics Data System (ADS)

    Wang, Yu-Ming

    2016-03-01

    I discuss the factorization-compatible definitions of transverse-momentumdependent (TMD) pion wave functions which are fundamental theory inputs entering QCD factorization formulae for many hard exclusive processes. I will first demonstrate that the soft subtraction factor introduced to remove both rapidity and pinch singularities can be greatly reduced by making the maximal use of the freedom to construct the Wilson-line paths when defining the TMD wave functions. I will then turn to show that the newly proposed TMD definition with non-dipolarWilson lines is equivalent to the one with dipolar gauge links and with a complicated soft function, to all orders of the perturbative expansion in the strong coupling, as far as the infrared behavior is concerned.

  16. Unconventional N-Linked Glycosylation Promotes Trimeric Autotransporter Function in Kingella kingae and Aggregatibacter aphrophilus

    PubMed Central

    Rempe, Katherine A.; Spruce, Lynn A.; Porsch, Eric A.; Seeholzer, Steven H.; Nørskov-Lauritsen, Niels

    2015-01-01

    ABSTRACT Glycosylation is a widespread mechanism employed by both eukaryotes and bacteria to increase the functional diversity of their proteomes. The nontypeable Haemophilus influenzae glycosyltransferase HMW1C mediates unconventional N-linked glycosylation of the adhesive protein HMW1, which is encoded in a two-partner secretion system gene cluster that also encodes HMW1C. In this system, HMW1 is modified in the cytoplasm by sequential transfer of hexose residues. In the present study, we examined Kingella kingae and Aggregatibacter aphrophilus homologues of HMW1C that are not encoded near a gene encoding an obvious acceptor protein. We found both homologues to be functional glycosyltransferases and identified their substrates as the K. kingae Knh and the A. aphrophilus EmaA trimeric autotransporter proteins. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed multiple sites of N-linked glycosylation on Knh and EmaA. Without glycosylation, Knh and EmaA failed to facilitate wild-type levels of bacterial autoaggregation or adherence to human epithelial cells, establishing that glycosylation is essential for proper protein function. PMID:26307167

  17. Linking Resting-State Networks in the Prefrontal Cortex to Executive Function: A Functional Near Infrared Spectroscopy Study

    PubMed Central

    Zhao, Jia; Liu, Jiangang; Jiang, Xin; Zhou, Guifei; Chen, Guowei; Ding, Xiao P.; Fu, Genyue; Lee, Kang

    2016-01-01

    Executive function (EF) plays vital roles in our everyday adaptation to the ever-changing environment. However, limited existing studies have linked EF to the resting-state brain activity. The functional connectivity in the resting state between the sub-regions of the brain can reveal the intrinsic neural mechanisms involved in cognitive processing of EF without disturbance from external stimuli. The present study investigated the relations between the behavioral executive function (EF) scores and the resting-state functional network topological properties in the Prefrontal Cortex (PFC). We constructed complex brain functional networks in the PFC from 90 healthy young adults using functional near infrared spectroscopy (fNIRS). We calculated the correlations between the typical network topological properties (regional topological properties and global topological properties) and the scores of both the Total EF and components of EF measured by computer-based Cambridge Neuropsychological Test Automated Battery (CANTAB). We found that the Total EF scores were positively correlated with regional properties in the right dorsal superior frontal gyrus (SFG), whereas the opposite pattern was found in the right triangular inferior frontal gyrus (IFG). Different EF components were related to different regional properties in various PFC areas, such as planning in the right middle frontal gyrus (MFG), working memory mainly in the right MFG and triangular IFG, short-term memory in the left dorsal SFG, and task switch in the right MFG. In contrast, there were no significant findings for global topological properties. Our findings suggested that the PFC plays an important role in individuals' behavioral performance in the executive function tasks. Further, the resting-state functional network can reveal the intrinsic neural mechanisms involved in behavioral EF abilities. PMID:27774047

  18. Adversity in childhood linked to elevated striatal dopamine function in adulthood.

    PubMed

    Egerton, Alice; Valmaggia, Lucia R; Howes, Oliver D; Day, Fern; Chaddock, Christopher A; Allen, Paul; Winton-Brown, Toby T; Bloomfield, Michael A P; Bhattacharyya, Sagnik; Chilcott, Jack; Lappin, Julia M; Murray, Robin M; McGuire, Philip

    2016-10-01

    Childhood adversity increases the risk of psychosis in adulthood. Theoretical and animal models suggest that this effect may be mediated by increased striatal dopamine neurotransmission. The primary objective of this study was to examine the relationship between adversity in childhood and striatal dopamine function in early adulthood. Secondary objectives were to compare exposure to childhood adversity and striatal dopamine function in young people at ultra high risk (UHR) of psychosis and healthy volunteers. Sixty-seven young adults, comprising 47 individuals at UHR for psychosis and 20 healthy volunteers were recruited from the same geographic area and were matched for age, gender and substance use. Presynaptic dopamine function in the associative striatum was assessed using 18F-DOPA positron emission tomography. Childhood adversity was assessed using the Childhood Experience of Care and Abuse questionnaire. Within the sample as a whole, both severe physical or sexual abuse (T63=2.92; P=0.005), and unstable family arrangements (T57=2.80; P=0.007) in childhood were associated with elevated dopamine function in the associative striatum in adulthood. Comparison of the UHR and volunteer subgroups revealed similar incidence of childhood adverse experiences, and there was no significant group difference in dopamine function. This study provides evidence that childhood adversity is linked to elevated striatal dopamine function in adulthood. PMID:27344984

  19. Linked-cluster expansion for the Green's function of the infinite-U Hubbard model.

    PubMed

    Khatami, Ehsan; Perepelitsky, Edward; Rigol, Marcos; Shastry, B Sriram

    2014-06-01

    We implement a highly efficient strong-coupling expansion for the Green's function of the Hubbard model. In the limit of extreme correlations, where the onsite interaction is infinite, the evaluation of diagrams simplifies dramatically enabling us to carry out the expansion to the eighth order in powers of the hopping amplitude. We compute the finite-temperature Green's function analytically in the momentum and Matsubara frequency space as a function of the electron density. Employing Padé approximations, we study the equation of state, Kelvin thermopower, momentum distribution function, quasiparticle fraction, and quasiparticle lifetime of the system at temperatures lower than, or of the order of, the hopping amplitude. We also discuss several different approaches for obtaining the spectral functions through analytic continuation of the imaginary frequency Green's function, and show results for the system near half filling. We benchmark our results for the equation of state against those obtained from a numerical linked-cluster expansion carried out to the eleventh order. PMID:25019906

  20. Intermediate closed state for glycine receptor function revealed by cysteine cross-linking

    PubMed Central

    Prevost, Marie S.; Moraga-Cid, Gustavo; Van Renterghem, Catherine; Edelstein, Stuart J.; Changeux, Jean-Pierre; Corringer, Pierre-Jean

    2013-01-01

    Pentameric ligand-gated ion channels (pLGICs) mediate signal transmission by coupling the binding of extracellular ligands to the opening of their ion channel. Agonist binding elicits activation and desensitization of pLGICs, through several conformational states, that are, thus far, incompletely characterized at the structural level. We previously reported for GLIC, a prokaryotic pLGIC, that cross-linking of a pair of cysteines at both sides of the extracellular and transmembrane domain interface stabilizes a locally closed (LC) X-ray structure. Here, we introduced the homologous pair of cysteines on the human α1 glycine receptor. We show by electrophysiology that cysteine cross-linking produces a gain-of-function phenotype characterized by concomitant constitutive openings, increased agonist potency, and equalization of efficacies of full and partial agonists. However, it also produces a reduction of maximal currents at saturating agonist concentrations without change of the unitary channel conductance, an effect reversed by the positive allosteric modulator propofol. The cross-linking thus favors a unique closed state distinct from the resting and longest-lived desensitized states. Fitting the data according to a three-state allosteric model suggests that it could correspond to a LC conformation. Its plausible assignment to a gating intermediate or a fast-desensitized state is discussed. Overall, our data show that relative movement of two loops at the extracellular-transmembrane interface accompanies orthosteric agonist-mediated gating. PMID:24085847

  1. Linking Executive Function and Peer Problems from Early Childhood Through Middle Adolescence.

    PubMed

    Holmes, Christopher J; Kim-Spoon, Jungmeen; Deater-Deckard, Kirby

    2016-01-01

    Peer interactions and executive function play central roles in the development of healthy children, as peer problems have been indicative of lower cognitive competencies such as self-regulatory behavior and poor executive function has been indicative of problem behaviors and social dysfunction. However, few studies have focused on the relation between peer interactions and executive function and the underlying mechanisms that may create this link. Using a national sample (n = 1164, 48.6% female) from the Study of Early Child Care and Youth Development (SECCYD), we analyzed executive function and peer problems (including victimization and rejection) across three waves within each domain (executive function or peer problems), beginning in early childhood and ending in middle adolescence. Executive function was measured as a multi-method, multi-informant composite including reports from parents on the Children's Behavior Questionnaire and Child Behavior Checklist and child's performance on behavioral tasks including the Continuous Performance Task, Woodcock-Johnson, Tower of Hanoi, Operation Span Task, Stroop, and Tower of London. Peer problems were measured as a multi-informant composite including self, teacher, and afterschool caregiver reports on multiple peer-relationship scales. Using a cross-lagged design, our Structural Equation Modeling findings suggested that experiencing peer problems contributed to lower executive function later in childhood and better executive function reduced the likelihood of experiencing peer problems later in childhood and middle adolescence, although these relations weakened as a child moves into adolescence. The results highlight that peer relationships are involved in the development of strengths and deficits in executive function and vice versa. PMID:26096194

  2. Linking Executive Function and Peer Problems from Early Childhood Through Middle Adolescence.

    PubMed

    Holmes, Christopher J; Kim-Spoon, Jungmeen; Deater-Deckard, Kirby

    2016-01-01

    Peer interactions and executive function play central roles in the development of healthy children, as peer problems have been indicative of lower cognitive competencies such as self-regulatory behavior and poor executive function has been indicative of problem behaviors and social dysfunction. However, few studies have focused on the relation between peer interactions and executive function and the underlying mechanisms that may create this link. Using a national sample (n = 1164, 48.6% female) from the Study of Early Child Care and Youth Development (SECCYD), we analyzed executive function and peer problems (including victimization and rejection) across three waves within each domain (executive function or peer problems), beginning in early childhood and ending in middle adolescence. Executive function was measured as a multi-method, multi-informant composite including reports from parents on the Children's Behavior Questionnaire and Child Behavior Checklist and child's performance on behavioral tasks including the Continuous Performance Task, Woodcock-Johnson, Tower of Hanoi, Operation Span Task, Stroop, and Tower of London. Peer problems were measured as a multi-informant composite including self, teacher, and afterschool caregiver reports on multiple peer-relationship scales. Using a cross-lagged design, our Structural Equation Modeling findings suggested that experiencing peer problems contributed to lower executive function later in childhood and better executive function reduced the likelihood of experiencing peer problems later in childhood and middle adolescence, although these relations weakened as a child moves into adolescence. The results highlight that peer relationships are involved in the development of strengths and deficits in executive function and vice versa.

  3. Linking EEG signals, brain functions and mental operations: Advantages of the Laplacian transformation.

    PubMed

    Vidal, Franck; Burle, Boris; Spieser, Laure; Carbonnell, Laurence; Meckler, Cédric; Casini, Laurence; Hasbroucq, Thierry

    2015-09-01

    Electroencephalography (EEG) is a very popular technique for investigating brain functions and/or mental processes. To this aim, EEG activities must be interpreted in terms of brain and/or mental processes. EEG signals being a direct manifestation of neuronal activity it is often assumed that such interpretations are quite obvious or, at least, straightforward. However, they often rely on (explicit or even implicit) assumptions regarding the structures supposed to generate the EEG activities of interest. For these assumptions to be used appropriately, reliable links between EEG activities and the underlying brain structures must be established. Because of volume conduction effects and the mixture of activities they induce, these links are difficult to establish with scalp potential recordings. We present different examples showing how the Laplacian transformation, acting as an efficient source separation method, allowed to establish more reliable links between EEG activities and brain generators and, ultimately, with mental operations. The nature of those links depends on the depth of inferences that can vary from weak to strong. Along this continuum, we show that 1) while the effects of experimental manipulation can appear widely distributed with scalp potentials, Laplacian transformation allows to reveal several generators contributing (in different manners) to these modulations, 2) amplitude variations within the same set of generators can generate spurious differences in scalp potential topographies, often interpreted as reflecting different source configurations. In such a case, Laplacian transformation provides much more similar topographies, evidencing the same generator(s) set, and 3) using the LRP as an index of response activation most often produces ambiguous results, Laplacian-transformed response-locked ERPs obtained over motor areas allow resolving these ambiguities. PMID:25958789

  4. Linking EEG signals, brain functions and mental operations: Advantages of the Laplacian transformation.

    PubMed

    Vidal, Franck; Burle, Boris; Spieser, Laure; Carbonnell, Laurence; Meckler, Cédric; Casini, Laurence; Hasbroucq, Thierry

    2015-09-01

    Electroencephalography (EEG) is a very popular technique for investigating brain functions and/or mental processes. To this aim, EEG activities must be interpreted in terms of brain and/or mental processes. EEG signals being a direct manifestation of neuronal activity it is often assumed that such interpretations are quite obvious or, at least, straightforward. However, they often rely on (explicit or even implicit) assumptions regarding the structures supposed to generate the EEG activities of interest. For these assumptions to be used appropriately, reliable links between EEG activities and the underlying brain structures must be established. Because of volume conduction effects and the mixture of activities they induce, these links are difficult to establish with scalp potential recordings. We present different examples showing how the Laplacian transformation, acting as an efficient source separation method, allowed to establish more reliable links between EEG activities and brain generators and, ultimately, with mental operations. The nature of those links depends on the depth of inferences that can vary from weak to strong. Along this continuum, we show that 1) while the effects of experimental manipulation can appear widely distributed with scalp potentials, Laplacian transformation allows to reveal several generators contributing (in different manners) to these modulations, 2) amplitude variations within the same set of generators can generate spurious differences in scalp potential topographies, often interpreted as reflecting different source configurations. In such a case, Laplacian transformation provides much more similar topographies, evidencing the same generator(s) set, and 3) using the LRP as an index of response activation most often produces ambiguous results, Laplacian-transformed response-locked ERPs obtained over motor areas allow resolving these ambiguities.

  5. Perception of affective prosody in major depression: a link to executive functions?

    PubMed

    Uekermann, Jennifer; Abdel-Hamid, Mona; Lehmkämper, Caroline; Vollmoeller, Wolfgang; Daum, Irene

    2008-07-01

    Major depression is associated with impairments of executive functions and affect perception deficits, both being linked to dysfunction of fronto-subcortical networks. So far, little is known about the relationship between cognitive and affective deficits in major depression. In the present investigation, affect perception and executive functions were assessed in 29 patients with a diagnosis of major depression (Dep) and 29 healthy controls (HC). Both groups were comparable on IQ, age, and gender distribution. Depressed patients showed deficits of perception of affective prosody, which were significantly related to inhibition, set shifting, and working memory. Our findings suggest a significant association between cognitive deficits and affect perception impairments in major depression, which may be of considerable clinical relevance and might be addressed in treatment approaches. Future studies are desirable to investigate the nature of the association in more detail.

  6. Efficient estimation and prediction for the Bayesian binary spatial model with flexible link functions.

    PubMed

    Roy, Vivekananda; Evangelou, Evangelos; Zhu, Zhengyuan

    2016-03-01

    Spatial generalized linear mixed models (SGLMMs) are popular models for spatial data with a non-Gaussian response. Binomial SGLMMs with logit or probit link functions are often used to model spatially dependent binomial random variables. It is known that for independent binomial data, the robit regression model provides a more robust (against extreme observations) alternative to the more popular logistic and probit models. In this article, we introduce a Bayesian spatial robit model for spatially dependent binomial data. Since constructing a meaningful prior on the link function parameter as well as the spatial correlation parameters in SGLMMs is difficult, we propose an empirical Bayes (EB) approach for the estimation of these parameters as well as for the prediction of the random effects. The EB methodology is implemented by efficient importance sampling methods based on Markov chain Monte Carlo (MCMC) algorithms. Our simulation study shows that the robit model is robust against model misspecification, and our EB method results in estimates with less bias than full Bayesian (FB) analysis. The methodology is applied to a Celastrus Orbiculatus data, and a Rhizoctonia root data. For the former, which is known to contain outlying observations, the robit model is shown to do better for predicting the spatial distribution of an invasive species. For the latter, our approach is doing as well as the classical models for predicting the disease severity for a root disease, as the probit link is shown to be appropriate. Though this article is written for Binomial SGLMMs for brevity, the EB methodology is more general and can be applied to other types of SGLMMs. In the accompanying R package geoBayes, implementations for other SGLMMs such as Poisson and Gamma SGLMMs are provided. PMID:26331903

  7. Efficient estimation and prediction for the Bayesian binary spatial model with flexible link functions.

    PubMed

    Roy, Vivekananda; Evangelou, Evangelos; Zhu, Zhengyuan

    2016-03-01

    Spatial generalized linear mixed models (SGLMMs) are popular models for spatial data with a non-Gaussian response. Binomial SGLMMs with logit or probit link functions are often used to model spatially dependent binomial random variables. It is known that for independent binomial data, the robit regression model provides a more robust (against extreme observations) alternative to the more popular logistic and probit models. In this article, we introduce a Bayesian spatial robit model for spatially dependent binomial data. Since constructing a meaningful prior on the link function parameter as well as the spatial correlation parameters in SGLMMs is difficult, we propose an empirical Bayes (EB) approach for the estimation of these parameters as well as for the prediction of the random effects. The EB methodology is implemented by efficient importance sampling methods based on Markov chain Monte Carlo (MCMC) algorithms. Our simulation study shows that the robit model is robust against model misspecification, and our EB method results in estimates with less bias than full Bayesian (FB) analysis. The methodology is applied to a Celastrus Orbiculatus data, and a Rhizoctonia root data. For the former, which is known to contain outlying observations, the robit model is shown to do better for predicting the spatial distribution of an invasive species. For the latter, our approach is doing as well as the classical models for predicting the disease severity for a root disease, as the probit link is shown to be appropriate. Though this article is written for Binomial SGLMMs for brevity, the EB methodology is more general and can be applied to other types of SGLMMs. In the accompanying R package geoBayes, implementations for other SGLMMs such as Poisson and Gamma SGLMMs are provided.

  8. Functional Divergence in the Role of N-Linked Glycosylation in Smoothened Signaling

    PubMed Central

    Marada, Suresh; Navarro, Gemma; Truong, Ashley; Stewart, Daniel P.; Arensdorf, Angela M.; Nachtergaele, Sigrid; Angelats, Edgar; Opferman, Joseph T.; Rohatgi, Rajat; McCormick, Peter J.; Ogden, Stacey K.

    2015-01-01

    The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice. PMID:26291458

  9. Current topics of functional links between primary cilia and cell cycle.

    PubMed

    Izawa, Ichiro; Goto, Hidemasa; Kasahara, Kousuke; Inagaki, Masaki

    2015-01-01

    Primary cilia, microtubule-based sensory structures, orchestrate various critical signals during development and tissue homeostasis. In view of the rising interest into the reciprocal link between ciliogenesis and cell cycle, we discuss here several recent advances to understand the molecular link between the individual step of ciliogenesis and cell cycle control. At the onset of ciliogenesis (the transition from centrosome to basal body), distal appendage proteins have been established as components indispensable for the docking of vesicles at the mother centriole. In the initial step of axonemal extension, CP110, Ofd1, and trichoplein, key negative regulators of ciliogenesis, are found to be removed by a kinase-dependent mechanism, autophagy, and ubiquitin-proteasome system, respectively. Of note, their disposal functions as a restriction point to decide that the axonemal nucleation and extension begin. In the elongation step, Nde1, a negative regulator of ciliary length, is revealed to be ubiquitylated and degraded by CDK5-SCF(Fbw7) in a cell cycle-dependent manner. With regard to ciliary length control, it has been uncovered in flagellar shortening of Chlamydomonas that cilia itself transmit a ciliary length signal to cytoplasm. At the ciliary resorption step upon cell cycle re-entry, cilia are found to be disassembled not only by Aurora A-HDAC6 pathway but also by Nek2-Kif24 and Plk1-Kif2A pathways through their microtubule-depolymerizing activity. On the other hand, it is becoming evident that the presence of primary cilia itself functions as a structural checkpoint for cell cycle re-entry. These data suggest that ciliogenesis and cell cycle intimately link each other, and further elucidation of these mechanisms will contribute to understanding the pathology of cilia-related disease including cancer and discovering targets of therapeutic interventions. PMID:26719793

  10. Regressive evolution of the arthropod tritocerebral segment linked to functional divergence of the Hox gene labial

    PubMed Central

    Pechmann, Matthias; Schwager, Evelyn E.; Turetzek, Natascha; Prpic, Nikola-Michael

    2015-01-01

    The intercalary segment is a limbless version of the tritocerebral segment and is present in the head of all insects, whereas other extant arthropods have retained limbs on their tritocerebral segment (e.g. the pedipalp limbs in spiders). The evolutionary origin of limb loss on the intercalary segment has puzzled zoologists for over a century. Here we show that an intercalary segment-like phenotype can be created in spiders by interfering with the function of the Hox gene labial. This links the origin of the intercalary segment to a functional change in labial. We show that in the spider Parasteatoda tepidariorum the labial gene has two functions: one function in head tissue maintenance that is conserved between spiders and insects, and a second function in pedipalp limb promotion and specification, which is only present in spiders. These results imply that labial was originally crucial for limb formation on the tritocerebral segment, but that it has lost this particular subfunction in the insect ancestor, resulting in limb loss on the intercalary segment. Such loss of a subfunction is a way to avoid adverse pleiotropic effects normally associated with mutations in developmental genes, and may thus be a common mechanism to accelerate regressive evolution. PMID:26311666

  11. Dopamine D2 receptor availability is linked to hippocampal–caudate functional connectivity and episodic memory

    PubMed Central

    Nyberg, Lars; Karalija, Nina; Salami, Alireza; Andersson, Micael; Wåhlin, Anders; Kaboovand, Neda; Köhncke, Ylva; Axelsson, Jan; Rieckmann, Anna; Papenberg, Goran; Garrett, Douglas D.; Riklund, Katrine; Lövdén, Martin; Bäckman, Lars

    2016-01-01

    D1 and D2 dopamine receptors (D1DRs and D2DRs) may contribute differently to various aspects of memory and cognition. The D1DR system has been linked to functions supported by the prefrontal cortex. By contrast, the role of the D2DR system is less clear, although it has been hypothesized that D2DRs make a specific contribution to hippocampus-based cognitive functions. Here we present results from 181 healthy adults between 64 and 68 y of age who underwent comprehensive assessment of episodic memory, working memory, and processing speed, along with MRI and D2DR assessment with [11C]raclopride and PET. Caudate D2DR availability was positively associated with episodic memory but not with working memory or speed. Whole-brain analyses further revealed a relation between hippocampal D2DR availability and episodic memory. Hippocampal and caudate D2DR availability were interrelated, and functional MRI-based resting-state functional connectivity between the ventral caudate and medial temporal cortex increased as a function of caudate D2DR availability. Collectively, these findings indicate that D2DRs make a specific contribution to hippocampus-based cognition by influencing striatal and hippocampal regions, and their interactions. PMID:27339132

  12. Dopamine D2 receptor availability is linked to hippocampal-caudate functional connectivity and episodic memory.

    PubMed

    Nyberg, Lars; Karalija, Nina; Salami, Alireza; Andersson, Micael; Wåhlin, Anders; Kaboovand, Neda; Köhncke, Ylva; Axelsson, Jan; Rieckmann, Anna; Papenberg, Goran; Garrett, Douglas D; Riklund, Katrine; Lövdén, Martin; Lindenberger, Ulman; Bäckman, Lars

    2016-07-12

    D1 and D2 dopamine receptors (D1DRs and D2DRs) may contribute differently to various aspects of memory and cognition. The D1DR system has been linked to functions supported by the prefrontal cortex. By contrast, the role of the D2DR system is less clear, although it has been hypothesized that D2DRs make a specific contribution to hippocampus-based cognitive functions. Here we present results from 181 healthy adults between 64 and 68 y of age who underwent comprehensive assessment of episodic memory, working memory, and processing speed, along with MRI and D2DR assessment with [(11)C]raclopride and PET. Caudate D2DR availability was positively associated with episodic memory but not with working memory or speed. Whole-brain analyses further revealed a relation between hippocampal D2DR availability and episodic memory. Hippocampal and caudate D2DR availability were interrelated, and functional MRI-based resting-state functional connectivity between the ventral caudate and medial temporal cortex increased as a function of caudate D2DR availability. Collectively, these findings indicate that D2DRs make a specific contribution to hippocampus-based cognition by influencing striatal and hippocampal regions, and their interactions. PMID:27339132

  13. Regressive evolution of the arthropod tritocerebral segment linked to functional divergence of the Hox gene labial.

    PubMed

    Pechmann, Matthias; Schwager, Evelyn E; Turetzek, Natascha; Prpic, Nikola-Michael

    2015-09-01

    The intercalary segment is a limbless version of the tritocerebral segment and is present in the head of all insects, whereas other extant arthropods have retained limbs on their tritocerebral segment (e.g. the pedipalp limbs in spiders). The evolutionary origin of limb loss on the intercalary segment has puzzled zoologists for over a century. Here we show that an intercalary segment-like phenotype can be created in spiders by interfering with the function of the Hox gene labial. This links the origin of the intercalary segment to a functional change in labial. We show that in the spider Parasteatoda tepidariorum the labial gene has two functions: one function in head tissue maintenance that is conserved between spiders and insects, and a second function in pedipalp limb promotion and specification, which is only present in spiders. These results imply that labial was originally crucial for limb formation on the tritocerebral segment, but that it has lost this particular subfunction in the insect ancestor, resulting in limb loss on the intercalary segment. Such loss of a subfunction is away to avoid adverse pleiotropic effects normally associated with mutations in developmental genes, and may thus be a common mechanism to accelerate regressive evolution.

  14. Using plant functional traits as a link between land use and bee foraging abundance

    NASA Astrophysics Data System (ADS)

    Pakeman, R. J.; Stockan, J.

    2013-07-01

    Many recent studies have shown that plant functional traits can be used to predict the response of plant assemblages to management or other environmental change. A further challenge is to use them to predict changes in the assemblages of other groups. Using data from a study of the impact of land use on biodiversity, the linkages between management drivers, a range of plant functional traits and the overall foraging numbers and assemblage of bees was assessed. Bee foraging numbers were only weakly predicted by plant traits, though bee foraging assemblage was closely related to a number of different groups of plant traits (flower colour and Forage Index, as well as taxonomic group). In turn, the selected traits were significantly correlated to some of the response traits that linked the plant assemblage to management, indicating that there was a predictive pathway from management to bee abundance and assemblage structure. However, models developed with just the environmental drivers proved superior at predicting both bee numbers and assemblage. Plant traits proved to be a moderately effective predictor of bee assemblage structure. However, the use of plant traits as a link between the bees and management did not offer any improvement on models directly developed from management variables. This suggests that the bee assemblage is responding to traits that have not been quantified and that developing these trophic linkage models may have to take a different approach.

  15. Removal of anionic azo dyes from aqueous solution by functional ionic liquid cross-linked polymer.

    PubMed

    Gao, Hejun; Kan, Taotao; Zhao, Siyuan; Qian, Yixia; Cheng, Xiyuan; Wu, Wenli; Wang, Xiaodong; Zheng, Liqiang

    2013-10-15

    A novel functional ionic liquid based cross-linked polymer (PDVB-IL) was synthesized from 1-aminoethyl-3-vinylimidazolium chloride and divinylbenzene for use as an adsorbent. The physicochemical properties of PDVB-IL were investigated by Fourier transform infrared spectroscopy, scanning electron microscopy and thermogravimetric analysis. The adsorptive capacity was investigated using anionic azo dyes of orange II, sunset yellow FCF, and amaranth as adsorbates. The maximum adsorption capacity could reach 925.09, 734.62, and 547.17 mg/g for orange II, sunset yellow FCF and amaranth at 25°C, respectively, which are much better than most of the other adsorbents reported earlier. The effect of pH value was investigated in the range of 1-8. The result shows that a low pH value is found to favor the adsorption of those anionic azo dyes. The adsorption kinetics and isotherms are well fitted by a pseudo second-order model and Langmuir model, respectively. The adsorption process is found to be dominated by physisorption. The introduction of functional ionic liquid moieties into cross-linked poly(divinylbenzene) polymer constitutes a new and efficient kind of adsorbent.

  16. Functional characterization of Sporothrix schenckii glycosidases involved in the N-linked glycosylation pathway.

    PubMed

    Lopes-Bezerra, Leila M; Lozoya-Pérez, Nancy E; López-Ramírez, Luz A; Martínez-Álvarez, José A; Teixeira, Marcus M; Felipe, Maria S S; Flores-Carreón, Arturo; Mora-Montes, Héctor M

    2015-01-01

    Protein glycosylation pathways are conserved metabolic processes in eukaryotic organisms and are required for cell fitness. In fungal pathogens, the N-linked glycosylation pathway is indispensable for proper cell wall composition and virulence. In Sporothrix schenckii sensu stricto, the causative agent of sporotrichosis, little is known about this glycosylation pathway. Here, using a genome-wide screening for putative members of the glycosyl hydrolase (CAZy - GH) families 47 and 63, which group enzymes involved in the processing step during N-linked glycan maturation, we found seven homologue genes belonging to family 47 and one to family 63. The eight genes were individually expressed in C. albicans null mutants lacking either MNS1 (for members of family 47) or CWH41 (for the member of family 63). Our results indicate that SsCWH41 is the functional ortholog of CaCWH41, whereas SsMNS1 is the functional ortholog of CaMNS1. The remaining genes of family 47 encode Golgi mannosidases and endoplasmic reticulum degradation-enhancing alpha-mannosidase-like proteins (EDEMs). Since these GH families gather proteins used as target for drugs to control cell growth, identification of these genes could help in the design of antifungals that could be used to treat sporotrichosis and other fungal diseases. In addition, to our knowledge, we are the first to report that Golgi mannosidases and EDEMs are expressed and characterized in yeast cells.

  17. Functional characterization of Sporothrix schenckii glycosidases involved in the N-linked glycosylation pathway.

    PubMed

    Lopes-Bezerra, Leila M; Lozoya-Pérez, Nancy E; López-Ramírez, Luz A; Martínez-Álvarez, José A; Teixeira, Marcus M; Felipe, Maria S S; Flores-Carreón, Arturo; Mora-Montes, Héctor M

    2015-01-01

    Protein glycosylation pathways are conserved metabolic processes in eukaryotic organisms and are required for cell fitness. In fungal pathogens, the N-linked glycosylation pathway is indispensable for proper cell wall composition and virulence. In Sporothrix schenckii sensu stricto, the causative agent of sporotrichosis, little is known about this glycosylation pathway. Here, using a genome-wide screening for putative members of the glycosyl hydrolase (CAZy - GH) families 47 and 63, which group enzymes involved in the processing step during N-linked glycan maturation, we found seven homologue genes belonging to family 47 and one to family 63. The eight genes were individually expressed in C. albicans null mutants lacking either MNS1 (for members of family 47) or CWH41 (for the member of family 63). Our results indicate that SsCWH41 is the functional ortholog of CaCWH41, whereas SsMNS1 is the functional ortholog of CaMNS1. The remaining genes of family 47 encode Golgi mannosidases and endoplasmic reticulum degradation-enhancing alpha-mannosidase-like proteins (EDEMs). Since these GH families gather proteins used as target for drugs to control cell growth, identification of these genes could help in the design of antifungals that could be used to treat sporotrichosis and other fungal diseases. In addition, to our knowledge, we are the first to report that Golgi mannosidases and EDEMs are expressed and characterized in yeast cells. PMID:25526779

  18. C2 Link Security for UAS: Technical Literature Study and Preliminary Functional Requirements. Version 0.9 (Working Draft)

    NASA Technical Reports Server (NTRS)

    2005-01-01

    This document provides a study of the technical literature related to Command and Control (C2) link security for Unmanned Aircraft Systems (UAS) for operation in the National Airspace System (NAS). Included is a preliminary set of functional requirements for C2 link security.

  19. Allocating structure to function: the strong links between neuroplasticity and natural selection

    PubMed Central

    Anderson, Michael L.; Finlay, Barbara L.

    2014-01-01

    A central question in brain evolution is how species-typical behaviors, and the neural function-structure mappings supporting them, can be acquired and inherited. Advocates of brain modularity, in its different incarnations across scientific subfields, argue that natural selection must target domain-dedicated, separately modifiable neural subsystems, resulting in genetically-specified functional modules. In such modular systems, specification of neuron number and functional connectivity are necessarily linked. Mounting evidence, however, from allometric, developmental, comparative, systems-physiological, neuroimaging and neurological studies suggests that brain elements are used and reused in multiple functional systems. This variable allocation can be seen in short-term neuromodulation, in neuroplasticity over the lifespan and in response to damage. We argue that the same processes are evident in brain evolution. Natural selection must preserve behavioral functions that may co-locate in variable amounts with other functions. In genetics, the uses and problems of pleiotropy, the re-use of genes in multiple networks have been much discussed, but this issue has been sidestepped in neural systems by the invocation of modules. Here we highlight the interaction between evolutionary and developmental mechanisms to produce distributed and overlapping functional architectures in the brain. These adaptive mechanisms must be robust to perturbations that might disrupt critical information processing and action selection, but must also recognize useful new sources of information arising from internal genetic or environmental variability, when those appear. These contrasting properties of “robustness” and “evolvability” have been discussed for the basic organization of body plan and fundamental cell physiology. Here we extend them to the evolution and development, “evo-devo,” of brain structure. PMID:24431995

  20. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.

    PubMed

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel W; Gontang, Erin A; McGlinchey, Ryan P; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric E; Moore, Bradley S; Jensen, Paul R

    2009-10-01

    Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.

  1. Ecologically valid support for the link between cognitive and psychosocial functioning in bipolar disorder

    PubMed Central

    Levy, Boaz; Medina, Anna Marie; Hintz, Kathryn; Weiss, Roger D.

    2011-01-01

    Prior research into the link between cognitive and psychosocial functioning in bipolar disorder has examined primarily asymptomatic patients, has measured these domains concurrently, and has failed to establish convergent validity in the assessment of psychosocial dysfunction. The present study examines the relation between cognitive and psychosocial functioning at the time of discharge from hospitalization for acute mood disturbance. We obtained measures of psychosocial functioning that were both close and distant to the time of neuropsychological testing; the former from the discharging psychiatrists, and the latter from reports of formally recognized disability status, determined by persons wholly unrelated to the present research. Sixty-three patients with bipolar I disorder, hospitalized for acute mood disturbance, completed a neuropsychological test battery 24 to 48 hours prior to discharge. We compared patients with versus without formal disability status on the Global Assessment of Functioning (GAF) scale and on scores of neuropsychological tests. We also tested associations between GAF scores and cognitive test scores. Results supported the convergent validity in the measurement of psychosocial disability, underscored the robust connection between cognitive and psychosocial impairment, and highlighted the presence of this connection during an important clinical state – time of discharge from psychiatric hospitalization. PMID:20674041

  2. Ecological-network models link diversity, structure and function in the plankton food-web.

    PubMed

    D'Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d'Alcalà, Maurizio

    2016-02-17

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named 'green' and 'blue' - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the 'adaptive' responses of plankton communities to perturbations.

  3. Ecological-network models link diversity, structure and function in the plankton food-web

    PubMed Central

    D’Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d’Alcalà, Maurizio

    2016-01-01

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named ‘green’ and ‘blue’ - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the ‘adaptive’ responses of plankton communities to perturbations. PMID:26883643

  4. Ecological-network models link diversity, structure and function in the plankton food-web.

    PubMed

    D'Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera d'Alcalà, Maurizio

    2016-01-01

    A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named 'green' and 'blue' - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the 'adaptive' responses of plankton communities to perturbations. PMID:26883643

  5. Scorpion Potassium Channel-blocking Defensin Highlights a Functional Link with Neurotoxin.

    PubMed

    Meng, Lanxia; Xie, Zili; Zhang, Qian; Li, Yang; Yang, Fan; Chen, Zongyun; Li, Wenxin; Cao, Zhijian; Wu, Yingliang

    2016-03-25

    The structural similarity between defensins and scorpion neurotoxins suggests that they might have evolved from a common ancestor. However, there is no direct experimental evidence demonstrating a functional link between scorpion neurotoxins and defensins. The scorpion defensin BmKDfsin4 from Mesobuthus martensiiKarsch contains 37 amino acid residues and a conserved cystine-stabilized α/β structural fold. The recombinant BmKDfsin4, a classical defensin, has been found to have inhibitory activity against Gram-positive bacteria such as Staphylococcus aureus, Bacillus subtilis, and Micrococcus luteusas well as methicillin-resistant Staphylococcus aureus Interestingly, electrophysiological experiments showed that BmKDfsin4,like scorpion potassium channel neurotoxins, could effectively inhibit Kv1.1, Kv1.2, and Kv1.3 channel currents, and its IC50value for the Kv1.3 channel was 510.2 nm Similar to the structure-function relationships of classical scorpion potassium channel-blocking toxins, basic residues (Lys-13 and Arg-19) of BmKDfsin4 play critical roles in peptide-Kv1.3 channel interactions. Furthermore, mutagenesis and electrophysiological experiments demonstrated that the channel extracellular pore region is the binding site of BmKDfsin4, indicating that BmKDfsin4 adopts the same mechanism for blocking potassium channel currents as classical scorpion toxins. Taken together, our work identifies scorpion BmKDfsin4 as the first invertebrate defensin to block potassium channels. These findings not only demonstrate that defensins from invertebrate animals are a novel type of potassium channel blockers but also provide evidence of a functional link between defensins and neurotoxins.

  6. Adolescent emotionality and effortful control: Core latent constructs and links to psychopathology and functioning

    PubMed Central

    Snyder, Hannah R.; Gulley, Lauren D.; Bijttebier, Patricia; Hartman, Catharina A.; Oldehinkel, Albertine J.; Mezulis, Amy; Young, Jami F.; Hankin, Benjamin L.

    2015-01-01

    Temperament is associated with important outcomes in adolescence, including academic and interpersonal functioning and psychopathology. Rothbart’s temperament model is among the most well-studied and supported approaches to adolescent temperament, and contains three main components: positive emotionality (PE), negative emotionality (NE), and effortful control (EC). However, the latent factor structure of Rothbart’s temperament measure for adolescents, the Early Adolescent Temperament Questionnaire Revised (EATQ-R, Ellis & Rothbart, 2001) has not been definitively established. To address this problem and investigate links between adolescent temperament and functioning, we used confirmatory factor analysis to examine the latent constructs of the EATQ-R in a large combined sample. For EC and NE, bifactor models consisting of a common factor plus specific factors for some sub-facets of each component fit best, providing a more nuanced understanding of these temperament dimensions. The nature of the PE construct in the EATQ-R is less clear. Models replicated in a hold-out dataset. The common components of high NE and low EC where broadly associated with increased psychopathology symptoms, and poor interpersonal and school functioning, while specific components of NE were further associated with corresponding specific components of psychopathology. Further questioning the construct validity of PE as measured by the EATQ-R, PE factors did not correlate with construct validity measures in a way consistent with theories of PE. Bringing consistency to the way the EATQ-R is modeled and using purer latent variables has the potential to advance the field in understanding links between dimensions of temperament and important outcomes of adolescent development. PMID:26011660

  7. Adolescent emotionality and effortful control: Core latent constructs and links to psychopathology and functioning.

    PubMed

    Snyder, Hannah R; Gulley, Lauren D; Bijttebier, Patricia; Hartman, Catharina A; Oldehinkel, Albertine J; Mezulis, Amy; Young, Jami F; Hankin, Benjamin L

    2015-12-01

    Temperament is associated with important outcomes in adolescence, including academic and interpersonal functioning and psychopathology. Rothbart's temperament model is among the most well-studied and supported approaches to adolescent temperament, and contains 3 main components: positive emotionality (PE), negative emotionality (NE), and effortful control (EC). However, the latent factor structure of Rothbart's temperament measure for adolescents, the Early Adolescent Temperament Questionnaire Revised (EATQ-R; Ellis & Rothbart, 2001) has not been definitively established. To address this problem and investigate links between adolescent temperament and functioning, we used confirmatory factor analysis to examine the latent constructs of the EATQ-R in a large combined sample. For EC and NE, bifactor models consisting of a common factor plus specific factors for some subfacets of each component fit best, providing a more nuanced understanding of these temperament dimensions. The nature of the PE construct in the EATQ-R is less clear. Models replicated in a hold-out dataset. The common components of high NE and low EC where broadly associated with increased psychopathology symptoms, and poor interpersonal and school functioning, while specific components of NE were further associated with corresponding specific components of psychopathology. Further questioning the construct validity of PE as measured by the EATQ-R, PE factors did not correlate with construct validity measures in a way consistent with theories of PE. Bringing consistency to the way the EATQ-R is modeled and using purer latent variables has the potential to advance the field in understanding links between dimensions of temperament and important outcomes of adolescent development. PMID:26011660

  8. Non-Invasive Brain-to-Brain Interface (BBI): Establishing Functional Links between Two Brains

    PubMed Central

    Yoo, Seung-Schik; Kim, Hyungmin; Filandrianos, Emmanuel; Taghados, Seyed Javid; Park, Shinsuk

    2013-01-01

    Transcranial focused ultrasound (FUS) is capable of modulating the neural activity of specific brain regions, with a potential role as a non-invasive computer-to-brain interface (CBI). In conjunction with the use of brain-to-computer interface (BCI) techniques that translate brain function to generate computer commands, we investigated the feasibility of using the FUS-based CBI to non-invasively establish a functional link between the brains of different species (i.e. human and Sprague-Dawley rat), thus creating a brain-to-brain interface (BBI). The implementation was aimed to non-invasively translate the human volunteer’s intention to stimulate a rat’s brain motor area that is responsible for the tail movement. The volunteer initiated the intention by looking at a strobe light flicker on a computer display, and the degree of synchronization in the electroencephalographic steady-state-visual-evoked-potentials (SSVEP) with respect to the strobe frequency was analyzed using a computer. Increased signal amplitude in the SSVEP, indicating the volunteer’s intention, triggered the delivery of a burst-mode FUS (350 kHz ultrasound frequency, tone burst duration of 0.5 ms, pulse repetition frequency of 1 kHz, given for 300 msec duration) to excite the motor area of an anesthetized rat transcranially. The successful excitation subsequently elicited the tail movement, which was detected by a motion sensor. The interface was achieved at 94.0±3.0% accuracy, with a time delay of 1.59±1.07 sec from the thought-initiation to the creation of the tail movement. Our results demonstrate the feasibility of a computer-mediated BBI that links central neural functions between two biological entities, which may confer unexplored opportunities in the study of neuroscience with potential implications for therapeutic applications. PMID:23573251

  9. Familial Alzheimer disease–linked mutations specifically disrupt Ca2+ leak function of presenilin 1

    PubMed Central

    Nelson, Omar; Tu, Huiping; Lei, Tianhua; Bentahir, Mostafa; de Strooper, Bart; Bezprozvanny, Ilya

    2007-01-01

    Mutations in presenilins are responsible for approximately 40% of all early-onset familial Alzheimer disease (FAD) cases in which a genetic cause has been identified. In addition, a number of mutations in presenilin-1 (PS1) have been suggested to be associated with the occurrence of frontal temporal dementia (FTD). Presenilins are highly conserved transmembrane proteins that support cleavage of the amyloid precursor protein by γ-secretase. Recently, we discovered that presenilins also function as passive ER Ca2+ leak channels. Here we used planar lipid bilayer reconstitution assays and Ca2+ imaging experiments with presenilin-null mouse embryonic fibroblasts to analyze ER Ca2+ leak function of 6 FAD-linked PS1 mutants and 3 known FTD-associated PS1 mutants. We discovered that L166P, A246E, E273A, G384A, and P436Q FAD mutations in PS1 abolished ER Ca2+ leak function of PS1. In contrast, A79V FAD mutation or FTD-associated mutations (L113P, G183V, and Rins352) did not appear to affect ER Ca2+ leak function of PS1 in our experiments. We validated our findings in Ca2+ imaging experiments with primary fibroblasts obtained from an FAD patient possessing mutant PS1-A246E. Our results indicate that many FAD mutations in presenilins are loss-of-function mutations affecting ER Ca2+ leak activity. In contrast, none of the FTD-associated mutations affected ER Ca2+ leak function of PS1, indicating that the observed effects are disease specific. Our observations are consistent with the potential role of disturbed Ca2+ homeostasis in Alzheimer disease pathogenesis. PMID:17431506

  10. Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils.

    PubMed

    Webster, Gordon; Embley, T Martin; Freitag, Thomas E; Smith, Zena; Prosser, James I

    2005-05-01

    Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.

  11. Modelling the multidimensional niche by linking functional traits to competitive performance.

    PubMed

    Maynard, Daniel S; Leonard, Kenneth E; Drake, John M; Hall, David W; Crowther, Thomas W; Bradford, Mark A

    2015-07-22

    Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified,and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts. PMID:26136444

  12. Modelling the multidimensional niche by linking functional traits to competitive performance

    PubMed Central

    Maynard, Daniel S.; Leonard, Kenneth E.; Drake, John M.; Hall, David W.; Crowther, Thomas W.; Bradford, Mark A.

    2015-01-01

    Linking competitive outcomes to environmental conditions is necessary for understanding species' distributions and responses to environmental change. Despite this importance, generalizable approaches for predicting competitive outcomes across abiotic gradients are lacking, driven largely by the highly complex and context-dependent nature of biotic interactions. Here, we present and empirically test a novel niche model that uses functional traits to model the niche space of organisms and predict competitive outcomes of co-occurring populations across multiple resource gradients. The model makes no assumptions about the underlying mode of competition and instead applies to those settings where relative competitive ability across environments correlates with a quantifiable performance metric. To test the model, a series of controlled microcosm experiments were conducted using genetically related strains of a widespread microbe. The model identified trait microevolution and performance differences among strains, with the predicted competitive ability of each organism mapped across a two-dimensional carbon and nitrogen resource space. Areas of coexistence and competitive dominance between strains were identified, and the predicted competitive outcomes were validated in approximately 95% of the pairings. By linking trait variation to competitive ability, our work demonstrates a generalizable approach for predicting and modelling competitive outcomes across changing environmental contexts. PMID:26136444

  13. Gene therapy improves immune function in preadolescents with X-linked severe combined immunodeficiency

    PubMed Central

    Chinen, Javier; Davis, Joie; De Ravin, Suk See; Hay, Beverly N.; Hsu, Amy P.; Linton, Gilda F.; Naumann, Nora; Nomicos, Effie Y. H.; Silvin, Christopher; Ulrick, Jean; Whiting-Theobald, Narda L.; Puck, Jennifer M.

    2007-01-01

    Retroviral gene therapy can restore immunity to infants with X-linked severe combined immunodeficiency (XSCID) caused by mutations in the IL2RG gene encoding the common gamma chain (γc) of receptors for interleukins 2 (IL-2), −4, −7, −9, −15, and −21. We investigated the safety and efficacy of gene therapy as salvage treatment for older XSCID children with inadequate immune reconstitution despite prior bone marrow transplant from a parent. Subjects received retrovirus-transduced autologous peripherally mobilized CD34+ hematopoietic cells. T-cell function significantly improved in the youngest subject (age 10 years), and multilineage retroviral marking occurred in all 3 children. PMID:17369490

  14. Joining the dots: neurobiological links in a functional analysis of depression

    PubMed Central

    2010-01-01

    Depression is one of the major contributors to the Total Disease Burden and afflicts about one-sixth of Western populations. One of the most effective treatments for depression focuses upon analysis of causal chains in overt behaviour, but does not include brain-related phenomena as steps along these causal pathways. Recent research findings regarding the neurobiological concomitants of depressive behaviour suggest a sequence of structural and functional alterations to the brain which may also produce a beneficial outcome for the depressed individual--that of adaptive withdrawal from uncontrollable aversive stressors. Linking these brain-based explanations to models of observable contingencies for depressive behaviour can provide a comprehensive explanation of how depressive behaviour occurs and why it persists in many patients. PMID:21143991

  15. Linking Cultural Competence to Functional Life Outcomes in Mental Health Care Settings.

    PubMed

    Michalopoulou, Georgia; Falzarano, Pamela; Butkus, Michael; Zeman, Lori; Vershave, Judy; Arfken, Cynthia

    2014-01-01

    Minorities in the United States have well-documented health disparities. Cultural barriers and biases by health care providers may contribute to lower quality of services which may contribute to these disparities. However, evidence linking cultural competency and health outcomes is lacking. This study, part of an ongoing quality improvement effort, tested the mediation hypothesis that patients' perception of provider cultural competency indirectly influences patients' health outcomes through process of care. Data were from patient satisfaction surveys collected in seven mental health clinics (n=94 minority patients). Consistent with our hypothesis, patients' perception of clinicians' cultural competency was indirectly associated with patients' self-reported improvements in social interactions, improvements in performance at work or school, and improvements in managing life problems through the patients' experience of respect, trust, and communication with the clinician. These findings indicate that process of care characteristics during the clinical encounter influence patients' perceptions of clinicians' cultural competency and affect functional outcomes.

  16. The Link between Dietary Protein Intake, Skeletal Muscle Function and Health in Older Adults

    PubMed Central

    Baum, Jamie I.; Wolfe, Robert R.

    2015-01-01

    Skeletal muscle mass and function are progressively lost with age, a condition referred to as sarcopenia. By the age of 60, many older adults begin to be affected by muscle loss. There is a link between decreased muscle mass and strength and adverse health outcomes such as obesity, diabetes and cardiovascular disease. Data suggest that increasing dietary protein intake at meals may counterbalance muscle loss in older individuals due to the increased availability of amino acids, which stimulate muscle protein synthesis by activating the mammalian target of rapamycin (mTORC1). Increased muscle protein synthesis can lead to increased muscle mass, strength and function over time. This review aims to address the current recommended dietary allowance (RDA) for protein and whether or not this value meets the needs for older adults based upon current scientific evidence. The current RDA for protein is 0.8 g/kg body weight/day. However, literature suggests that consuming protein in amounts greater than the RDA can improve muscle mass, strength and function in older adults. PMID:27417778

  17. Endothelial Markers May Link Kidney Function to Cardiovascular Events in Type 2 Diabetes

    PubMed Central

    Maier, Christina; Clodi, Martin; Neuhold, Stephanie; Resl, Michael; Elhenicky, Marie; Prager, Rudolf; Moertl, Deddo; Strunk, Guido; Luger, Anton; Struck, Joachim; Pacher, Richard; Hülsmann, Martin

    2009-01-01

    OBJECTIVE The increased cardiovascular risk in diabetes has been linked to endothelial and renal dysfunction. The aim of this study was to investigate the role of stable fragments of the precursors of adrenomedullin, endothelin-1, vasopressin, and atrial natriuretic peptide in progression of cardiovascular disease in patients with diabetes. RESEARCH DESIGN AND METHODS This was a prospective, observational study design with a composite end point (death or unexpected admission to hospital due to a cardiovascular event) on 781 patients with type 2 diabetes (54 events, median duration of observation 15 months). The four stable precursor peptides midregional adrenomedullin (MR-proADM), midregional proatrial natriuretic peptide (MR-proANP), COOH-terminal proendothelin-1 (CT-proET-1), and COOH-terminal provasopressin or copeptin (CT-proAVP) were determined at baseline, and their association to renal function and cardiovascular events was studied using stepwise linear and Cox logistic regression analysis and receiver operating characteristic analysis, respectively. RESULTS MR-proADM, CT-proET-1, CT-proAVP, and MR-proANP were all elevated in patients with future cardiovascular events and independently correlated to serum creatinine. MR-proADM and MR-proANP were significant predictors of a future cardiovascular event, with MR-proANP being the stronger (area under the curve 0.802 ± 0.034, sensitivity 0.833, specificity 0.576, positive predictive value 0.132, and negative predictive value 0.978 with a cutoff value of 75 pmol/l). CONCLUSIONS The four serum markers of vasoactive and natriuretic peptides are related to both kidney function and cardiovascular events, thus linking two major complications of diabetes, diabetic nephropathy and cardiovascular disease. PMID:19564455

  18. Ecosystem functional properties - useful links to organism and to global scale?

    NASA Astrophysics Data System (ADS)

    Reichstein, M.

    2015-12-01

    Classical biogeographical observations tell us that ecosystems (vegetation and soils) strongly respond to climate variation in terms of their structure and function. On the other hand the influence of vegetation function on climate via exchange of matter and energy with the atmosphere has become evident in the last decades via observational and modeling studies. Recent continuous observations of this exchange of CO2, H2O and sensible heat within the global observation network FLUXNET have enabled us to quantify ecosystem function in response to large eco-climatological spatio-temporal variability of climate. We see that ecosystem function co-varies strongly with climate, but that climate alone does not suffice to explain the variation in total. Instead vegetation biophysical and structural parameters co-determine the exchange of carbon, water and energy between the ecosystem and the atmosphere. By combining ecosystem level observation and information of spatial meteorological and vegetation remote sensing covariates we can infer global patterns of ecosystem atmosphere fluxes and derive key ecosystem functional properties globally. While this approach is powerful and meteorological and vegetation structural predictors explain more than 70% of the spatial variation of monthly fluxes at FLUXNET sites, it ignores the effect of ecophysiological vegetation properties, which is expected from plant physiological leaf or whole-plant studies. Hence, future research has to more strongly link the organismic trait information with ecosystem functional properties. For this we propose a framework that involves 1) the correlation of community aggregated traits with flux-derived ecosystem properties across a range of ecosystems, 2) the up-scaling of vegetation traits using spatially distributed geo-ecological co-variates and the comparison with global ecosystem functional properties and their co-variation with climate, 3) the use of vegetation traits instead of vegetation classes

  19. Linking of Sensor Molecules with Amino Groups to Amino-Functionalized AFM Tips

    PubMed Central

    2011-01-01

    The measuring tip of an atomic force microscope (AFM) can be upgraded to a specific biosensor by attaching one or a few biomolecules to the apex of the tip. The biofunctionalized tip is then used to map cognate target molecules on a sample surface or to study biophysical parameters of interaction with the target molecules. The functionality of tip-bound sensor molecules is greatly enhanced if they are linked via a thin, flexible polymer chain. In a typical scheme of tip functionalization, reactive groups are first generated on the tip surface, a bifunctional cross-linker is then attached with one of its two reactive ends, and finally the probe molecule of interest is coupled to the free end of the cross-linker. Unfortunately, the most popular functional group generated on the tip surface is the amino group, while at the same time, the only useful coupling functions of many biomolecules (such as antibodies) are also NH2 groups. In the past, various tricks or detours were applied to minimize the undesired bivalent reaction of bifunctional linkers with adjacent NH2 groups on the tip surface. In the present study, an uncompromising solution to this problem was found with the help of a new cross-linker (“acetal-PEG-NHS”) which possesses one activated carboxyl group and one acetal-protected benzaldehyde function. The activated carboxyl ensures rapid unilateral attachment to the amino-functionalized tip, and only then is the terminal acetal group converted into the amino-reactive benzaldehyde function by mild treatment (1% citric acid, 1–10 min) which does not harm the AFM tip. As an exception, AFM tips with magnetic coating become demagnetized in 1% citric acid. This problem was solved by deprotecting the acetal group before coupling the PEG linker to the AFM tip. Bivalent binding of the corresponding linker (“aldehyde-PEG-NHS”) to adjacent NH2 groups on the tip was largely suppressed by high linker concentrations. In this way, magnetic AFM tips could be

  20. Linking suspended sediment transport metrics with fish functional traits in the Northwestern Great Plains (Invited)

    NASA Astrophysics Data System (ADS)

    Schwartz, J. S.; Simon, A.; Klimetz, L.

    2009-12-01

    Loss of ecological integrity due to excessive suspended sediment in rivers and streams is a major cause of water quality impairment in the United States. Although 32 states have developed numeric criteria for turbidity or suspended solids, or both according to the USEPA (2006), criteria is typically written as a percent exceedance above background and what constitutes background is not well defined. Defining a background level is problematic considering suspended sediments and related turbidity levels change with flow stage and season, and limited scientific data exists on relationships between sediment exposure and biotic response. Current assessment protocols for development of sediment total maximum daily loads (TMDLs) lack a means to link temporally-variable sediment transport rates with specific losses of ecological functions as loads increase. This study, within the in Northwestern Great Plains Ecoregion, co-located 58 USGS gauging stations with existing flow and suspended sediment data, and fish data from federal and state agencies. Suspended sediment concentration (SSC) transport metrics were quantified into exceedance frequencies of a given magnitude, duration as the number of consecutive days a given concentration was equaled or exceeded, dosage as concentration x duration, and mean annual suspended sediment yields. A functional traits-based approach was used to correlate SSC transport metrics with site occurrences of 20 fish traits organized into four main groups: preferred rearing mesohabitat, trophic structure, feeding habits, and spawning behavior. Negative correlations between SSC metrics and trait occurrences were assumed to represent potential conditions for impairment, specifically identifying an ecological loss by functional trait. Potential impairment conditions were linked with presence of the following traits: habitat preferences for stream pool and river shallow waters; feeding generalists, omnivores, piscivores; and several spawning

  1. GRK2 – A Link Between Myocardial Contractile Function and Cardiac Metabolism

    PubMed Central

    Woodall, Meryl C.; Ciccarelli, Michele; Woodall, Benjamin P.; Koch, Walter J.

    2014-01-01

    Heart failure (HF) causes a tremendous burden on the worldwide healthcare system, affecting more than 23 million people. There are many cardiovascular disorders that contribute to the development of HF and multiple risk factors that accelerate its occurrence, but regardless of its underlying cause, HF is characterized by a marked decrease in myocardial contractility and loss of pump function. One biomarker molecule consistently shown to be upregulated in human HF and several animal models is G protein-coupled receptor (GPCR) kinase 2 (GRK2), a kinase originally discovered to be involved in GPCR desensitization, especially β-adrenergic receptors (βARs). Indeed, higher levels of GRK2 can impair βAR-mediated inotropic reserve and its inhibition or molecular reduction has shown to improve pump function in several animal models including a pre-clinical pig model of HF. Recently, non-classical roles for GRK2 in cardiovascular disease have been described, including negative regulation of insulin signaling, a role in myocyte cell survival and apoptotic signaling, and it has been shown to be localized in/on mitochondria. These new roles of GRK2 suggest that GRK2 may be a nodal link in the myocyte, influencing both cardiac contractile function and cell metabolism and survival and contributing to HF independent of its canonical role on GPCR desensitization. In this review, classical and non-classical roles for GRK2 will be discussed, focusing on recently discovered roles for GRK2 in cardiomyocyte metabolism and the effects that these roles may have on myocardial contractile function and HF development. PMID:24812353

  2. Links between plant litter chemistry, species diversity, and below-ground ecosystem function.

    PubMed

    Meier, Courtney L; Bowman, William D

    2008-12-16

    Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics of plant species diversity. We amended native soils with litter mixtures containing up to 4 alpine plant species, and we used 9 litter chemical traits to evaluate the chemical composition (i.e., the identity and quantity of compounds) and chemical diversity of the litter mixtures. The chemical composition of the litter mixtures was the strongest predictor of soil respiration, net N mineralization, and microbial biomass N. Soil respiration and net N mineralization rates were also significantly correlated with the chemical diversity of the litter mixtures. In contrast, soil C and N cycling rates were poorly correlated with plant species richness, and there was no relationship between species richness and the chemical diversity of the litter mixtures. These results indicate that the composition and diversity of chemical compounds in litter are potentially important functional traits affecting decomposition, and simple metrics like plant species richness may fail to capture variation in these traits. Litter chemical traits therefore provide a mechanistic link between organisms, species diversity, and key components of below-ground ecosystem function.

  3. Hermite Functional Link Neural Network for Solving the Van der Pol-Duffing Oscillator Equation.

    PubMed

    Mall, Susmita; Chakraverty, S

    2016-08-01

    Hermite polynomial-based functional link artificial neural network (FLANN) is proposed here to solve the Van der Pol-Duffing oscillator equation. A single-layer hermite neural network (HeNN) model is used, where a hidden layer is replaced by expansion block of input pattern using Hermite orthogonal polynomials. A feedforward neural network model with the unsupervised error backpropagation principle is used for modifying the network parameters and minimizing the computed error function. The Van der Pol-Duffing and Duffing oscillator equations may not be solved exactly. Here, approximate solutions of these types of equations have been obtained by applying the HeNN model for the first time. Three mathematical example problems and two real-life application problems of Van der Pol-Duffing oscillator equation, extracting the features of early mechanical failure signal and weak signal detection problems, are solved using the proposed HeNN method. HeNN approximate solutions have been compared with results obtained by the well known Runge-Kutta method. Computed results are depicted in term of graphs. After training the HeNN model, we may use it as a black box to get numerical results at any arbitrary point in the domain. Thus, the proposed HeNN method is efficient. The results reveal that this method is reliable and can be applied to other nonlinear problems too. PMID:27348738

  4. Hermite Functional Link Neural Network for Solving the Van der Pol-Duffing Oscillator Equation.

    PubMed

    Mall, Susmita; Chakraverty, S

    2016-08-01

    Hermite polynomial-based functional link artificial neural network (FLANN) is proposed here to solve the Van der Pol-Duffing oscillator equation. A single-layer hermite neural network (HeNN) model is used, where a hidden layer is replaced by expansion block of input pattern using Hermite orthogonal polynomials. A feedforward neural network model with the unsupervised error backpropagation principle is used for modifying the network parameters and minimizing the computed error function. The Van der Pol-Duffing and Duffing oscillator equations may not be solved exactly. Here, approximate solutions of these types of equations have been obtained by applying the HeNN model for the first time. Three mathematical example problems and two real-life application problems of Van der Pol-Duffing oscillator equation, extracting the features of early mechanical failure signal and weak signal detection problems, are solved using the proposed HeNN method. HeNN approximate solutions have been compared with results obtained by the well known Runge-Kutta method. Computed results are depicted in term of graphs. After training the HeNN model, we may use it as a black box to get numerical results at any arbitrary point in the domain. Thus, the proposed HeNN method is efficient. The results reveal that this method is reliable and can be applied to other nonlinear problems too.

  5. An exploration of links between early parenting experiences and personality disorder type and disordered personality functioning.

    PubMed

    Parker, G; Roy, K; Wilhelm, K; Mitchell, P; Austin, M P; Hadzi-Pavlovic, D

    1999-01-01

    Reports of early parenting were assessed using two measures, the Parental Bonding Index (PBI) and the Measure of Parenting Style (MOPS), in a sample of 265 patients with DSM-defined major depressive disorder. Psychiatrists then rated the extent to which sample members evidenced the personality "styles" underpinning 15 separate personality disorders, returning personality vignette scores. The extent of disordered functioning was also assessed across "parameters" and "domains" by psychiatrists, referrers, and family members, using a range of measures. Those with higher scores on vignettes measuring borderline, anxious, depressive, and self-defeating personality style rated parents as uncaring, overcontrolling, and abusive. When vignettes were consolidated into scores akin to the DSM clusters, the most consistent links between perceived dysfunctional parenting were with the Cluster C (anxious), and Cluster B (dramatic) styles and were nonsignificant for Cluster A (eccentric) style. Meeting criteria for an increasing number of personality disorder clusters was associated with increasing levels of adverse parenting. Multiple regression analyses indicated that disordered functioning (as assessed by the three independent rater groups) was most distinctly associated with paternal indifference and maternal overcontrol. PMID:10633316

  6. RTTN Mutations Link Primary Cilia Function to Organization of the Human Cerebral Cortex

    PubMed Central

    Kheradmand Kia, Sima; Verbeek, Elly; Engelen, Erik; Schot, Rachel; Poot, Raymond A.; de Coo, Irenaeus F.M.; Lequin, Maarten H.; Poulton, Cathryn J.; Pourfarzad, Farzin; Grosveld, Frank G.; Brehm, António; de Wit, Marie Claire Y.; Oegema, Renske; Dobyns, William B.; Verheijen, Frans W.; Mancini, Grazia M.S.

    2012-01-01

    Polymicrogyria is a malformation of the developing cerebral cortex caused by abnormal organization and characterized by many small gyri and fusion of the outer molecular layer. We have identified autosomal-recessive mutations in RTTN, encoding Rotatin, in individuals with bilateral diffuse polymicrogyria from two separate families. Rotatin determines early embryonic axial rotation, as well as anteroposterior and dorsoventral patterning in the mouse. Human Rotatin has recently been identified as a centrosome-associated protein. The Drosophila melanogaster homolog of Rotatin, Ana3, is needed for structural integrity of centrioles and basal bodies and maintenance of sensory neurons. We show that Rotatin colocalizes with the basal bodies at the primary cilium. Cultured fibroblasts from affected individuals have structural abnormalities of the cilia and exhibit downregulation of BMP4, WNT5A, and WNT2B, which are key regulators of cortical patterning and are expressed at the cortical hem, the cortex-organizing center that gives rise to Cajal-Retzius (CR) neurons. Interestingly, we have shown that in mouse embryos, Rotatin colocalizes with CR neurons at the subpial marginal zone. Knockdown experiments in human fibroblasts and neural stem cells confirm a role for RTTN in cilia structure and function. RTTN mutations therefore link aberrant ciliary function to abnormal development and organization of the cortex in human individuals. PMID:22939636

  7. PDGFRβ expression and function in fibroblasts derived from pluripotent cells is linked to DNA demethylation

    PubMed Central

    Hewitt, Kyle J.; Shamis, Yulia; Knight, Elana; Smith, Avi; Maione, Anna; Alt-Holland, Addy; Sheridan, Steven D.; Haggarty, Stephen J.; Garlick, Jonathan A.

    2012-01-01

    Platelet-derived growth factor receptor-beta (PDGFRβ) is required for the development of mesenchymal cell types, and plays a diverse role in the function of fibroblasts in tissue homeostasis and regeneration. In this study, we characterized the expression of PDGFRβ in fibroblasts derived from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), and showed that this expression is important for cellular functions such as migration, extracellular matrix production and assembly in 3D self-assembled tissues. To determine potential regulatory regions predictive of expression of PDGFRβ following differentiation from ESCs and iPSCs, we analyzed the DNA methylation status of a region of the PDGFRB promoter that contains multiple CpG sites, before and after differentiation. We demonstrated that this promoter region is extensively demethylated following differentiation, and represents a developmentally regulated, differentially methylated region linked to PDGFRβ expression. Understanding the epigenetic regulation of genes such as PDGFRB, and identifying sites of active DNA demethylation, is essential for future applications of iPSC-derived fibroblasts for regenerative medicine. PMID:22344267

  8. Integrin-Linked Kinase Is Indispensable for Keratinocyte Differentiation and Epidermal Barrier Function.

    PubMed

    Sayedyahossein, Samar; Rudkouskaya, Alena; Leclerc, Valerie; Dagnino, Lina

    2016-02-01

    A functional permeability barrier is essential to prevent the passage of water and electrolytes, macromolecules, and pathogens through the epidermis. This is accomplished in terminally differentiated keratinocytes through formation of a cornified envelope and the assembly of tight intercellular junctions. Integrin-linked kinase (ILK) is a scaffold protein essential for hair follicle morphogenesis and epidermal attachment to the basement membrane. However, the biological functions of ILK in differentiated keratinocytes remain poorly understood. Furthermore, whether ILK is implicated in keratinocyte differentiation and intercellular junction formation has remained an unresolved issue. Here we describe a pivotal role for ILK in keratinocyte differentiation responses to increased extracellular Ca(2+), regulation of adherens and tight junction assembly, and the formation of an outside-in permeability barrier toward macromolecules. In the absence of ILK, the calcium sensing receptor, E-cadherin, and ZO-1 fail to translocate to the cell membrane, through mechanisms that involve abnormalities in microtubules and in RhoA activation. In situ, ILK-deficient epidermis exhibits reduced tight junction formation and increased outside-in permeability to a dextran tracer, indicating reduced barrier properties toward macromolecules. Therefore, ILK is an essential component of keratinocyte differentiation programs that contribute to epidermal integrity and the establishment of its barrier properties. PMID:26967476

  9. Effect of Nitro-Functionalization on the Cross-Linking and Bioadhesion of Biomimetic Adhesive Moiety

    PubMed Central

    2015-01-01

    Dopamine mimics the exceptional moisture-resistant adhesive properties of the amino acid, DOPA, found in adhesive proteins secreted by marine mussels. The catechol side chain of dopamine was functionalized with a nitro-group, and the effect of the electron withdrawing group modification on the cross-linking chemistry and bioadhesive properties of the adhesive moiety was evaluated. Both nitrodopamine and dopamine were covalently attached as a terminal group onto an inert, 4-armed poly(ethylene glygol) (PEG-ND and PEG-D, respectively). PEG-ND and PEG-D exhibited different dependence on the concentration of NaIO4 and pH, which affected the curing rate, mechanical properties, and adhesive performance of these biomimetic adhesives differently. PEG-ND cured instantly and its bioadhesive properties were minimally affected by the change in pH (5.7–8) within the physiological range. Under mildly acidic conditions (pH 5.7 and 6.7), PEG-ND outperformed PEG-D in lap shear adhesion testing using wetted pericardium tissues. However, nitrodopamine only formed dimers, which resulted in the formation of loosely cross-linked network and adhesive with reduced cohesive properties. UV–vis spectroscopy further confirmed nitrodopamine’s ability for rapid dimer formation. The ability for nitrodopamine to rapidly cure and adhere to biological substrates in an acidic pH make it suitable for designing adhesive biomaterials targeted at tissues that are more acidic (i.e., subcutaneous, dysoxic, or tumor tissues). PMID:25495043

  10. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    PubMed Central

    Al-Najjar, Mohammad A. A.; Ramette, Alban; Kühl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. PMID:25147548

  11. Microtubule-Actin Cross-Linking Factor 1: Domains, Interaction Partners, and Tissue-Specific Functions.

    PubMed

    Goryunov, Dmitry; Liem, Ronald K H

    2016-01-01

    The cytoskeleton of most eukaryotic cells is composed of three principal filamentous components: actin filaments, microtubules (MTs), and intermediate filaments. It is a highly dynamic system that plays crucial roles in a wide range of cellular processes, including migration, adhesion, cytokinesis, morphogenesis, intracellular traffic and signaling, and structural flexibility. Among the large number of cytoskeleton-associated proteins characterized to date, microtubule-actin cross-linking factor 1 (MACF1) is arguably the most versatile integrator and modulator of cytoskeleton-related processes. MACF1 belongs to the plakin family of proteins, and within it, to the spectraplakin subfamily. These proteins are characterized by the ability to bridge MT and actin cytoskeletal networks in a dynamic fashion, which underlies their involvement in the regulation of cell migration, axonal extension, and vesicular traffic. Studying MACF1 functions has provided insights not only into the regulation of the cytoskeleton but also into molecular mechanisms of both normal cellular physiology and cellular pathology. Multiple MACF1 isoforms exist, composed of a large variety of alternatively spliced domains. Each of these domains mediates a specific set of interactions and functions. These functions are manifested in tissue and cell-specific phenotypes observed in conditional MACF1 knockout mice. The conditional models described to date reveal critical roles of MACF1 in mammalian skin, nervous system, heart muscle, and intestinal epithelia. Complete elimination of MACF1 is early embryonic lethal, indicating an essential role for MACF1 in early development. Further studies of MACF1 domains and their interactions will likely reveal multiple new roles of this protein in various tissues.

  12. Positioning Multiple Proteins at the Nanoscale with Electron Beam Cross-Linked Functional Polymers

    PubMed Central

    Christman, Karen L.; Schopf, Eric; Broyer, Rebecca M.; Li, Ronald C.; Chen, Yong; Maynard, Heather D.

    2009-01-01

    Constructing multicomponent protein structures that match the complexity of those found in Nature is essential for the next generation of medical materials. In this report, a versatile method to precisely arrange multicomponent protein nanopatterns in two-dimensional single-layer or three-dimensional multilayer formats using electron beam lithography is described. Eight arm poly(ethylene glycol)s were modified at the chain ends with either biotin, maleimide, aminooxy, or nitrilotriacetic acid. Analysis by 1H NMR spectroscopy revealed that the reactions were efficient and that end group conversions were 91-100%. The polymers were then cross-linked onto Si surfaces using electron beams to form micron sized patterns of the functional groups. Proteins with biotin binding sites, a free cysteine, an N-terminal α-oxoamide, and a histidine tag, respectively, were then incubated with the substrate in aqueous solutions without the addition of any other reagents. By fluorescence microscopy experiments it was determined that proteins reacted site-specifically with the exposed functional groups to form protein micropatterns. Multicomponent nanoscale protein patterns were then fabricated. Different PEGs with orthogonal reactivity were sequentially patterned on the same chip. Simultaneous assembly of two different proteins from a mixture of the biomolecules formed the multicomponent two dimensional patterns. Atomic force microscopy demonstrated that nanometer sized patterns of polymer were formed and fluorescence microscopy demonstrated that side-by-side patterns of the different proteins were obtained. Moreover, multilayer PEG fabrication produced micron and nanometer sized patterns of one functional group on top of the other. Precise three-dimensional arrangements of different proteins were then realized. PMID:19160460

  13. Linking Carbonic Anhydrase Abundance and Diversity in Soils to Ecological Function

    NASA Astrophysics Data System (ADS)

    Pang, E.; Meredith, L. K.; Welander, P. V.

    2015-12-01

    Carbonic anhydrase (CA) is an ancient enzyme widespread among bacteria, archaea, and eukarya that catalyzes the following reaction: CO2 + H2O ⇌ HCO3- + H+. Its functions are critical for key cellular processes such as concentrating CO2 for autotrophic growth, pH regulation, and pathogen survival in hosts. Currently, there are six known CA classes (α, β, γ, δ, η, ζ) arising from several distinct evolutionary lineages. CA are widespread in sequenced genomes, with many organisms containing multiple classes of CA or multiple CA of the same class. Soils host rich microbial communities with diverse and important ecological functions, but the diversity and abundance of CA in soils has not been explored. CA appears to play an important, but poorly understood, role in some biogeochemical cycles such as those of CO2 and its oxygen isotope composition and also carbonyl sulfide (COS), which are potential tracers in predictive carbon cycle models. Recognizing the prevalence and functional significance of CA in soils, we used a combined bioinformatics and molecular biology approach to address fundamental questions regarding the abundance, diversity, and function of CA in soils. To characterize the abundance and diversity of the different CA classes in soils, we analyzed existing soil metagenomic and metatranscriptomic data from the DOE Joint Genome Institute databases. Out of the six classes of CA, we only found the α, β, and γ classes to be present in soils, with the β class being the most abundant. We also looked at genomes of sequenced soil microorganisms to learn what combination of CA classes they contain, from which we can begin to predict the physiological role of CA. To characterize the functional roles of the different CA classes in soils, we collected soil samples from a variety of biomes with diverse chemical and physical properties and quantified the rate of two CA-mediated processes: soil uptake of COS and acceleration of the oxygen isotope exchange

  14. Non-random distribution of homo-repeats: links with biological functions and human diseases

    PubMed Central

    Lobanov, Michail Yu.; Klus, Petr; Sokolovsky, Igor V.; Tartaglia, Gian Gaetano; Galzitskaya, Oxana V.

    2016-01-01

    The biological function of multiple repetitions of single amino acids, or homo-repeats, is largely unknown, but their occurrence in proteins has been associated with more than 20 hereditary diseases. Analysing 122 bacterial and eukaryotic genomes, we observed that the number of proteins containing homo-repeats is significantly larger than expected from theoretical estimates. Analysis of statistical significance indicates that the minimal size of homo-repeats varies with amino acid type and proteome. In an attempt to characterize proteins harbouring long homo-repeats, we found that those containing polar or small amino acids S, P, H, E, D, K, Q and N are enriched in structural disorder as well as protein- and RNA-interactions. We observed that E, S, Q, G, L, P, D, A and H homo-repeats are strongly linked with occurrence in human diseases. Moreover, S, E, P, A, Q, D and T homo-repeats are significantly enriched in neuronal proteins associated with autism and other disorders. We release a webserver for further exploration of homo-repeats occurrence in human pathology at http://bioinfo.protres.ru/hradis/. PMID:27256590

  15. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

    PubMed Central

    Shafer, Paul; Isganitis, Timothy; Yona, Golan

    2006-01-01

    Background Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. Results We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. Conclusion Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at . PMID:16480496

  16. Clinical aspects and adrenal functions in eleven Japanese children with X-linked adrenoleukodystrophy.

    PubMed

    Miyoshi, Yoko; Sakai, Norio; Hamada, Yusuke; Tachibana, Makiko; Hasegawa, Yasuhiro; Kiyohara, Yuki; Yamada, Hiroyuki; Murakami, Mari; Kondou, Hiroki; Kimura-Ohba, Shihoko; Mine, Junji; Sato, Tatsuharu; Kamio, Noriko; Ueda, Hitoshi; Suzuki, Yasuhiro; Shiomi, Masashi; Ohta, Hideaki; Shimozawa, Nobuyuki; Ozono, Keiichi

    2010-01-01

    X-linked adrenoleukodystrophy (X-ALD) is a genetic disease associated with demyelination of the central nervous system, adrenocortical insufficiency and accumulation of very long chain fatty acids. It is a clinically heterogeneous disorder ranging from a severe childhood cerebral form to an asymptomatic form. The incidence in Japan is estimated to be between 1:30,000 and 1:50,000 boys as determined by a nationwide retrospective survey between 1990 and 1999, which found no cases with Addison's form. We reviewed the medical records of eleven Japanese boys with X-ALD from 1990 to 2010 in our institute. Eight patients were detected by neuropsychological abnormalities, whereas a higher prevalence of unrecognized adrenocortical insufficiency (5/11: 45%) was observed than previously recognized. While no neurological abnormalities were demonstrated in two brothers, the elder brother had moderate Addison's disease at diagnosis and the presymptomatic younger brother progressed to Addison's disease six months after the diagnosis of X-ALD. Early detection of impaired adrenal function as well as early identification of neurologically presymptomatic patients by genetic analysis is essential for better prognosis. Addison's form might be overlooked in Japan; therefore, X-ALD should be suspected in patients with adrenocortical insufficiency.

  17. Functional Characterization of Bacterial Oligosaccharyltransferases Involved in O-Linked Protein Glycosylation▿

    PubMed Central

    Faridmoayer, Amirreza; Fentabil, Messele A.; Mills, Dominic C.; Klassen, John S.; Feldman, Mario F.

    2007-01-01

    Protein glycosylation is an important posttranslational modification that occurs in all domains of life. Pilins, the structural components of type IV pili, are O glycosylated in Neisseria meningitidis, Neisseria gonorrhoeae, and some strains of Pseudomonas aeruginosa. In this work, we characterized the P. aeruginosa 1244 and N. meningitidis MC58 O glycosylation systems in Escherichia coli. In both cases, sugars are transferred en bloc by an oligosaccharyltransferase (OTase) named PglL in N. meningitidis and PilO in P. aeruginosa. We show that, like PilO, PglL has relaxed glycan specificity. Both OTases are sufficient for glycosylation, but they require translocation of the undecaprenol-pyrophosphate-linked oligosaccharide substrates into the periplasm for activity. Whereas PilO activity is restricted to short oligosaccharides, PglL is able to transfer diverse oligo- and polysaccharides. This functional characterization supports the concept that despite their low sequence similarity, PilO and PglL belong to a new family of “O-OTases” that transfer oligosaccharides from lipid carriers to hydroxylated amino acids in proteins. To date, such activity has not been identified for eukaryotes. To our knowledge, this is the first report describing recombinant O glycoproteins synthesized in E. coli. PMID:17890310

  18. Linking mother and youth parenting attitudes: indirect effects via maltreatment, parent involvement, and youth functioning.

    PubMed

    Thompson, Richard; Jones, Deborah J; Litrownik, Alan J; English, Diana J; Kotch, Jonathan B; Lewis, Terri; Dubowitz, Howard

    2014-01-01

    Evidence suggests that parenting attitudes are transmitted within families. However, limited research has examined this prospectively. The current prospective study examined direct effects of early maternal attitudes toward parenting (as measured at child age 4 by the Adult-Adolescent Parenting Inventory [AAPI]) on later youth parenting attitudes (as measured by the AAPI at youth age 18). Indirect effects via child maltreatment (physical abuse, sexual abuse, neglect, and emotional maltreatment), parent involvement, and youth functioning (internalizing and externalizing problems) were also assessed. Analyses were conducted on data from 412 families enrolled in the Longitudinal Studies of Child Abuse and Neglect (LONGSCAN). There were significant direct effects for three of the four classes of mother parenting attitudes (appropriate developmental expectations of children, empathy toward children, and appropriate family roles) on youth attitudes but not for rejection of punishment. In addition, the following indirect effects were obtained: Mother expectations influenced youth expectations via neglect; mother empathy influenced youth empathy via both parental involvement and youth externalizing problems; and mother rejection of punishment influenced youth rejection of punishment via youth internalizing problems. None of the child or family process variables, however, affected the link between mother and youth attitudes about roles.

  19. Possible functional links among brain- and skull-related genes selected in modern humans.

    PubMed

    Benítez-Burraco, Antonio; Boeckx, Cedric

    2015-01-01

    The sequencing of the genomes from extinct hominins has revealed that changes in some brain-related genes have been selected after the split between anatomically-modern humans and Neanderthals/Denisovans. To date, no coherent view of these changes has been provided. Following a line of research we initiated in Boeckx and Benítez-Burraco (2014a), we hypothesize functional links among most of these genes and their products, based on the existing literature for each of the gene discussed. The genes we focus on are found mutated in different cognitive disorders affecting modern populations and their products are involved in skull and brain morphology, and neural connectivity. If our hypothesis turns out to be on the right track, it means that the changes affecting most of these proteins resulted in a more globular brain and ultimately brought about modern cognition, with its characteristic generativity and capacity to form and exploit cross-modular concepts, properties most clearly manifested in language.

  20. Possible functional links among brain- and skull-related genes selected in modern humans

    PubMed Central

    Benítez-Burraco, Antonio; Boeckx, Cedric

    2015-01-01

    The sequencing of the genomes from extinct hominins has revealed that changes in some brain-related genes have been selected after the split between anatomically-modern humans and Neanderthals/Denisovans. To date, no coherent view of these changes has been provided. Following a line of research we initiated in Boeckx and Benítez-Burraco (2014a), we hypothesize functional links among most of these genes and their products, based on the existing literature for each of the gene discussed. The genes we focus on are found mutated in different cognitive disorders affecting modern populations and their products are involved in skull and brain morphology, and neural connectivity. If our hypothesis turns out to be on the right track, it means that the changes affecting most of these proteins resulted in a more globular brain and ultimately brought about modern cognition, with its characteristic generativity and capacity to form and exploit cross-modular concepts, properties most clearly manifested in language. PMID:26136701

  1. Linking Mother and Youth Parenting Attitudes: Indirect Effects via Maltreatment, Parent Involvement, and Youth Functioning

    PubMed Central

    Thompson, Richard; Jones, Deborah J.; Litrownik, Alan J.; English, Diana J.; Kotch, Jonathan B.; Lewis, Terri; Dubowitz, Howard

    2014-01-01

    Evidence suggests that parenting attitudes are transmitted within families. However, limited research has examined this prospectively. The current prospective study examined direct effects of early maternal attitudes toward parenting (as measured at child age 4 by the Adult-Adolescent Parenting Inventory [AAPI]) on later youth parenting attitudes (as measured by the AAPI at youth age 18). Indirect effects via child maltreatment (physical abuse, sexual abuse, neglect, and emotional maltreatment), parent involvement, and youth functioning (internalizing and externalizing problems) were also assessed. Analyses were conducted on data from 412 families enrolled in the Longitudinal Studies of Child Abuse and Neglect (LONGSCAN). There were significant direct effects for three of the four classes of mother parenting attitudes (appropriate developmental expectations of children, empathy toward children, and appropriate family roles) on youth attitudes but not for rejection of punishment. In addition, the following indirect effects were obtained: Mother expectations influenced youth expectations via neglect; mother empathy influenced youth empathy via both parental involvement and youth externalizing problems; and mother rejection of punishment influenced youth rejection of punishment via youth internalizing problems. None of the child or family process variables, however, affected the link between mother and youth attitudes about roles. PMID:25113632

  2. Application of Radial Basis Functional Link Networks to Exploration for Proterozoic Mineral Deposits in Central Iran

    SciTech Connect

    Behnia, Pouran

    2007-06-15

    The metallogeny of Central Iran is characterized mainly by the presence of several iron, apatite, and uranium deposits of Proterozoic age. Radial Basis Function Link Networks (RBFLN) were used as a data-driven method for GIS-based predictive mapping of Proterozoic mineralization in this area. To generate the input data for RBFLN, the evidential maps comprising stratigraphic, structural, geophysical, and geochemical data were used. Fifty-eight deposits and 58 'nondeposits' were used to train the network. The operations for the application of neural networks employed in this study involve both multiclass and binary representation of evidential maps. Running RBFLN on different input data showed that an increase in the number of evidential maps and classes leads to a larger classification sum of squared error (SSE). As a whole, an increase in the number of iterations resulted in the improvement of training SSE. The results of applying RBFLN showed that a successful classification depends on the existence of spatially well distributed deposits and nondeposits throughout the study area.

  3. Canonical Nlrp3 inflammasome links systemic low grade inflammation to functional decline in aging

    PubMed Central

    Youm, Yun-Hee; Grant, Ryan W.; McCabe, Laura R.; Albarado, Diana C.; Nguyen, Kim Yen; Ravussin, Anthony; Pistell, Paul; Newman, Susan; Carter, Renee; Laque, Amanda; Münzberg, Heike; Rosen, Clifford J.; Ingram, Donald K.; Salbaum, J. Michael; Dixit, Vishwa Deep

    2014-01-01

    SUMMARY Despite a wealth of clinical data showing an association between inflammation and degenerative disorders in elderly, the immune sensors that causally link systemic inflammation to aging remain unclear. Here we detail a mechanism that the Nlrp3 inflammasome controls systemic low grade age-related ‘sterile’ inflammation in both periphery and brain independently of the non-canonical caspase-11 inflammasome. Ablation of Nlrp3 inflammasome protected mice from age-related increases in the innate immune activation, alterations in CNS transcriptome and astrogliosis. Consistent with the hypothesis that systemic low grade inflammation promotes age-related degenerative changes, the deficient Nlrp3 inflammasome mediated caspase-1 activity improved glycemic control and attenuated bone loss and thymic demise. Notably, IL-1 mediated only Nlrp3 inflammasome dependent improvement in cognitive function and motor performance in aged mice. These studies reveal Nlrp3 inflammasome as an upstream target that controls age-related inflammation and offer innovative therapeutic strategy to lower Nlrp3 activity to delay multiple age-related chronic diseases. PMID:24093676

  4. Purification of a vesicle-vacuole fraction functionally linked to aflatoxin synthesis in Aspergillus parasiticus.

    PubMed

    Chanda, Anindya; Roze, Ludmila V; Pastor, Alicia; Frame, Melinda K; Linz, John E

    2009-07-01

    Current studies in our laboratory demonstrate a functional link between vesicles, vacuoles and aflatoxin biosynthesis in the filamentous fungus, Aspergillus parasiticus. Under aflatoxin inducing conditions in liquid yeast-extract sucrose medium, A. parasiticus undergoes a shift from vacuole biogenesis to accumulation of an enhanced number of vesicles which exhibit significant heterogeneity in size and density. As a first step in conducting a detailed analysis of the role of these organelles in aflatoxin synthesis, we developed a novel method to purify the vesicle and vacuole fraction using protoplasts prepared from cells harvested during aflatoxin synthesis. The method includes the following steps: 1] preparation of protoplasts from mycelia grown for 36 h under aflatoxin inducing conditions; 2] release of vesicles and vacuoles from purified protoplasts in the presence of Triton X-100; and 3] fractionation of the vesicles and vacuoles using a "one-step high density cushion". The vesicle-vacuole fraction showed a 35 fold enrichment in alpha-mannosidase activity (vacuole marker) and non-detectable succinate dehydrogenase and lactate dehydrogenase activities (mitochondrial and cytoplasmic markers, respectively). Confocal laser scanning microscopy with the vacuole dyes MDY-64 and CMAC demonstrated that the fraction contained pure vesicles and vacuoles and was devoid of membranous debris. Transmission electron microscopy (TEM) confirmed that no mitochondria or unbroken protoplasts contaminated the purified fraction. The purified organelles exhibited significant size heterogeneity with a range of sizes similar to that observed in whole cells and protoplasts.

  5. FACILE CHEMICAL FUNCTIONALIZATION OF PROTEINS THROUGH INTEIN-LINKED YEAST DISPLAY

    PubMed Central

    Marshall, Carrie J.; Agarwal, Nitin; Kalia, Jeet; Grosskopf, Vanessa A.; McGrath, Nicholas A.; Abbott, Nicholas L.; Raines, Ronald T.; Shusta, Eric V.

    2013-01-01

    Intein-mediated expressed protein ligation (EPL) permits the site-specific chemical customization of proteins. While traditional techniques have used purified, soluble proteins, we have extended these methods to release and modify intein fusion proteins expressed on the yeast surface, thereby eliminating the need for soluble protein expression and purification. To this end, we sought to simultaneously release yeast surface-displayed proteins and selectively conjugate with chemical functionalities compatible with EPL and click chemistry. Single-chain antibodies (scFv) and green fluorescent protein (GFP) were displayed on the yeast surface as fusions to the N-terminus of the Mxe GyrA intein. ScFv and GFP were released from the yeast surface with either a sulfur nucleophile (MESNA) or a nitrogen nucleophile (hydrazine) linked to an azido group. The hydrazine azide permitted the simultaneous release and azido functionalization of displayed proteins, but nonspecific reactions with other yeast proteins were detected, and cleavage efficiency was limited. In contrast, MESNA released significantly more protein from the yeast surface while also generating a unique thioester at the carboxy-terminus of the released protein. These protein thioesters were subsequently reacted with a cysteine alkyne in an EPL reaction and then employed in an azide–alkyne cycloaddition to immobilize the scFv and GFP on an azide-decorated surface with >90% site-specificity. Importantly, the immobilized proteins retained their activity. Since yeast surface display is also a protein engineering platform, these approaches provide a particularly powerful tool for the rapid assessment of engineered proteins. PMID:23924245

  6. Translational informatics approach for identifying the functional molecular communicators linking coronary artery disease, infection and inflammation

    PubMed Central

    SHARMA, ANKIT; GHATGE, MADANKUMAR; MUNDKUR, LAKSHMI; VANGALA, RAJANI KANTH

    2016-01-01

    Translational informatics approaches are required for the integration of diverse and accumulating data to enable the administration of effective translational medicine specifically in complex diseases such as coronary artery disease (CAD). In the current study, a novel approach for elucidating the association between infection, inflammation and CAD was used. Genes for CAD were collected from the CAD-gene database and those for infection and inflammation were collected from the UniProt database. The cytomegalovirus (CMV)-induced genes were identified from the literature and the CAD-associated clinical phenotypes were obtained from the Unified Medical Language System. A total of 55 gene ontologies (GO) termed functional communicator ontologies were identifed in the gene sets linking clinical phenotypes in the diseasome network. The network topology analysis suggested that important functions including viral entry, cell adhesion, apoptosis, inflammatory and immune responses networked with clinical phenotypes. Microarray data was extracted from the Gene Expression Omnibus (dataset: GSE48060) for highly networked disease myocardial infarction. Further analysis of differentially expressed genes and their GO terms suggested that CMV infection may trigger a xenobiotic response, oxidative stress, inflammation and immune modulation. Notably, the current study identified γ-glutamyl transferase (GGT)-5 as a potential biomarker with an odds ratio of 1.947, which increased to 2.561 following the addition of CMV and CMV-neutralizing antibody (CMV-NA) titers. The C-statistics increased from 0.530 for conventional risk factors (CRFs) to 0.711 for GGT in combination with the above mentioned infections and CRFs. Therefore, the translational informatics approach used in the current study identified a potential molecular mechanism for CMV infection in CAD, and a potential biomarker for risk prediction. PMID:27035874

  7. Normal birth weight variation and children's neuropsychological functioning: links between language, executive functioning, and theory of mind.

    PubMed

    Wade, M; Browne, D T; Madigan, S; Plamondon, A; Jenkins, J M

    2014-10-01

    The effect of low birth weight on children's development has been documented for a range of neurocognitive outcomes. However, few previous studies have examined the effect of birth weight variability within the normal range on children's neuropsychological development. The current study examined birth weight variation amongst children weighing ≥2500 g in relation to their language, executive functioning (EF), and theory of mind (ToM), and specified a developmental pathway in which birth weight was hypothesized to be associated with children's EF and ToM through their intermediary language skills. The current study used a prospective community birth cohort of 468 children. Families were recruited when children were newborns and followed up every 18 months until children were age 4.5. Language was assessed at age 3 using a standardized measure of receptive vocabulary (PPVT), and EF and ToM were measured at age 4.5 using previously validated and developmentally appropriate tasks. After controlling for potential confounding variables (family income, parent education, gestational age), birth weight within the normal range was associated with language ability at age 3 (β=.17; p=.012); and the effect of birth weight on both EF (z=2.09; p=.03) and ToM (z=2.07; p=.03) at age 4.5 operated indirectly through their language ability at age 3. Our findings indicate that the effects of birth weight on child neurocognition extend into the normal range of birth weight, and specific developmental mechanisms may link these skills over time.

  8. Pathway analysis supports association of nonsyndromic cryptorchidism with genetic loci linked to cytoskeleton-dependent functions

    PubMed Central

    Barthold, Julia Spencer; Wang, Yanping; Kolon, Thomas F.; Kollin, Claude; Nordenskjöld, Agneta; Olivant Fisher, Alicia; Figueroa, T. Ernesto; BaniHani, Ahmad H.; Hagerty, Jennifer A.; Gonzaléz, Ricardo; Noh, Paul H.; Chiavacci, Rosetta M.; Harden, Kisha R.; Abrams, Debra J.; Kim, Cecilia E.; Li, Jin; Hakonarson, Hakon; Devoto, Marcella

    2015-01-01

    STUDY QUESTION What are the genetic loci that increase susceptibility to nonsyndromic cryptorchidism, or undescended testis? SUMMARY ANSWER A genome-wide association study (GWAS) suggests that susceptibility to cryptorchidism is heterogeneous, with a subset of suggestive signals linked to cytoskeleton-dependent functions and syndromic forms of the disease. WHAT IS KNOWN ALREADY Population studies suggest moderate genetic risk of cryptorchidism and possible maternal and environmental contributions to risk. Previous candidate gene analyses have failed to identify a major associated locus, although variants in insulin-like 3 (INSL3), relaxin/insulin-like family peptide receptor 2 (RXFP2) and other hormonal pathway genes may increase risk in a small percentage of patients. STUDY DESIGN, SIZE, DURATION This is a case–control GWAS of 844 boys with nonsyndromic cryptorchidism and 2718 control subjects without syndromes or genital anomalies, all of European ancestry. PARTICIPANTS/MATERIALS, SETTING, METHODS All boys with cryptorchidism were diagnosed and treated by a pediatric specialist. In the discovery phase, DNA was extracted from tissue or blood samples and genotyping performed using the Illumina HumanHap550 and Human610-Quad (Group 1) or OmniExpress (Group 2) platform. We imputed genotypes genome-wide, and combined single marker association results in meta-analyses for all cases and for secondary subphenotype analyses based on testis position, laterality and age, and defined genome-wide significance as P = 7 × 10−9 to correct for multiple testing. Selected markers were genotyped in an independent replication group of European cases (n = 298) and controls (n = 324). We used several bioinformatics tools to analyze top (P < 10−5) and suggestive (P < 10−3) signals for significant enrichment of signaling pathways, cellular functions and custom gene lists after multiple testing correction. MAIN RESULTS AND THE ROLE OF CHANCE In the full analysis, we identified 20

  9. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    PubMed

    Bromage, Timothy G; Idaghdour, Youssef; Lacruz, Rodrigo S; Crenshaw, Thomas D; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  10. Occupational exposure to aluminum and its amyloidogenic link with cognitive functions.

    PubMed

    Zawilla, N H; Taha, F M; Kishk, N A; Farahat, S A; Farghaly, M; Hussein, M

    2014-10-01

    As many other metals, aluminum is a widely recognized neurotoxicant and its link with neurodegenerative disorders has been the subject of scientific debate. One proposal focuses on amyloid β deposition (amyloidogenesis) as the key player in triggering neuronal dysfunction the so-called amyloid cascade hypothesis. We undertook this study first to investigate the cognition status of workers exposed to Al dust in an Al factory in Southern Cairo, second, to evaluate serum amyloid precursor protein (APP) and cathepsin D (CD) enzyme activity to study the possible role of Al in amyloidogenesis, and finally to explore the relation between these potential biomarkers and cognitive functions. The study was conducted on 54 exposed workers and 51 matched controls. They were subjected to questionnaire, neurological examination and a cognitive test battery, Addenbrooke's Cognitive Examination - Revised (ACE-R). Serum Al, APP and CD enzyme activity were measured. A significant increase of serum Al was found in the exposed workers with an associated increase in serum APP and decrement in CD activity. The exposed workers displayed poor performance on the ACE-R test. No significant correlation was detected between ACE-R test total score and either APP or CD activity. We concluded that occupational exposure to Al is associated with cognitive impairment. The effect of occupational Al exposure on the serum levels of APP and CD activity may be regarded as a possible mechanism of Al in amyloidogenesis. However, our findings do not support the utility of serum APP and CD activity as screening markers for early or preclinical cognitive impairment.

  11. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth

    PubMed Central

    Bromage, Timothy G.; Idaghdour, Youssef; Lacruz, Rodrigo S.; Crenshaw, Thomas D.; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  12. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    PubMed Central

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  13. Understanding Riparian Ecosystem Function: Linking Biogeochemistry and Hydrology at Multiple Scales

    NASA Astrophysics Data System (ADS)

    Schade, J. D.; Grimm, N. B.; Lewis, D. B.; Villinski, J.; Welter, J. R.; Conklin, M.; Huth, A. K.

    2002-12-01

    ). Developing a detailed view of hydrological exchange is also more tractable at this scale. Our work on Sycamore Creek and the San Pedro River demonstrates the importance of interfaces between landscape elements that differ strongly in redox potential and the form of N available, and the importance of direction of hydrologic exchange in determining N retention and dominant N cycling processes. The key to understanding riparian function is to improve our ability to scale up from small-scale, mechanistic studies to larger scales. Thus, our great challenge is to develop theoretical and empirical approaches that will link hydrology and biogeochemistry across multiple scales.

  14. Determining the Anchor Composition for a Mixed-Format Test: Evaluation of Subpopulation Invariance of Linking Functions

    ERIC Educational Resources Information Center

    Kim, Sooyeon; Walker, Michael

    2012-01-01

    This study examined the appropriateness of the anchor composition in a mixed-format test, which includes both multiple-choice (MC) and constructed-response (CR) items, using subpopulation invariance indices. Linking functions were derived in the nonequivalent groups with anchor test (NEAT) design using two types of anchor sets: (a) MC only and (b)…

  15. Specifying Links between Executive Functioning and Theory of Mind during Middle Childhood: Cognitive Flexibility Predicts Social Understanding

    ERIC Educational Resources Information Center

    Bock, Allison M.; Gallaway, Kristin C.; Hund, Alycia M.

    2015-01-01

    The purpose of this study was to specify the development of and links between executive functioning and theory of mind during middle childhood. One hundred four 7- to 12-year-old children completed a battery of age-appropriate tasks measuring working memory, inhibition, flexibility, theory of mind, and vocabulary. As expected, spatial working…

  16. Executive Function as a Mediator in the Link between Attention-Deficit/Hyperactivity Disorder and Social Problems

    ERIC Educational Resources Information Center

    Tseng, Wan-Ling; Gau, Susan Shur-Fen

    2013-01-01

    Background: Cognitive processes and mechanisms underlying the strong link between attention-deficit/hyperactivity disorder (ADHD) and social problems remain unclear. Limited knowledge also exists regarding a subgroup of youth with ADHD who do not have social problems. This study investigated the extent to which executive function (EF) mediated the…

  17. The Broader Context of Relational Aggression in Adolescent Romantic Relationships: Predictions from Peer Pressure and Links to Psychosocial Functioning

    ERIC Educational Resources Information Center

    Schad, Megan M.; Szwedo, David E.; Antonishak, Jill; Hare, Amanda; Allen, Joseph P.

    2008-01-01

    The broader context of relational aggression in adolescent romantic relationships was assessed by considering the ways such aggression emerged from prior experiences of peer pressure and was linked to concurrent difficulties in psychosocial functioning. Longitudinal, multi-reporter data were obtained from 97 adolescents and their best friends at…

  18. Bridging Multiple Lines Of Evidence To Quantify Plant Phenology And Assess Links To Dryland Ecosystem Function

    NASA Astrophysics Data System (ADS)

    Browning, D. M.; Tweedie, C. E.; Vivoni, E. R.; Maynard, J. J.; Karl, J.

    2015-12-01

    The clear and pressing need to reliably identify and predict shifts in plant phenology at landscape scales requires a critical link between mechanistic understanding of climate drivers and broad scale forecasts of plant responses to climate change. A multi-scale phenology study co-located with two eddy covariance towers was initiated on the Jornada Basin LTER in New Mexico in 2010 to bridge phenology patterns at the plant level with those representing aggregated signals at the landscape level. The study integrates phenology observations collected in the field along with those collected via remotely using imagery from phenocams, unmanned aerial vehicles (UAVs), and satellite sensors along with estimates of carbon flux. We applied the Breaks for Additive Seasonal and Trend (BFAST) time series algorithm to MODIS 250-m NDVI greenness index values to partition the NDVI signal into components representing the long-term trend, seasonal periodicity, and residuals and identified significant shifts in the NDVI signal (i.e., "breaks"). Previous work verified breaks representing significant deviations from the BFAST seasonal and trend models using field-estimated plant biomass collected between 2000 and 2014. We subsequently examine estimates of fractional cover by functional group derived from UAV images acquired 2010 through 2015. At a mixed grassland site, the BFAST algorithm detected four breaks in the trend model denoting significant increases in NDVI in May 2004, July 2006, and March 2010 and a significant decrease in May 2012. The 2004 and 2006 breaks corresponded to herbaceous vegetation responses to rainfall following prolonged periods of drought. The 2012 decrease in NDVI corresponded to the marked reduction of herbaceous biomass following an exceptionally dry period in late 2010-2011. Seasonal breaks representing changes in the timing and magnitude of NDVI identified in July 2006 and September 2008 coincide with rapid increases in production of annual species in

  19. Three Brachypodium distachyon Uev1s Promote Ubc13-Mediated Lys63-Linked Polyubiquitination and Confer Different Functions

    PubMed Central

    Guo, Huiping; Wen, Rui; Wang, Qianqian; Datla, Raju; Xiao, Wei

    2016-01-01

    In this study, we report the identification and functional characterization of three Brachypodium distachyon UEV genes. All three BdUev1s form heterodimers with BdUbc13s, which are capable of catalyzing Lys63-linked polyubiquitination in vitro. The three BdUEV1 genes are also able to functionally complement the budding yeast mms2 mutant defective in DNA-damage tolerance. BdUev1A differs from the other two BdUev1s in that it contains an 18-amino acid tail, which appears to compromise its function in yeast, as deletion of this tail restores full function. BdUev1A is excluded from the nucleus, whereas BdUev1B, BdUev1C and the C-terminally truncated BdUev1A are mainly found in the nucleus. These and the BdUEV1 gene expression analysis allow us to speculate that although all three BdUev1s function by promoting Lys63-linked polyubiquitination, BdUev1B and BdUev1C are involved in DNA-damage response and possibly other nuclear functions, while BdUev1A is required for non-nuclear function(s). PMID:27803708

  20. Linking Remotely Sensed Functional Diversity of Structural Traits to the Radiative Regime of a Temperate Mixed Forest

    NASA Astrophysics Data System (ADS)

    Schneider, F. D.; Morsdorf, F.; Furrer, R.; Schmid, B.; Schaepman, M. E.

    2015-12-01

    Patterns of functional diversity reflect the inter- and intraspecific variability of plant traits and are linked to other aspects of biodiversity, environmental factors and ecosystem function. To study the patterns at plot and stand level, spatially continuous trait measurements are required. Remote sensing methods based on airborne observations can offer such continuous high-resolution measurements, resolving individual trees of a forest at a regional extent. The study was performed at the Laegern forest, a temperate mixed forest dominated by deciduous and coniferous trees (Fagus sylvatica, Picea abies; 47°28'42.0" N, 8°21'51.8" E, 682 m asl; Switzerland). Canopy height, plant area index and foliage height diversity were derived from full-waveform airborne laser scanning data. These structural traits were used to calculate functional richness, functional evenness and functional divergence at a range of scales. A Bayesian multiresolution scale analysis was used to infer the scales at which functional diversity patterns occur. The radiative regime of the forest was simulated using the 3D radiative transfer model DART. Using a voxel-based forest reconstruction allowed us to derive top of canopy, bottom of canopy and absorbed photosynthetically active radiation. The results of this study will provide new insights on linking forest canopy structure to the radiative regime of the forest. Light availability is a critical factor determining plant growth and competition. Within canopy light scattering is mainly driven by the arrangement of leaves and their leaf optical properties. Therefore, we expect a link between the structural complexity of the forest as encompassed by functional diversity and the light availability within and below the canopy. Ultimately, this information can be used in dynamic ecosystem models such as ED2, allowing us to predict the influence of functional diversity and radiative properties on ecosystem functioning under current conditions and

  1. Influence of Cross-Linker Concentration on the Functionality of Carbodiimide Cross-Linked Gelatin Membranes for Retinal Sheet Carriers.

    PubMed

    Lai, Jui-Yang; Li, Ya-Ting

    2011-01-01

    Carbodiimide cross-linking can easily regulate the functionality of gelatin carriers used for retinal sheet delivery. This paper investigates the effect of cross-linker concentrations (0-0.4 mmol EDC/mg gelatin membrane (GM)) on the properties of the chemically-modified GMs. ATR-FT-IR and ninhydrin analyses results consistently indicated that the EDC cross-linking reaction approaches saturation at concentrations around 0.02 mmol EDC/mg GM. The thermal stability and resistance to water dissolution and collagenase digestion were significantly enhanced with increasing cross-linker concentration from 0.001 to 0.02 mmol EDC/mg GM. In addition, the chemical cross-linking did not affect the ability to form a tissue-encapsulating structure at 37°C. Irrespective of their cross-linking degree, the GMs had an appropriate degradation rate sufficient to allow tissue integration. It was noted that, although high cross-linker concentrations can be used to improve the delivery efficiency of gelatin samples, the treatment with 0.1-0.4 mmol EDC/mg GM may lead to poor biocompatibility. Results of Live/Dead and pro-inflammatory cytokine expression analyses showed that the exposure of ARPE-19 cultures to the test materials cross-linked with a concentration ≥0.1 mmol EDC/mg GM induces significant cytotoxicity and high levels of interleukin-1β and interleukin-6. However, the presence of EDC cross-linked gelatin membranes in the culture medium had no effect on the glutamate uptake capacity. It is concluded that among the cross-linked gelatin samples studied, 0.02 mmol EDC/mg GM is the best cross-linker concentration for preparation of retinal sheet delivery carriers.

  2. Sleep and Cognition in Preschool Years: Specific Links to Executive Functioning

    ERIC Educational Resources Information Center

    Bernier, Annie; Beauchamp, Miriam H.; Bouvette-Turcot, Andrée-Anne; Carlson, Stephanie M.; Carrier, Julie

    2013-01-01

    This study investigated the prospective links between sleep in infancy and preschoolers' cognitive performance. Mothers of 65 infants completed a sleep diary when infants were aged 1 year, and children completed two subscales of the Wechsler Preschool and Primary Scale of Intelligence at 4 years, indexing general cognitive ability and complex…

  3. Developing functional musculoskeletal tissues through hypoxia and lysyl oxidase-induced collagen cross-linking

    PubMed Central

    Makris, Eleftherios A.; Responte, Donald J.; Hu, Jerry C.; Athanasiou, Kyriacos A.

    2014-01-01

    The inability to recapitulate native tissue biomechanics, especially tensile properties, hinders progress in regenerative medicine. To address this problem, strategies have focused on enhancing collagen production. However, manipulating collagen cross-links, ubiquitous throughout all tissues and conferring mechanical integrity, has been underinvestigated. A series of studies examined the effects of lysyl oxidase (LOX), the enzyme responsible for the formation of collagen cross-links. Hypoxia-induced endogenous LOX was applied in multiple musculoskeletal tissues (i.e., cartilage, meniscus, tendons, ligaments). Results of these studies showed that both native and engineered tissues are enhanced by invoking a mechanism of hypoxia-induced pyridinoline (PYR) cross-links via intermediaries like LOX. Hypoxia was shown to enhance PYR cross-linking 1.4- to 6.4-fold and, concomitantly, to increase the tensile properties of collagen-rich tissues 1.3- to 2.2-fold. Direct administration of exogenous LOX was applied in native cartilage and neocartilage generated using a scaffold-free, self-assembling process of primary chondrocytes. Exogenous LOX was found to enhance native tissue tensile properties 1.9-fold. LOX concentration- and time-dependent increases in PYR content (∼16-fold compared with controls) and tensile properties (approximately fivefold compared with controls) of neocartilage were also detected, resulting in properties on par with native tissue. Finally, in vivo subcutaneous implantation of LOX-treated neocartilage in nude mice promoted further maturation of the neotissue, enhancing tensile and PYR content approximately threefold and 14-fold, respectively, compared with in vitro controls. Collectively, these results provide the first report, to our knowledge, of endogenous (hypoxia-induced) and exogenous LOX applications for promoting collagen cross-linking and improving the tensile properties of a spectrum of native and engineered tissues both in vitro and in

  4. Developing functional musculoskeletal tissues through hypoxia and lysyl oxidase-induced collagen cross-linking.

    PubMed

    Makris, Eleftherios A; Responte, Donald J; Paschos, Nikolaos K; Hu, Jerry C; Athanasiou, Kyriacos A

    2014-11-11

    The inability to recapitulate native tissue biomechanics, especially tensile properties, hinders progress in regenerative medicine. To address this problem, strategies have focused on enhancing collagen production. However, manipulating collagen cross-links, ubiquitous throughout all tissues and conferring mechanical integrity, has been underinvestigated. A series of studies examined the effects of lysyl oxidase (LOX), the enzyme responsible for the formation of collagen cross-links. Hypoxia-induced endogenous LOX was applied in multiple musculoskeletal tissues (i.e., cartilage, meniscus, tendons, ligaments). Results of these studies showed that both native and engineered tissues are enhanced by invoking a mechanism of hypoxia-induced pyridinoline (PYR) cross-links via intermediaries like LOX. Hypoxia was shown to enhance PYR cross-linking 1.4- to 6.4-fold and, concomitantly, to increase the tensile properties of collagen-rich tissues 1.3- to 2.2-fold. Direct administration of exogenous LOX was applied in native cartilage and neocartilage generated using a scaffold-free, self-assembling process of primary chondrocytes. Exogenous LOX was found to enhance native tissue tensile properties 1.9-fold. LOX concentration- and time-dependent increases in PYR content (∼ 16-fold compared with controls) and tensile properties (approximately fivefold compared with controls) of neocartilage were also detected, resulting in properties on par with native tissue. Finally, in vivo subcutaneous implantation of LOX-treated neocartilage in nude mice promoted further maturation of the neotissue, enhancing tensile and PYR content approximately threefold and 14-fold, respectively, compared with in vitro controls. Collectively, these results provide the first report, to our knowledge, of endogenous (hypoxia-induced) and exogenous LOX applications for promoting collagen cross-linking and improving the tensile properties of a spectrum of native and engineered tissues both in vitro and in

  5. Link functions and Matérn kernel in the estimation of reflectance spectra from RGB responses.

    PubMed

    Heikkinen, Ville; Mirhashemi, Arash; Alho, Juha

    2013-11-01

    We evaluate three link functions (square root, logit, and copula) and Matérn kernel in the kernel-based estimation of reflectance spectra of the Munsell Matte collection in the 400-700 nm region. We estimate reflectance spectra from RGB camera responses in case of real and simulated responses and show that a combination of link function and a kernel regression model with a Matérn kernel decreases spectral errors when compared to a Gaussian mixture model or kernel regression with the Gaussian kernel. Matérn kernel produces performance similar to the thin plate spline model, but does not require a parametric polynomial part in the model.

  6. Nitrocinnamate-functionalized gelatin: synthesis and "smart"hydrogel formation via photo-cross-linking.

    PubMed

    Gattás-Asfura, Kerim M; Weisman, Eric; Andreopoulos, Fotios M; Micic, Miodrag; Muller, Bill; Sirpal, Sanjeev; Pham, Si M; Leblanc, Roger M

    2005-01-01

    Gelatin having p-nitrocinnamate pendant groups (Gel-NC) was prepared via an efficient one-pot synthesis, yield >87%. (1)H NMR data indicated that 1 mol of gelatin was modified with 18 +/- 6 mol of the photosensitive group. Upon exposure to low-intensity 365 nm UV light and in the absence of photoinitiators or catalysts, Gel-NC cross-linked within minutes into a gelatin-based hydrogel as monitored by UV-vis spectroscopy. The degree of swelling of this biodegradable hydrogel in aqueous solutions responded to changes in Gel-NC concentration levels, the ionic strength of the aqueous solutions, and photo-cross-linking time. Topography changes associated with phase transition resulting from "photocleavage" of the hydrogel network with 254 nm UV light were studied with AFM. Both Gel-NC and its hydrogel expressed low toxicity to human neonatal fibroblast cells. In addition, gelatin-based microgels were prepared via the photo-cross-linking of Gel-NC within inverse micelles. PMID:15877371

  7. The use of controlled microbial cenoses in producers' link to increase steady functioning of artificial ecosystems

    NASA Astrophysics Data System (ADS)

    Somova, Lydia; Mikheeva, Galina; Somova, Lydia

    The life support systems (LSS) for long-term missions are to use cycling-recycling systems, including biological recycling. Simple ecosystems include 3 links: producers (plants), consumers (man, animals) and reducers (microorganisms). Microorganisms are substantial component of every link of LSS. Higher plants are the traditional regenerator of air and producer of food. They should be used in many successive generations of their reproduction in LSS. Controlled microbiocenoses can increase productivity of producer's link and protect plants from infections. The goal of this work was development of methodological bases of formation of stable, controlled microbiocenoses, intended for increase of productivity of plants and for obtaining ecologically pure production of plants. Main results of our investigations: 1. Experimental microbiocenoses, has been produced in view of the developed methodology on the basis of natural association of microorganisms by long cultivation on specially developed medium. Dominating groups are bacteria of genera: Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Rhodopseudomonas and yeast of genera: Kluyveromyces, Saccharomyces, Torulopsis. 2. Optimal parameters of microbiocenosis cultivation (t, pH, light exposure, biogenic elements concentrations) were experimentally established. Conditions of cultivation on which domination of different groups of microbiocenosis have been found. 3. It was shown, that processing of seeds of wheat, oats, bulbs and plants Allium cepa L. (an onions) with microbial association raised energy of germination of seeds and bulbs and promoted the increase (on 20-30 %) of growth green biomass and root system of plants in comparison with the control. This work is supported by grant, Yenissey , 07-04-96806

  8. Physicochemical, in vitro digestibility and functional properties of carboxymethyl rice starch cross-linked with epichlorohydrin.

    PubMed

    Kittipongpatana, Ornanong S; Kittipongpatana, Nisit

    2013-11-15

    Cross-linked carboxymethyl rice starches (CL-CMRSs) were prepared from reactions between native rice starch and varied concentrations (0.1-15%w/w, M-0.1 to M-15) of epichlorohydrin (ECH) in a simultaneous carboxymethylation-crosslinking reaction setup using methanol as the solvent. The degree of carboxymethyl substitution was between 0.24 and 0.28, while apparent amylose contents were lowered due to modification. SEM images showed minor change on the granule surface, while XRD profiles indicated slight loss of crystallinity. DSC thermograms revealed no transition peak in all treated samples. The water uptake (WU), swelling volume (SV) and free swelling capacity (FSC) of CL-CMRSs increased significantly as a result of the modification, while swelling of CMRSs cross-linked with 2% (M-2) and 3% (M-3) ECH yielded FSC values and WU values that were much greater than those of native starches and were comparable to that of Explotab®. All modified starch samples showed increased amount of rapidly digestible starch (RDS), while cross-linking with 5-7.5% ECH raised the resistant starch (RS) content, compared to native starch. M-2 also showed promising results in tablet disintegration test. ECH-CL-CMRSs could potentially be used as an excipient in pharmaceutical and food/food supplement products.

  9. Bottom up modeling of the connectome: linking structure and function in the resting brain and their changes in aging.

    PubMed

    Nakagawa, Tristan T; Jirsa, Viktor K; Spiegler, Andreas; McIntosh, Anthony R; Deco, Gustavo

    2013-10-15

    With the increasing availability of advanced imaging technologies, we are entering a new era of neuroscience. Detailed descriptions of the complex brain network enable us to map out a structural connectome, characterize it with graph theoretical methods, and compare it to the functional networks with increasing detail. To link these two aspects and understand how dynamics and structure interact to form functional brain networks in task and in the resting state, we use theoretical models. The advantage of using theoretical models is that by recreating functional connectivity and time series explicitly from structure and pre-defined dynamics, we can extract critical mechanisms by linking structure and function in ways not directly accessible in the real brain. Recently, resting-state models with varying local dynamics have reproduced empirical functional connectivity patterns, and given support to the view that the brain works at a critical point at the edge of a bifurcation of the system. Here, we present an overview of a modeling approach of the resting brain network and give an application of a neural mass model in the study of complexity changes in aging.

  10. Factors Determining Roles and Functions of Educational Linking Agents with Implications for Training and Support Systems. Educational Knowledge, Dissemination, and Utilization: Occasional Paper Series.

    ERIC Educational Resources Information Center

    Butler, Matilda; Paisley, William

    Relationships are examined among linking functions and the linking agent role in the context of factors that determine the function and affect the role. The historical context in which educational dissemination has evolved is described, and three major clusters of dissemination concepts that have been identified and analyzed since 1966 are…

  11. Radiation cross-linking of ethylene vinyl alcohol copolymer functionalized with m-isopropenyl-{alpha},{alpha}-dimethyl benzyl isocyanate

    SciTech Connect

    Ekman, K.B.; Naesman, J.H.

    1993-12-31

    In order to allow radiation cross-linking at low radiation doses, pendant unsaturation was introduced by reactive processing of ethylene vinyl alcohol copolymer and m-isopropenyl-{alpha},{alpha}-dimethyl benzyl isocyanate. Oxygen permeability of ethylene vinyl alcohol copolymer decreased with increasing degree of functionalization, while irradiation of the samples form trapped radicals, which act as oxygen scavengers and consequently no oxygen permeability was detected. However, radical activity was inhibited by annealing the samples at 110{degrees}C for 2.5 h, resulting in a 24% higher oxygen permeability value for the irradiated unfunctionalized copolymer, while the oxygen permeability values of the irradiated functionalized samples were 13% lower. Laminates, of m-isopropenyl-{alpha},{alpha}-dimethyl benzyl isocyanate functionalized ethylene vinyl alcohol copolymer and m-isopropenyl-{alpha},{alpha}-dimethyl benzyl isocyanate functionalized ethylene hydroxyethyl methacrylate copolymer acquired improved adhesive strength both at dry and wet conditions as well as at elevated temperatures upon exposure to radiation.

  12. Removing Cr(VI) from aqueous solutions using a functional ionic liquid-based cross-linked polymer.

    PubMed

    Gao, Hejun; Wang, Yun; Zheng, Liqiang

    2014-05-01

    A novel functional ionic liquid-based cross-linked polymer was synthesized from 1-aminoethyl-3-vinylimidazolium chloride hydrochloride and divinylbenzene. The physicochemical properties of the adsorbent were investigated using scanning electron microscopy, thermogravimetric analysis, and Fourier transform infrared spectroscopy. The adsorption capacity of the novel cross-linked polymer with respect to Cr(VI) was investigated using a batch adsorption procedure and the kinetics and thermodynamics of the adsorption process were further investigated. It was found that the adsorption kinetics was well fitted by a pseudo-second-order model and the adsorption isotherms agreed well with the Langmuir model. The maximum adsorption capacity after 5 min at room temperature (25 °C) was found to be 391.4 mg/g, which was much better than the most of the previously reported adsorbents. The adsorption process was found to be dominated by electrostatic interactions. The introduction of functional ionic liquid moieties into cross-linked poly(divinylbenzene) polymer constitutes a new and efficient kind of adsorbent.

  13. Crucial role of detailed function, task, timeline, link and human vulnerability analyses in HRA. [Human Reliability Analysis (HRA)

    SciTech Connect

    Ryan, T.G.; Haney, L.N.; Ostrom, L.T.

    1992-01-01

    This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.

  14. Executive function moderates the intention-behavior link for physical activity and dietary behavior.

    PubMed

    Hall, Peter A; Fong, Geoffrey T; Epp, Lynette J; Elias, Lorin J

    2008-01-01

    Dominant theories of health behavior posit that social-cognitive and conative variables are sufficient to explain health behavior tendencies. The current studies challenge this assumption in two ways: (1) by demonstrating that unique variance in health protective behavior is predictable by knowing about individual differences in executive functioning, and (2) by demonstrating that executive function moderates the association between intention and behavior. In Studies 1 and 2, participants completed a computer-based task of executive function (Go/NoGo task) and articulated 1-week behavioral intentions for physical activity (Study 1) and dietary behavior (Study 2). Hierarchical regression analyses revealed that executive function predicts unique variance in both behaviors, and strongly moderates the association between behavioral intention and behavioral performance. Together behavioral intention and executive function explain more variance in health protective behavior than 'rational actor' models that have been widely adopted and disseminated. PMID:25160480

  15. N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

    PubMed Central

    Ding, Yan; Meyer, Benjamin H.; Albers, Sonja-Verena; Kaminski, Lina; Eichler, Jerry

    2014-01-01

    SUMMARY N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus. PMID:24847024

  16. Application of systems engineering techniques to component design - Capturing functionality and linking part 'critical to quality' features to requirements

    SciTech Connect

    Patel, C. M.; Moorby, J. S.; Sulley, J. L.

    2012-07-01

    A systems engineering approach - focusing upon functionality - has predominantly been applied in industry to the design of complex systems with many functional interactions, inputs and outputs, eg the design of a decay heat removal system. This paper presents how systems engineering techniques can be applied to component design, i.e. treating the component as a system in its own right, and using functionality as the 'bridge' between the customer requirements and accepted performance. A pressure relief valve is used as an example to present the techniques of: Functional Modelling to establish the functional requirements and Functional Failure Modes and Effects Analysis to establish any emergent functionality to reduce the risk of adverse behaviour. A key aspect of component design is capturing the design intent and establishing the 'Critical to Quality 'features that can critically affect quality and performance. This paper details 'Quality Function Deployment' being applied to a component to capture such features and to establish a clear link to the overarching performance requirements. This approach is particularly useful in ensuring continuity of design understanding throughout the component life cycle, assessing the effects of any proposed changes to the design and the effects of changes in system or customer requirements, or for using the design in a different application. (authors)

  17. Ferroportin diseases: functional studies, a link between genetic and clinical phenotype.

    PubMed

    Détivaud, Lénaïck; Island, Marie-Laure; Jouanolle, Anne-Marie; Ropert, Martine; Bardou-Jacquet, Edouard; Le Lan, Caroline; Mosser, Annick; Leroyer, Patricia; Deugnier, Yves; David, Véronique; Brissot, Pierre; Loréal, Olivier

    2013-11-01

    Ferroportin (FPN) mediates iron export from cells and this function is modulated by serum hepcidin. Mutations in the FPN gene (SLC40A1) lead to autosomal dominant iron overload diseases related either to loss or to gain of function, and usually characterized by normal or low transferrin saturation versus elevated transferrin saturation, respectively. However, for the same mutation, the phenotypic expression may vary from one patient to another. Using in vitro overexpression of wild-type or mutant FPN proteins, we characterized the functional impact of five recently identified FPN gene mutations regarding FPN localization, cell iron status, and hepcidin sensitivity. Our aim was to integrate functional results and biological findings in probands and relatives. We show that while the p.Arg371Gln (R371Q) mutation had no impact on studied parameters, the p.Trp158Leu (W158L), p.Arg88Gly (R88G), and p.Asn185Asp (N185D) mutations caused an iron export defect and were classified as loss-of-function mutations. The p.Gly204Ser (G204S) mutation induced a gain of FPN function. Functional studies are useful to determine whether or not a FPN gene mutation found in an iron overloaded patient is deleterious and to characterize its biological impact, especially when family studies are not fully informative and/or additional confounding factors may affect bio-clinical expression.

  18. Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis--evaluation framework.

    PubMed

    Boersma, Kate S; Dee, Laura E; Miller, Steve J; Bogan, Michael T; Lytle, David A; Gitelman, Alix I

    2016-03-01

    Functional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions ("trait space") and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis-driven approach will increase the rigor and transparency of applied functional trait studies. PMID:27197386

  19. Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis--evaluation framework.

    PubMed

    Boersma, Kate S; Dee, Laura E; Miller, Steve J; Bogan, Michael T; Lytle, David A; Gitelman, Alix I

    2016-03-01

    Functional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions ("trait space") and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis-driven approach will increase the rigor and transparency of applied functional trait studies.

  20. Converging genetic and functional brain imaging evidence links neuronal excitability to working memory, psychiatric disease, and brain activity

    PubMed Central

    Heck, A.; Fastenrath, M.; Ackermann, S.; Auschra, B.; Bickel, H.; Coynel, D.; Gschwind, L.; Jessen, F.; Kaduszkiewicz, H.; Maier, W.; Milnik, A.; Pentzek, M.; Riedel-Heller, S.G.; Ripke, S.; Spalek, K.; Sullivan, P.; Vogler, C.; Wagner, M.; Weyerer, S.; Wolfsgruber, S.; de Quervain, D.; Papassotiropoulos, A.

    2014-01-01

    Summary Working memory, the capacity of actively maintaining task-relevant information during a cognitive task, is a heritable trait. Working memory deficits are characteristic for many psychiatric disorders. We performed genome-wide gene-set enrichment analyses in multiple independent data sets of young and aged cognitively healthy subjects (n = 2’824), and in a large schizophrenia case-control sample (n = 32’143). The voltage-gated cation channel activity gene-set, consisting of genes related to neuronal excitability, was robustly linked to performance in working memory-related tasks across ages, and to schizophrenia. Functional brain imaging in 707 healthy participants linked this gene-set also to working memory-related activity in the parietal cortex and the cerebellum. Gene-set analyses may help to dissect the molecular underpinnings of cognitive dimensions, brain activity and psychopathology. PMID:24529980

  1. The application of a mathematical model linking structural and functional connectomes in severe brain injury

    PubMed Central

    Kuceyeski, A.; Shah, S.; Dyke, J.P.; Bickel, S.; Abdelnour, F.; Schiff, N.D.; Voss, H.U.; Raj, A.

    2016-01-01

    Following severe injuries that result in disorders of consciousness, recovery can occur over many months or years post-injury. While post-injury synaptogenesis, axonal sprouting and functional reorganization are known to occur, the network-level processes underlying recovery are poorly understood. Here, we test a network-level functional rerouting hypothesis in recovery of patients with disorders of consciousness following severe brain injury. This hypothesis states that the brain recovers from injury by restoring normal functional connections via alternate structural pathways that circumvent impaired white matter connections. The so-called network diffusion model, which relates an individual's structural and functional connectomes by assuming that functional activation diffuses along structural pathways, is used here to capture this functional rerouting. We jointly examined functional and structural connectomes extracted from MRIs of 12 healthy and 16 brain-injured subjects. Connectome properties were quantified via graph theoretic measures and network diffusion model parameters. While a few graph metrics showed groupwise differences, they did not correlate with patients' level of consciousness as measured by the Coma Recovery Scale — Revised. There was, however, a strong and significant partial Pearson's correlation (accounting for age and years post-injury) between level of consciousness and network diffusion model propagation time (r = 0.76, p < 0.05, corrected), i.e. the time functional activation spends traversing the structural network. We concluded that functional rerouting via alternate (and less efficient) pathways leads to increases in network diffusion model propagation time. Simulations of injury and recovery in healthy connectomes confirmed these results. This work establishes the feasibility for using the network diffusion model to capture network-level mechanisms in recovery of consciousness after severe brain injury. PMID:27200264

  2. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

    PubMed Central

    Meyer, Mona; Reimand, Jüri; Lan, Xiaoyang; Head, Renee; Zhu, Xueming; Kushida, Michelle; Bayani, Jane; Pressey, Jessica C.; Lionel, Anath C.; Clarke, Ian D.; Cusimano, Michael; Squire, Jeremy A.; Scherer, Stephen W.; Bernstein, Mark; Woodin, Melanie A.; Bader, Gary D.; Dirks, Peter B.

    2015-01-01

    Glioblastoma (GBM) is a cancer comprised of morphologically, genetically, and phenotypically diverse cells. However, an understanding of the functional significance of intratumoral heterogeneity is lacking. We devised a method to isolate and functionally profile tumorigenic clones from patient glioblastoma samples. Individual clones demonstrated unique proliferation and differentiation abilities. Importantly, naïve patient tumors included clones that were temozolomide resistant, indicating that resistance to conventional GBM therapy can preexist in untreated tumors at a clonal level. Further, candidate therapies for resistant clones were detected with clone-specific drug screening. Genomic analyses revealed genes and pathways that associate with specific functional behavior of single clones. Our results suggest that functional clonal profiling used to identify tumorigenic and drug-resistant tumor clones will lead to the discovery of new GBM clone-specific treatment strategies. PMID:25561528

  3. Linking Changes in Management and Riparian Physical Functionality to Water Quality and Aquatic Habitat

    EPA Science Inventory

    Wildlife and aquatic habitats are dependent on the development of riparian area management strategies. Land management strategies consider certain basic ecological and economic relationships. These relationships are functions of riparian and te rrestrial ecosystems, which include...

  4. Extending CATH: increasing coverage of the protein structure universe and linking structure with function.

    PubMed

    Cuff, Alison L; Sillitoe, Ian; Lewis, Tony; Clegg, Andrew B; Rentzsch, Robert; Furnham, Nicholas; Pellegrini-Calace, Marialuisa; Jones, David; Thornton, Janet; Orengo, Christine A

    2011-01-01

    CATH version 3.3 (class, architecture, topology, homology) contains 128,688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework.

  5. Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation

    PubMed Central

    Agarwal, Vinayak; Peck, Spencer C.; Chen, Jui-Hui; Borisova, Svetlana A.; Chekan, Jonathan R.; van der Donk, Wilfred A.; Nair, Satish K.

    2015-01-01

    Summary Phosphonates (C-PO32−) have application as antibiotics, herbicides and detergents. In some environments, these molecules represent the predominant source for phosphorus, and several microbes have evolved dedicated enzymatic machineries for phosphonate degradation. For example, most common naturally occurring phosphonates can be catabolized to either phosphonoacetaldehyde or phosphonoacetate, which can then be hydrolyzed to generate inorganic phosphate and acetaldehyde or acetate, respectively. The phosphonoacetaldehyde oxidase gene (phnY) links these two hydrolytic processes and provides a previously unknown catabolic mechanism for phosphonoacetate production in the microbial metabolome. Here, we present biochemical characterization of PhnY and high-resolution crystal structures of the apo state, as well as complexes with substrate, cofactor and product. Kinetic analysis of active site mutants demonstrates how a highly conserved aldehyde dehydrogenase active site has been modified in nature to generate activity with a phosphonate substrate. PMID:24361046

  6. Functional links between Aβ toxicity, endocytic trafficking, and Alzheimer's disease risk factors in yeast.

    PubMed

    Treusch, Sebastian; Hamamichi, Shusei; Goodman, Jessica L; Matlack, Kent E S; Chung, Chee Yeun; Baru, Valeriya; Shulman, Joshua M; Parrado, Antonio; Bevis, Brooke J; Valastyan, Julie S; Han, Haesun; Lindhagen-Persson, Malin; Reiman, Eric M; Evans, Denis A; Bennett, David A; Olofsson, Anders; DeJager, Philip L; Tanzi, Rudolph E; Caldwell, Kim A; Caldwell, Guy A; Lindquist, Susan

    2011-12-01

    Aβ (beta-amyloid peptide) is an important contributor to Alzheimer's disease (AD). We modeled Aβ toxicity in yeast by directing the peptide to the secretory pathway. A genome-wide screen for toxicity modifiers identified the yeast homolog of phosphatidylinositol binding clathrin assembly protein (PICALM) and other endocytic factors connected to AD whose relationship to Aβ was previously unknown. The factors identified in yeast modified Aβ toxicity in glutamatergic neurons of Caenorhabditis elegans and in primary rat cortical neurons. In yeast, Aβ impaired the endocytic trafficking of a plasma membrane receptor, which was ameliorated by endocytic pathway factors identified in the yeast screen. Thus, links between Aβ, endocytosis, and human AD risk factors can be ascertained with yeast as a model system.

  7. X-linked inhibitor of apoptosis protein functions as a cofactor in transforming growth factor-beta signaling.

    PubMed

    Birkey Reffey, S; Wurthner, J U; Parks, W T; Roberts, A B; Duckett, C S

    2001-07-13

    X-linked inhibitor of apoptosis protein (XIAP) is a potent suppressor of apoptotic cell death, which functions by directly inhibiting caspases, the principal effectors of apoptosis. Here we report that XIAP can also function as a cofactor in the regulation of gene expression by transforming growth factor-beta (TGF-beta). XIAP, but not the related proteins c-IAP1 or c-IAP2, associated with several members of the type I class of the TGF-beta receptor superfamily and potentiated TGF-beta-induced signaling. Although XIAP-mediated activation of c-Jun N-terminal kinase and nuclear factor kappa B was found to require the TGF-beta signaling intermediate Smad4, the ability of XIAP to suppress apoptosis was found to be Smad4-independent. These data implicate a role for XIAP in TGF-beta-mediated signaling that is distinct from its anti-apoptotic functions.

  8. Possible pathways linking ploidy level to cell elongation and cuticular function in hypocotyls of dark-grown Arabidopsis seedlings

    PubMed Central

    Narukawa, Hideki; Yokoyama, Ryusuke; Nishitani, Kazuhiko

    2016-01-01

    abstract The mechanisms underlying correlations between ploidy level and cell size in eukaryotes remain unclear. Recently, we showed that cell length was higher in tetraploid than in diploid dark-grown Arabidopsis hypocotyls. Cuticular function was aberrant, and expression of genes of cuticle formation was reduced. Here, the links between cell elongation, cuticular function, and ploidy level in the etiolated hypocotyl were examined. Seedlings defective in cuticle formation exhibited shorter hypocotyls. This was due to inhibition of cell elongation rather than cell proliferation, indicating that the reduced cuticular function was a consequence of tetraploidy-induced cell elongation rather than its cause. Inhibition of hypocotyl elongation by impaired cuticles was lower in tetraploid than diploid, indicating that tetraploid hypocotyls were less sensitive to cuticular damage. PMID:26618780

  9. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.

    PubMed

    Mao, Hailiang; Sun, Shengyuan; Yao, Jialing; Wang, Chongrong; Yu, Sibin; Xu, Caiguo; Li, Xianghua; Zhang, Qifa

    2010-11-01

    Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function; loss-of-function mutations of these domains produced very short grain. This study linked the functional domains of the GS3 protein to natural variation of grain size in rice. PMID:20974950

  10. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

    PubMed

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-12-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).

  11. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis

    PubMed Central

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-01-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or ‘expressology’, thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). PMID:24147765

  12. Highly stable pyridinium-functionalized cross-linked anion exchange membranes for all vanadium redox flow batteries

    NASA Astrophysics Data System (ADS)

    Zeng, L.; Zhao, T. S.; Wei, L.; Zeng, Y. K.; Zhang, Z. H.

    2016-11-01

    It has recently been demonstrated that the use of anion exchange membranes (AEMs) in vanadium redox flow batteries (VRFBs) can reduce the migration of vanadium ions through the membrane due to the Donnan exclusion effect among the positively charged functional groups and vanadium ions. However, AEMs are plagued by low chemical stability in harsh chemical environments. Here we propose and fabricate a pyridinium-functionalized cross-linked AEM for VRFBs. The pyridinium-functionalized bromomethylated poly (2,6-dimethyl-1,4-phenylene oxide) exhibits a superior chemical stability as a result of the strengthened internal cross-linking networks and the chemical inertness of the polymer backbone. Therefore, the membrane exhibits littler decay in a harsh environment for 20 days during the course of an ex situ immersion test. A cycling test also demonstrates that the VRFB assembled with the membrane enable to retain 80% of the initial discharge capacity over 537 cycles with a capacity decay rate of 0.037% cycle-1. Meanwhile, the membrane also shows a low vanadium permeability and a reasonably high conductivity in supporting electrolytes. Hence, all the measurements and performance tests reported in this work suggest that the membrane is a promising AEM for redox flow batteries to achieve excellent cycling stability and superior cell performance.

  13. Callosal Function in Pediatric Traumatic Brain Injury Linked to Disrupted White Matter Integrity

    PubMed Central

    Dennis, Emily L.; Ellis, Monica U.; Marion, Sarah D.; Jin, Yan; Moran, Lisa; Olsen, Alexander; Kernan, Claudia; Babikian, Talin; Mink, Richard; Babbitt, Christopher; Johnson, Jeffrey; Giza, Christopher C.; Asarnow, Robert F.

    2015-01-01

    Traumatic brain injury (TBI) often results in traumatic axonal injury and white matter (WM) damage, particularly to the corpus callosum (CC). Damage to the CC can lead to impaired performance on neurocognitive tasks, but there is a high degree of heterogeneity in impairment following TBI. Here we examined the relation between CC microstructure and function in pediatric TBI. We used high angular resolution diffusion-weighted imaging (DWI) to evaluate the structural integrity of the CC in humans following brain injury in a sample of 32 children (23 males and 9 females) with moderate-to-severe TBI (msTBI) at 1–5 months postinjury, compared with well matched healthy control children. We assessed CC function through interhemispheric transfer time (IHTT) as measured using event-related potentials (ERPs), and related this to DWI measures of WM integrity. Finally, the relation between DWI and IHTT results was supported by additional results of neurocognitive performance assessed using a single composite performance scale. Half of the msTBI participants (16 participants) had significantly slower IHTTs than the control group. This slow IHTT group demonstrated lower CC integrity (lower fractional anisotropy and higher mean diffusivity) and poorer neurocognitive functioning than both the control group and the msTBI group with normal IHTTs. Lower fractional anisotropy—a common sign of impaired WM—and slower IHTTs also predicted poor neurocognitive function. This study reveals that there is a subset of pediatric msTBI patients during the post-acute phase of injury who have markedly impaired CC functioning and structural integrity that is associated with poor neurocognitive functioning. SIGNIFICANCE STATEMENT Traumatic brain injury (TBI) is the primary cause of death and disability in children and adolescents. There is considerable heterogeneity in postinjury outcome, which is only partially explained by injury severity. Imaging biomarkers may help explain some of this

  14. The proton-linked monocarboxylate transporter (MCT) family: structure, function and regulation.

    PubMed Central

    Halestrap, A P; Price, N T

    1999-01-01

    Monocarboxylates such as lactate and pyruvate play a central role in cellular metabolism and metabolic communication between tissues. Essential to these roles is their rapid transport across the plasma membrane, which is catalysed by a recently identified family of proton-linked monocarboxylate transporters (MCTs). Nine MCT-related sequences have so far been identified in mammals, each having a different tissue distribution, whereas six related proteins can be recognized in Caenorhabditis elegans and 4 in Saccharomyces cerevisiae. Direct demonstration of proton-linked lactate and pyruvate transport has been demonstrated for mammalian MCT1-MCT4, but only for MCT1 and MCT2 have detailed analyses of substrate and inhibitor kinetics been described following heterologous expression in Xenopus oocytes. MCT1 is ubiquitously expressed, but is especially prominent in heart and red muscle, where it is up-regulated in response to increased work, suggesting a special role in lactic acid oxidation. By contrast, MCT4 is most evident in white muscle and other cells with a high glycolytic rate, such as tumour cells and white blood cells, suggesting it is expressed where lactic acid efflux predominates. MCT2 has a ten-fold higher affinity for substrates than MCT1 and MCT4 and is found in cells where rapid uptake at low substrate concentrations may be required, including the proximal kidney tubules, neurons and sperm tails. MCT3 is uniquely expressed in the retinal pigment epithelium. The mechanisms involved in regulating the expression of different MCT isoforms remain to be established. However, there is evidence for alternative splicing of the 5'- and 3'-untranslated regions and the use of alternative promoters for some isoforms. In addition, MCT1 and MCT4 have been shown to interact specifically with OX-47 (CD147), a member of the immunoglobulin superfamily with a single transmembrane helix. This interaction appears to assist MCT expression at the cell surface. There is still

  15. Modified enzyme-linked immunosorbent assay strategy using graphene oxide sheets and gold nanoparticles functionalized with different antibody types.

    PubMed

    Lin, Hongjun; Liu, Yingfu; Huo, Jingrui; Zhang, Aihong; Pan, Yiting; Bai, Haihong; Jiao, Zhang; Fang, Tian; Wang, Xin; Cai, Yun; Wang, Qingming; Zhang, Yangjun; Qian, Xiaohong

    2013-07-01

    Gold nanoparticles (GNPs) and graphene oxide (GO) sheets are excellent nano carriers in many analytical methods. In this study, a modified enzyme-linked immunosorbent assay (ELISA) strategy was developed using antibody-functionalized GO sheets and GNPs. This modification significantly reduced the limit of detection (LOD) and cost greatly of this assay. The applicability of the method was demonstrated by detecting HSP70 in a human serum sample. This result suggests that the 3G-ELISA method is feasible to detect an antigen in a complex mixture, and the LOD is up to 64-fold and the cost is as low as one-tenth of the conventional ELISA method.

  16. Sex Differences in Mental Ability: A Proposed Means to Link Them to Brain Structure and Function

    ERIC Educational Resources Information Center

    Johnson, Wendy; Bouchard, Thomas J., Jr.

    2007-01-01

    Recent work with the 42 mental ability tests administered to participants of the Minnesota Study of Twins Reared Apart (MISTRA) has suggested that there are important dimensions of mental ability that function independently of "g". Two of these dimensions, rotation-verbal and focus-diffusion, appear to involve trade-offs: greater residual rotation…

  17. Nonoccupational environmental exposure to manganese is linked to deficits in peripheral and central olfactory function.

    PubMed

    Guarneros, Marco; Ortiz-Romo, Nahum; Alcaraz-Zubeldia, Mireya; Drucker-Colín, René; Hudson, Robyn

    2013-11-01

    Manganese is of growing concern as a toxic air pollutant. It is readily transported from the olfactory epithelium to the olfactory bulb, and unlike other metals, it is transported transynaptically to structures deep within the brain. However, little is known regarding the possible effect of nonoccupational exposure to manganese on olfactory function. Using the Sniffin' Sticks test battery, we compared the olfactory performance of subjects from a manganese mining district living <1 km from a manganese processing plant, with nonexposed subjects living 50 km from the closest source of exposure (N = 30/group). Groups were matched for age, sex, and schooling, and none had ever worked in mining-related activities. Concentrations of manganese in hair were measured as a biomarker of exposure; exposed subjects had significantly higher concentrations than nonexposed subjects. They were also significantly outperformed by the nonexposed subjects on all olfactory measures (threshold, discrimination, and identification), indicating adverse effects of manganese exposure on a range of olfactory functions, including those involving higher order cognitive processes. This contrasts with previous findings showing adverse peripheral but not central effects on olfactory function of big city air pollution, which mostly consists of toxicants known to affect the olfactory epithelium but with lower transynaptic transport capacity compared with manganese. We conclude that nonoccupational exposure to airborne manganese is associated with decrements in both peripheral and central olfactory function. PMID:24097266

  18. The speed of sound in silk: linking material performance to biological function.

    PubMed

    Mortimer, Beth; Gordon, Shira D; Holland, Chris; Siviour, Clive R; Vollrath, Fritz; Windmill, James F C

    2014-08-13

    Sonic properties of spider silks are measured independent of the web using laser vibrometry and ballistic impact providing insights into Nature's design of functionalized high-performance materials. Through comparison to cocoon silk and other industrial fibers, we find that major ampullate silk has the largest wavespeed range of any known material.

  19. Does cognitive self-consciousness link older adults' cognitive functioning to obsessive-compulsive symptoms?

    PubMed

    Prouvost, Caroline; Calamari, John E; Woodard, John L

    2016-10-01

    To elucidate how obsessional symptoms might develop or intensify in late-life, we tested a risk model. We posited that cognitive self-consciousness (CSC), a tendency to be aware of and monitor thinking, would increase reactivity to aging-related cognitive changes and mediate the relationship between cognitive functioning and obsessive-compulsive disorder (OCD) symptoms. Older adults (Mage = 76.7 years) completed the Dementia Rating Scale-2 (DRS-2), a CSC measure, and an OCD symptom measure up to four times over 18 months. A model that included DRS-2 age and education adjusted total score as the indicator of cognitive functioning fit the data well, and CSC score change mediated the relationship between initial cognitive functioning and changes in OCD symptoms. In tests of a model that included DRS-2 Initiation/Perseveration (I/P) and Conceptualization subscale scores, the model again fit the data well. Conceptualization scores, but not I/P scores, were related to later OCD symptoms, and change in CSC scores again mediated the relationship. Lower scores on initial cognitive functioning measures predicted increases in CSC scores over time, which in turn predicted increases in OCD symptoms over the 18 months of the study. Implications for understanding late-life obsessional problems are discussed. PMID:27541572

  20. "Bad Romance": Links between Psychological and Physical Aggression and Relationship Functioning in Adolescent Couples.

    PubMed

    Seiffge-Krenke, Inge; Burk, William J

    2015-06-09

    Assortative mating is an important issue in explaining antisocial, aggressive behavior. It is yet unclear, whether the similarity paradigm fully explains frequent displays of aggression in adolescents' romantic relationships. In a sample of 194 romantic partner dyads, differences between female and male partners' reports of aggression (psychological and physical) and different measures of relationship functioning (e.g., jealousy, conflicts, and the affiliative and romantic quality of the relationship) were assessed. A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of psychological and physical aggression: nonaggressive couples, couples with higher perceived aggressiveness (both physical and psychological) by females, couples with higher aggressiveness perceived by males and mutually aggressive couples. A substantial number of non-aggressive dyads emerged. Of note was the high number of females showing one-sided aggression, which was, however, not countered by their partner. The mutually aggressive couples showed the least adaptive relationship functioning, with a lack of supportive, trusting relationship qualities, high conflict rates and high jealousy. The discussion focuses on the different functions of aggression in these early romantic relations, and the aggravating impact of mutual aggression on relationship functioning and its potential antisocial outcomes.

  1. Linking avian communities and avian influenza ecology in southern Africa using epidemiological functional groups.

    PubMed

    Caron, Alexandre; de Garine-Wichatitsky, Michel; Ndlovu, Mduduzi; Cumming, Graeme S

    2012-01-01

    The ecology of pathogens, and particularly their emergence in multi-host systems, is complex. New approaches are needed to reduce superficial complexities to a level that still allows scientists to analyse underlying and more fundamental processes. One promising approach for simplification is to use an epidemiological-function classification to describe ecological diversity in a way that relates directly to pathogen dynamics. In this article, we develop and apply the epidemiological functional group (EFG) concept to explore the relationships between wild bird communities and avian influenza virus (AIV) in three ecosystems in southern Africa. Using a two year dataset that combined bird counts and bimonthly sampling for AIV, we allocated each bird species to a set of EFGs that captured two overarching epidemiological functions: the capacity of species to maintain AIV in the system, and their potential to introduce the virus. Comparing AIV prevalence between EFGs suggested that the hypothesis that anseriforms (ducks) and charadriiforms (waders) drive AIV epidemiology cannot entirely explain the high prevalence observed in some EFGs. If anseriforms do play an important role in AIV dynamics in each of the three ecosystems, the role of other species in the local maintenance of AIV cannot be ruled out. The EFG concept thus helped us to identify gaps in knowledge and to highlight understudied bird groups that might play a role in AIV epidemiology. In general, the use of EFGs has potential for generating a range of valuable insights in epidemiology, just as functional group approaches have done in ecology. PMID:23101696

  2. Stability and Change in Kindergartners' Friendships: Examination of Links with Social Functioning

    ERIC Educational Resources Information Center

    Proulx, Marie-France; Poulin, Francois

    2013-01-01

    Stability and change in kindergartners' friendships were examined based on a typology of profiles (stable, fluid, loss, gain, friendless). Our purpose was to determine whether children belonging to the five profiles differed in their social functioning. The sample was composed of 2353 kindergartners. Reciprocal friendships and social functioning…

  3. “Bad Romance”: Links between Psychological and Physical Aggression and Relationship Functioning in Adolescent Couples

    PubMed Central

    Seiffge-Krenke, Inge; Burk, William J.

    2015-01-01

    Assortative mating is an important issue in explaining antisocial, aggressive behavior. It is yet unclear, whether the similarity paradigm fully explains frequent displays of aggression in adolescents’ romantic relationships. In a sample of 194 romantic partner dyads, differences between female and male partners’ reports of aggression (psychological and physical) and different measures of relationship functioning (e.g., jealousy, conflicts, and the affiliative and romantic quality of the relationship) were assessed. A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of psychological and physical aggression: nonaggressive couples, couples with higher perceived aggressiveness (both physical and psychological) by females, couples with higher aggressiveness perceived by males and mutually aggressive couples. A substantial number of non-aggressive dyads emerged. Of note was the high number of females showing one-sided aggression, which was, however, not countered by their partner. The mutually aggressive couples showed the least adaptive relationship functioning, with a lack of supportive, trusting relationship qualities, high conflict rates and high jealousy. The discussion focuses on the different functions of aggression in these early romantic relations, and the aggravating impact of mutual aggression on relationship functioning and its potential antisocial outcomes. PMID:26067515

  4. Linking Ecosystem Services Benefit Transfer Databases and Ecosystem Services Production Function Libraries

    EPA Science Inventory

    The quantification or estimation of the economic and non-economic values of ecosystem services can be done from a number of distinct approaches. For example, practitioners may use ecosystem services production function models (ESPFMs) for a particular location, or alternatively, ...

  5. The Link between Functional Behavioral Assessments (FBAs) and Behavioral Intervention Plans (BIPs). ERIC Digest E592.

    ERIC Educational Resources Information Center

    Jolivette, Kristine; Scott, Terrance M.; Nelson, C. Michael

    This Digest discusses provisions in the Individuals with Disabilities Education Act (IDEA) that require functional behavioral assessments (FBAs) and behavioral intervention plans (BIPs) to be conducted prior to a change in placement or suspension for more than 10 days, based on inappropriate behaviors for students with disabilities. It presents…

  6. "Bad Romance": Links between Psychological and Physical Aggression and Relationship Functioning in Adolescent Couples.

    PubMed

    Seiffge-Krenke, Inge; Burk, William J

    2015-01-01

    Assortative mating is an important issue in explaining antisocial, aggressive behavior. It is yet unclear, whether the similarity paradigm fully explains frequent displays of aggression in adolescents' romantic relationships. In a sample of 194 romantic partner dyads, differences between female and male partners' reports of aggression (psychological and physical) and different measures of relationship functioning (e.g., jealousy, conflicts, and the affiliative and romantic quality of the relationship) were assessed. A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of psychological and physical aggression: nonaggressive couples, couples with higher perceived aggressiveness (both physical and psychological) by females, couples with higher aggressiveness perceived by males and mutually aggressive couples. A substantial number of non-aggressive dyads emerged. Of note was the high number of females showing one-sided aggression, which was, however, not countered by their partner. The mutually aggressive couples showed the least adaptive relationship functioning, with a lack of supportive, trusting relationship qualities, high conflict rates and high jealousy. The discussion focuses on the different functions of aggression in these early romantic relations, and the aggravating impact of mutual aggression on relationship functioning and its potential antisocial outcomes. PMID:26067515

  7. Does cognitive self-consciousness link older adults' cognitive functioning to obsessive-compulsive symptoms?

    PubMed

    Prouvost, Caroline; Calamari, John E; Woodard, John L

    2016-10-01

    To elucidate how obsessional symptoms might develop or intensify in late-life, we tested a risk model. We posited that cognitive self-consciousness (CSC), a tendency to be aware of and monitor thinking, would increase reactivity to aging-related cognitive changes and mediate the relationship between cognitive functioning and obsessive-compulsive disorder (OCD) symptoms. Older adults (Mage = 76.7 years) completed the Dementia Rating Scale-2 (DRS-2), a CSC measure, and an OCD symptom measure up to four times over 18 months. A model that included DRS-2 age and education adjusted total score as the indicator of cognitive functioning fit the data well, and CSC score change mediated the relationship between initial cognitive functioning and changes in OCD symptoms. In tests of a model that included DRS-2 Initiation/Perseveration (I/P) and Conceptualization subscale scores, the model again fit the data well. Conceptualization scores, but not I/P scores, were related to later OCD symptoms, and change in CSC scores again mediated the relationship. Lower scores on initial cognitive functioning measures predicted increases in CSC scores over time, which in turn predicted increases in OCD symptoms over the 18 months of the study. Implications for understanding late-life obsessional problems are discussed.

  8. Polysiloxane Functionalized Carbon Dots and Their Cross-Linked Flexible Silicone Rubbers for Color Conversion and Encapsulation of White LEDs.

    PubMed

    Wang, Yunfeng; Yin, Zhengmao; Xie, Zheng; Zhao, Xinxin; Zhou, Chuanjian; Zhou, Shuyun; Chen, Ping

    2016-04-20

    In this work, aminopropylmethylpolysiloxane (AMS) functionalized luminescent carbon dots (AMS-CDs) were prepared via a one-step solvothermal method. AMS-CDs could be self- or co-cross-linking with AMS to form 3D flexible transparent silicone rubbers (SRs) where CDs acted as cross-linking points, so the loading fraction of AMS-CDs could be adjusted from 10 to 100 wt %, thus modulating fluorescence properties and flexibility of silicone rubbers. Because of the self-curing property and high thermal stability, AMS-CDs were also studied in white LEDs (WLEDs), serving as a color conversion and encapsulation layer of GaN based blue LEDs simultaneously that would avoid the traditional problem of poor compatibility between emitting and packaging materials. And the color coordinate of AMS-CDs based WLEDs (0.33, 0.28) was very close to the pure white light. In addition, the obtained CDs cross-linked SRs had good transparency (T > 80%) at 510-1400 nm and high refractive indexes (1.33-1.54) that could meet the need of commercial packaging materials and optical application. AMS-CDs were also promising to be used in the UV LEDs based WLEDs according to their wide wavelength emission and flexible optoelectronic device. PMID:27035213

  9. Linking hydrology, ecosystem function, and livelihood sustainability in African papyrus wetlands using a Bayesian Network Model

    NASA Astrophysics Data System (ADS)

    van Dam, A.; Gettel, G. M.; Kipkemboi, J.; Rahman, M. M.

    2011-12-01

    Papyrus wetlands in East Africa provide ecosystem services supporting the livelihoods of millions but are rapidly degrading due to economic development. For ecosystem conservation, an integrated understanding of the natural and social processes driving ecosystem change is needed. This research focuses on integrating the causal relationships between hydrology, ecosystem function, and livelihood sustainability in Nyando wetland, western Kenya. Livelihood sustainability is based on ecosystem services that include plant and animal harvest for building material and food, conversion of wetlands to crop and grazing land, water supply, and water quality regulation. Specific objectives were: to integrate studies of hydrology, ecology, and livelihood activities using a Bayesian Network (BN) model and include stakeholder involvement in model development. The BN model (Netica 4.16) had 35 nodes with seven decision nodes describing demography, economy, papyrus market, and rainfall, and two target nodes describing ecosystem function (defined by groundwater recharge, nutrient and sediment retention, and biodiversity) and livelihood sustainability (drinking water supply, crop production, livestock production, and papyrus yield). The conditional probability tables were populated using results of ecohydrological and socio-economic field work and consultations with stakeholders. The model was evaluated for an average year with decision node probabilities set according to data from research, expert opinion, and stakeholders' views. Then, scenarios for dry and wet seasons and for economic development (low population growth and unemployment) and policy development (more awareness of wetland value) were evaluated. In an average year, the probability for maintaining a "good" level of sediment and nutrient retention functions, groundwater recharge, and biodiversity was about 60%. ("Good" is defined by expert opinion based on ongoing field research.) In the dry season, the probability was

  10. Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111

    PubMed Central

    Inhülsen, Silja; Aguilar, Claudio; Schmid, Nadine; Suppiger, Angela; Riedel, Kathrin; Eberl, Leo

    2012-01-01

    Burkholderia cenocepacia has emerged as an important pathogen for patients suffering from cystic fibrosis (CF). Previous work has shown that this organism employs the CepIR quorum-sensing (QS) system to control the expression of virulence factors as well as the formation of biofilms. To date, however, very little is known about the QS-regulated virulence factors and virtually nothing about the factors that link QS and biofilm formation. Here, we have employed a combined transcriptomic and proteomic approach to precisely define the QS regulon in our model strain B. cenocepacia H111, a CF isolate. Among the identified CepR-activated loci, three were analyzed in better detail for their roles in biofilm development: (i) a gene cluster coding for the BclACB lectins, (ii) the large surface protein BapA, and (iii) a type I pilus. The analysis of defined mutants revealed that BapA plays a major role in biofilm formation on abiotic surfaces while inactivation of the type I pilus showed little effect both in a static microtitre dish-based biofilm assay and in flow-through cells. Inactivation of the bclACB lectin genes resulted in biofilms containing hollow microcolonies, suggesting that the lectins are important for biofilm structural development. PMID:22950027

  11. Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111.

    PubMed

    Inhülsen, Silja; Aguilar, Claudio; Schmid, Nadine; Suppiger, Angela; Riedel, Kathrin; Eberl, Leo

    2012-06-01

    Burkholderia cenocepacia has emerged as an important pathogen for patients suffering from cystic fibrosis (CF). Previous work has shown that this organism employs the CepIR quorum-sensing (QS) system to control the expression of virulence factors as well as the formation of biofilms. To date, however, very little is known about the QS-regulated virulence factors and virtually nothing about the factors that link QS and biofilm formation. Here, we have employed a combined transcriptomic and proteomic approach to precisely define the QS regulon in our model strain B. cenocepacia H111, a CF isolate. Among the identified CepR-activated loci, three were analyzed in better detail for their roles in biofilm development: (i) a gene cluster coding for the BclACB lectins, (ii) the large surface protein BapA, and (iii) a type I pilus. The analysis of defined mutants revealed that BapA plays a major role in biofilm formation on abiotic surfaces while inactivation of the type I pilus showed little effect both in a static microtitre dish-based biofilm assay and in flow-through cells. Inactivation of the bclACB lectin genes resulted in biofilms containing hollow microcolonies, suggesting that the lectins are important for biofilm structural development. PMID:22950027

  12. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity.

    PubMed

    Rabbi, S M F; Daniel, H; Lockwood, P V; Macdonald, C; Pereg, L; Tighe, M; Wilson, B R; Young, I M

    2016-01-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

  13. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

    PubMed Central

    Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; Macdonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

    2016-01-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

  14. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

    NASA Astrophysics Data System (ADS)

    Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; MacDonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

    2016-09-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

  15. Decoding the conformation-linked functional properties of nucleic acids by the use of computational tools.

    PubMed

    Iacovelli, Federico; Falconi, Mattia

    2015-09-01

    DNA and RNA are large and flexible polymers selected by nature to transmit information. The most common DNA three-dimensional structure is represented by the double helix, but this biopolymer is extremely flexible and polymorphic, and can easily change its conformation to adapt to different interactions and purposes. DNA can also adopt singular topologies, giving rise, for instance, to supercoils, formed because of the limited free rotation of the DNA domain flanking a replication or transcription complex. Our understanding of the importance of these unusual or transient structures is growing, as recent studies of DNA topology, supercoiling, knotting and linking have shown that the geometric changes can drive, or strongly influence, the interactions between protein and DNA, so altering its own metabolism. On the other hand, the unique self-recognition properties of DNA, determined by the strict Watson-Crick rules of base pairing, make this material ideal for the creation of self-assembling, predesigned nanostructures. The construction of such structures is one of the main focuses of the thriving area of DNA nanotechnology, where several assembly strategies have been employed to build increasingly complex DNA nanostructures. DNA nanodevices can have direct applications in biomedicine, but also in the materials science field, requiring the immersion of DNA in an environment far from the physiological one. Crucial help in the understanding and planning of natural and artificial nanostructures is given by modern computer simulation techniques, which are able to provide a reliable structural and dynamic description of nucleic acids. PMID:25940731

  16. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology.

    PubMed

    Fleet, Tiffany; Stashi, Erin; Zhu, Bokai; Rajapakshe, Kimal; Marcelo, Kathrina L; Kettner, Nicole M; Gorman, Blythe K; Coarfa, Cristian; Fu, Loning; O'Malley, Bert W; York, Brian

    2016-10-01

    Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver.

  17. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology.

    PubMed

    Fleet, Tiffany; Stashi, Erin; Zhu, Bokai; Rajapakshe, Kimal; Marcelo, Kathrina L; Kettner, Nicole M; Gorman, Blythe K; Coarfa, Cristian; Fu, Loning; O'Malley, Bert W; York, Brian

    2016-10-01

    Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver. PMID:27432117

  18. Linking Environmental Régimes, Space and Time: Interpretations of Structural and Functional Connectivity

    NASA Astrophysics Data System (ADS)

    Wainwright, J.; Ibrahim, T. G.; Lexartza-Artza, I.; Turnbull, L.

    2008-12-01

    Traditional approaches to environmental systems have been heavily constrained by separate disciplinary frameworks within ecology, hydrology and geomorphology. Within these disciplines, there has been a significant amount of attention recently to different ideas of connectivity. These differences have reflected different concepts of structural and functional connectivity, and problems of interpretation have been further exacerbated by a lack of attention to systems connectivity. For example, structural connectivity has tended to focus on static representations of the state of the environment and thereby fail to capture the dynamic behaviour of the system. Approaches to functional connectivity have usually failed to appreciate that this connectivity is process-specific and it is thus difficult to generalize from one disciplinary area to another, and indeed in some cases even within the same disciplinary framework (e.g. dissolved pollutants or eroded soil moving in different ways from the water body). A lack of consideration of connectivity between systems can cause serious misinterpretations of system function due to the importance of what essentially become ill- posed boundary conditions. We argue that a more holistic and transdisciplinary approach to connectivity, based on the integration of a range of structural, functional and systems approaches is fundamental for improved understanding of environmental systems across a wide range of scales. We will illustrate the potential of this holistic approach with reference to a wide range of examples relating to our ongoing work. These examples will include groundwater-stream interactions, slope-channel interactions and land degradation. In all of these settings, there are important interactions in the longitudinal, lateral and vertical dimensions. For the former, the capacity of the hyporheic zone to control the fate of contaminants of stream and groundwater origin in contact with riverbed sediments is critical. Key

  19. Obesity and Alzheimer's disease: a link between body weight and cognitive function in old age.

    PubMed

    Naderali, Ebrahim K; Ratcliffe, Stuart H; Dale, Mark C

    Obesity is now a global health hazard. It not only predisposes to an array of risk factors leading to increased morbidity and mortality amongst adults but it also has a major negative impact on children's health. The deleterious effects of obesity on cardiovascular system have now been well acknowledged. It causes insulin resistance that in turn leads to diabetes, hypertension and cardiovascular abnormalities. The vascular effects of obesity may have a role in the development of a rapidly growing disease of late life, Alzheimer's disease. The precise mechanisms of the association between adiposity and impairment of cognitive performance remain to be elucidated. However, negative impact of obesity on cognitive function may be, at least in part, due to vascular defects, impaired insulin metabolism and signaling pathway or a defect in glucose transport mechanisms in brain. This review examines the available data regarding the impact of obesity on cognitive function.

  20. Linking structure to function: Recent lessons from inositol 1,4,5-trisphosphate receptor mutagenesis.

    PubMed

    Yule, David I; Betzenhauser, Matthew J; Joseph, Suresh K

    2010-06-01

    Great insight has been gained into the structure and function of the inositol 1,4,5 trisphosphate receptor (InsP(3)R) by studies employing mutagenesis of the cDNA encoding the receptor. Notably, early studies using this approach defined the key constituents required for InsP(3) binding in the N-terminus and the membrane spanning regions in the C-terminal domain responsible for channel formation, targeting and function. In this article we evaluate recent studies which have used a similar approach to investigate key residues underlying the in vivo modulation by select regulatory factors. In addition, we review studies defining the structural requirements in the channel domain which comprise the conduction pathway and are suggested to be involved in the gating of the channel.

  1. Physical activity and memory functions: are neurotrophins and cerebral gray matter volume the missing link?

    PubMed

    Flöel, A; Ruscheweyh, R; Krüger, K; Willemer, C; Winter, B; Völker, K; Lohmann, H; Zitzmann, M; Mooren, F; Breitenstein, C; Knecht, S

    2010-02-01

    Epidemiological studies reveal better cognitive function in physically active individuals. Possible mediators for this effect are neurotrophins, which are up-regulated through physical exercise and induce neuronal growth and synaptogenesis in the animal model. Here we cross-sectionally assessed 75 healthy older individuals for levels of physical activity, aerobic fitness, and memory encoding, as well as neurotrophin levels and cerebral gray matter volume. We found that physical activity, but not cardiovascular fitness, was associated with better memory encoding after controlling for age, sex, education, depression, alcohol consumption, and smoking. Higher levels of physical activity were associated with higher levels of the neurotrophin granulocyte colony stimulating factor (G-CSF) and increased cerebral gray matter volume in prefrontal and cingulate cortex as assessed by magnetic resonance voxel-based morphometry. While mediating factors will need to be further elucidated, these findings indicate that even low-level physical activity exerts beneficial effects on memory functions in older individuals.

  2. Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.

    PubMed

    Mahajan, Anubha; Rodan, Aylin R; Le, Thu H; Gaulton, Kyle J; Haessler, Jeffrey; Stilp, Adrienne M; Kamatani, Yoichiro; Zhu, Gu; Sofer, Tamar; Puri, Sanjana; Schellinger, Jeffrey N; Chu, Pei-Lun; Cechova, Sylvia; van Zuydam, Natalie; Arnlov, Johan; Flessner, Michael F; Giedraitis, Vilmantas; Heath, Andrew C; Kubo, Michiaki; Larsson, Anders; Lindgren, Cecilia M; Madden, Pamela A F; Montgomery, Grant W; Papanicolaou, George J; Reiner, Alex P; Sundström, Johan; Thornton, Timothy A; Lind, Lars; Ingelsson, Erik; Cai, Jianwen; Martin, Nicholas G; Kooperberg, Charles; Matsuda, Koichi; Whitfield, John B; Okada, Yukinori; Laurie, Cathy C; Morris, Andrew P; Franceschini, Nora

    2016-09-01

    We analyzed genome-wide association studies (GWASs), including data from 71,638 individuals from four ancestries, for estimated glomerular filtration rate (eGFR), a measure of kidney function used to define chronic kidney disease (CKD). We identified 20 loci attaining genome-wide-significant evidence of association (p < 5 × 10(-8)) with kidney function and highlighted that allelic effects on eGFR at lead SNPs are homogeneous across ancestries. We leveraged differences in the pattern of linkage disequilibrium between diverse populations to fine-map the 20 loci through construction of "credible sets" of variants driving eGFR association signals. Credible variants at the 20 eGFR loci were enriched for DNase I hypersensitivity sites (DHSs) in human kidney cells. DHS credible variants were expression quantitative trait loci for NFATC1 and RGS14 (at the SLC34A1 locus) in multiple tissues. Loss-of-function mutations in ancestral orthologs of both genes in Drosophila melanogaster were associated with altered sensitivity to salt stress. Renal mRNA expression of Nfatc1 and Rgs14 in a salt-sensitive mouse model was also reduced after exposure to a high-salt diet or induced CKD. Our study (1) demonstrates the utility of trans-ethnic fine mapping through integration of GWASs involving diverse populations with genomic annotation from relevant tissues to define molecular mechanisms by which association signals exert their effect and (2) suggests that salt sensitivity might be an important marker for biological processes that affect kidney function and CKD in humans. PMID:27588450

  3. Soil restoration with organic amendments: linking cellular functionality and ecosystem processes

    NASA Astrophysics Data System (ADS)

    Bastida, F.; Selevsek, N.; Torres, I. F.; Hernández, T.; García, C.

    2015-10-01

    A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality, and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures.

  4. Soil restoration with organic amendments: linking cellular functionality and ecosystem processes.

    PubMed

    Bastida, F; Selevsek, N; Torres, I F; Hernández, T; García, C

    2015-10-27

    A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality, and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures.

  5. Soil restoration with organic amendments: linking cellular functionality and ecosystem processes

    PubMed Central

    Bastida, F.; Selevsek, N.; Torres, I. F.; Hernández, T.; García, C.

    2015-01-01

    A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality, and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures. PMID:26503516

  6. Soil restoration with organic amendments: linking cellular functionality and ecosystem processes.

    PubMed

    Bastida, F; Selevsek, N; Torres, I F; Hernández, T; García, C

    2015-01-01

    A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality, and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures. PMID:26503516

  7. Linking functional and relational service quality to customer satisfaction and loyalty: differences between men and women.

    PubMed

    Sánchez-Hernández, Rosa M; Martínez-Tur, Vicente; Peiró, José M; Moliner, Carolina

    2010-04-01

    This study assessed differences between men and women in the association of perceptions of service quality with customer evaluations. Functional (efficiency with which the service is delivered) and relational (customers' emotional benefits, beyond the core performance, related to the social interaction of customers with employees) dimensions of service quality were measured as well as customer satisfaction and loyalty. The sample of 277 customers (191 men, 86 women), surveyed in 29 Mexican hotels, had a mean age of 38.1 yr. (SD=9.7) for men and 34.5 yr. (SD=11.0) for women. To be eligible for survey, customers had to have spent at least one night in the hotel in question. Analysis indicated that the women and men differed in the association of functional and relational dimensions of service quality with their satisfaction and loyalty. Functional service quality was higher for the men than the women, while relational service quality showed greater predictive power for women than for men, although these accounted for only 4% of the customers' satisfaction variance and 6% of the loyalty variance. PMID:20524565

  8. Linking functional and relational service quality to customer satisfaction and loyalty: differences between men and women.

    PubMed

    Sánchez-Hernández, Rosa M; Martínez-Tur, Vicente; Peiró, José M; Moliner, Carolina

    2010-04-01

    This study assessed differences between men and women in the association of perceptions of service quality with customer evaluations. Functional (efficiency with which the service is delivered) and relational (customers' emotional benefits, beyond the core performance, related to the social interaction of customers with employees) dimensions of service quality were measured as well as customer satisfaction and loyalty. The sample of 277 customers (191 men, 86 women), surveyed in 29 Mexican hotels, had a mean age of 38.1 yr. (SD=9.7) for men and 34.5 yr. (SD=11.0) for women. To be eligible for survey, customers had to have spent at least one night in the hotel in question. Analysis indicated that the women and men differed in the association of functional and relational dimensions of service quality with their satisfaction and loyalty. Functional service quality was higher for the men than the women, while relational service quality showed greater predictive power for women than for men, although these accounted for only 4% of the customers' satisfaction variance and 6% of the loyalty variance.

  9. Linking carbon storage with functional diversity in tropical rainforest in the central Congo Basin

    NASA Astrophysics Data System (ADS)

    Verbeeck, Hans; Kearsley, Elizabeth; Bauters, Marijn; Beeckman, Hans; Huygens, Dries; Steppe, Kathy; Boeckx, Pascal

    2015-04-01

    This presentation will show an overview of results of the COBIMFO project (Congo basin integrated monitoring for forest carbon mitigation and biodiversity). In the framework of this project we have established 21 permanent 1 ha sampling plots in different forest types in the Yangambi reserve. This UNESCO Man and Biosphere reserve has an area of more than 6000 km² and is located in the heart of the Congo Basin near the Yangambi research station (DR Congo). Analysis of the inventory data of these plots revealed that carbon stocks in mature forests in this area of the Congo Basin are significantly lower (24%) than stocks recorded in the outer regions of the basin. These lower stocks are attributed to a lower maximal tree height (Kearsley et al. 2013). In addition to the carbon inventories we collected leaf and wood samples on all species within 95% basal area of each of the Yangambi plots. A total of 995 individuals were sampled, covering 123 tree species. On the samples we measured 15 traits related to leaf and wood morphology and functioning. In the presented study, relationships between the observed functional diversity and biomass are analysed. One of the remarkable results of our analysis is that species with a high functional distinctiveness have a low contribution to the basal area and the carbon stocks. In contrast, species with a high contribution to the carbon stock have a low contribution to the functional diversity. Similar patterns have been observed elsewhere (e.g. Amazon basin), but are now for the first time confirmed for central African rainforest. Finally, we also present the first results of an analysis of carbons stocks and functional diversity in tropical plantations from a unique 70-years old tree diversity experiment that was established during the colonial period at the Yangambi research station. Kearsley, E., de Haulleville, T., Hufkens, K., Kidimbu, A., Toirambe, B., Baert, G., Huygens, D., Kebede, Y., Defourny, P., Bogaert, J., Beeckman, H

  10. Aliphatic polycarbonates based on carbon dioxide, furfuryl glycidyl ether, and glycidyl methyl ether: reversible functionalization and cross-linking.

    PubMed

    Hilf, Jeannette; Scharfenberg, Markus; Poon, Jeffrey; Moers, Christian; Frey, Holger

    2015-01-01

    Well-defined poly((furfuryl glycidyl ether)-co-(glycidyl methyl ether) carbonate) (P((FGE-co-GME)C)) copolymers with varying furfuryl glycidyl ether (FGE) content in the range of 26% to 100% are prepared directly from CO2 and the respective epoxides in a solvent-free synthesis. All materials are characterized by size-exclusion chromatography (SEC), (1)H NMR spectroscopy, and differential scanning calorimetry (DSC). The furfuryl-functional samples exhibit monomodal molecular weight distributions with Mw/Mn in the range of 1.16 to 1.43 and molecular weights (Mn) between 2300 and 4300 g mol(-1). Thermal properties reflect the amorphous structure of the polymers. Both post-functionalization and cross-linking are performed via Diels-Alder chemistry using maleimide derivatives, leading to reversible network formation. This transformation is shown to be thermally reversible at 110 °C.

  11. Aliphatic polycarbonates based on carbon dioxide, furfuryl glycidyl ether, and glycidyl methyl ether: reversible functionalization and cross-linking.

    PubMed

    Hilf, Jeannette; Scharfenberg, Markus; Poon, Jeffrey; Moers, Christian; Frey, Holger

    2015-01-01

    Well-defined poly((furfuryl glycidyl ether)-co-(glycidyl methyl ether) carbonate) (P((FGE-co-GME)C)) copolymers with varying furfuryl glycidyl ether (FGE) content in the range of 26% to 100% are prepared directly from CO2 and the respective epoxides in a solvent-free synthesis. All materials are characterized by size-exclusion chromatography (SEC), (1)H NMR spectroscopy, and differential scanning calorimetry (DSC). The furfuryl-functional samples exhibit monomodal molecular weight distributions with Mw/Mn in the range of 1.16 to 1.43 and molecular weights (Mn) between 2300 and 4300 g mol(-1). Thermal properties reflect the amorphous structure of the polymers. Both post-functionalization and cross-linking are performed via Diels-Alder chemistry using maleimide derivatives, leading to reversible network formation. This transformation is shown to be thermally reversible at 110 °C. PMID:25407342

  12. Genetic variation in AKT1 is linked to dopamine-associated prefrontal cortical structure and function in humans

    PubMed Central

    Tan, Hao-Yang; Nicodemus, Kristin K.; Chen, Qiang; Li, Zhen; Brooke, Jennifer K.; Honea, Robyn; Kolachana, Bhaskar S.; Straub, Richard E.; Meyer-Lindenberg, Andreas; Sei, Yoshitasu; Mattay, Venkata S.; Callicott, Joseph H.; Weinberger, Daniel R.

    2008-01-01

    AKT1-dependent molecular pathways control diverse aspects of cellular development and adaptation, including interactions with neuronal dopaminergic signaling. If AKT1 has an impact on dopaminergic signaling, then genetic variation in AKT1 would be associated with brain phenotypes related to cortical dopaminergic function. Here, we provide evidence that a coding variation in AKT1 that affects protein expression in human B lymphoblasts influenced several brain measures related to dopaminergic function. Cognitive performance linked to frontostriatal circuitry, prefrontal physiology during executive function, and frontostriatal gray-matter volume on MRI were altered in subjects with the AKT1 variation. Moreover, on neuroimaging measures with a main effect of the AKT1 genotype, there was significant epistasis with a functional polymorphism (Val158Met) in catechol-O-methyltransferase [COMT], a gene that indexes cortical synaptic dopamine. This genetic interaction was consistent with the putative role of AKT1 in dopaminergic signaling. Supportive of an earlier tentative association of AKT1 with schizophrenia, we also found that this AKT1 variant was associated with risk for schizophrenia. These data implicate AKT1 in modulating human prefrontal-striatal structure and function and suggest that the mechanism of this effect may be coupled to dopaminergic signaling and relevant to the expression of psychosis. PMID:18497887

  13. Highly efficient copper(II) ion sorbents obtained by calcium carbonate mineralization on functionalized cross-linked copolymers.

    PubMed

    Mihai, Marcela; Bunia, Ion; Doroftei, Florica; Varganici, Cristian-Dragos; Simionescu, Bogdan C

    2015-03-23

    A new type of Cu(II) ion sorbents is presented. These are obtained by CaCO3 mineralization from supersaturated solutions on gel-like cross-linked polymeric beads as insoluble templates. A divinylbenzene-ethylacrylate-acrylonitrile cross-linked copolymer functionalized with weakly acidic, basic, or amphoteric functional groups has been used, as well as different initial inorganic concentrations and addition procedures for CaCO3 crystal growth. The morphology of the new composites was investigated by SEM and compared to that of the unmodified beads, and the polymorph content was established by X-ray diffraction. The beads, before and after CaCO3 mineralization, were tested as sorbents for Cu(II) ions. The newly formed patterns on the bead surface after Cu(II) sorption were observed by SEM, and the elemental distribution on the composites and the chemical structure of crystals after interaction with Cu(II) were investigated by EDAX elemental mapping and by FTIR-ATR spectroscopy, respectively. The sorption capacity increased significantly after CaCO3 crystals growth on the weak anionic bead surface (up to 1041.5 mg Cu(II) /g sample) compared to that of unmodified beads (491.5 mg Cu(II) /g sample). PMID:25675892

  14. Functional analysis of seven genes linked to body mass index and adiposity by genome-wide association studies: a review.

    PubMed

    Speakman, John R

    2013-01-01

    Genome-wide association studies (GWAS) have identified a total of about 40 single nucleotide polymorphisms (SNPs) that show significant linkage to body mass index, a widely utilised surrogate measure of adiposity. However, only 8 of these associations have been confirmed by follow-up GWAS using more sophisticated measures of adiposity (computed tomography). Among these 8, there is a SNP close to the gene FTO which has been the subject of considerable work to diagnose its function. The remaining 7 SNPs are adjacent to, or within, the genes NEGR1, TMEM18, ETV5, FLJ35779, LINGO2, SH2B1 and GIPR, most of which are less well studied than FTO, particularly in the context of obesity. This article reviews the available data on the functions of these genes, including information gleaned from studies in humans and animal models. At present, we have virtually no information on the putative mechanism associating the genes FLJ35779 and LINGO2 to obesity. All of these genes are expressed in the brain, and for 2 of them (SH2B1 and GIPR), a direct link to the appetite regulation system is known. SH2B1 is an enhancer of intracellular signalling in the JAK-STAT pathway, and GIPR is the receptor for an appetite-linked hormone (GIP) produced by the alimentary tract. NEGR1, ETV5 and SH2B1 all have suggested roles in neurite outgrowth, and hence SNPs adjacent to these genes may affect development of the energy balance circuitry. Although the genes have central patterns of gene expression, implying a central neuronal connection to energy balance, for at least 4 of them (NEGR1, TMEM18, SH2B1 and GIPR), there are also significant peripheral functions related to adipose tissue biology. These functions may contribute to their effects on the obese phenotype.

  15. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts

    PubMed Central

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0–3 mm, transitional zone (TZ) 3–7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98–0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86–113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem. PMID:27625645

  16. Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function

    PubMed Central

    Lee, Shirley Y.; Pullen, Lester; Virgil, Daniel J.; Castañeda, Carlos A.; Abeykoon, Dulith; Bolon, Daniel N. A.; Fushman, David

    2014-01-01

    Mutations at solvent inaccessible core positions in proteins can impact function through many biophysical mechanisms including alterations to thermodynamic stability and protein dynamics. As these properties of proteins are difficult to investigate, the impacts of core mutations on protein function are poorly understood for most systems. Here, we determined the effects of alanine mutations at all 15 core positions in ubiquitin on function in yeast. The majority (13 of 15) of alanine substitutions supported yeast growth as the sole ubiquitin. The two null mutants (I30A and L43A) were both less stable to temperature-induced unfolding in vitro than wild-type, but were well folded at physiological temperatures. Heteronuclear NMR studies indicated that the L43A mutation reduces temperature stability while retaining a ground-state structure similar to wild-type. This structure enables L43A to bind to common ubiquitin receptors in vitro. Many of the core alanine ubiquitin mutants, including one of the null variants (I30A), exhibited an increased accumulation of high molecular weight species, suggesting that these mutants caused a defect in the processing of ubiquitin-substrate conjugates. In contrast, L43A exhibited a unique accumulation pattern with reduced levels of high molecular weight species and undetectable levels of free ubiquitin. When conjugation to other proteins was blocked, L43A ubiquitin accumulated as free ubiquitin in yeast. Based on these findings we speculate that ubiquitin's stability to unfolding may be required for efficient recycling during proteasome-mediated substrate degradation. PMID:24361330

  17. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts.

    PubMed

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0-3 mm, transitional zone (TZ) 3-7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98-0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86-113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem. PMID:27625645

  18. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts

    PubMed Central

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0–3 mm, transitional zone (TZ) 3–7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98–0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86–113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem.

  19. Circadian clock functioning is linked to acute stress reactivity in rats.

    PubMed

    Weibel, L; Maccari, S; Van Reeth, O

    2002-10-01

    At least two major physiological systems are involved in the adaptation of the organism to environmental challenges: the circadian system and the stress reaction. This study addressed the possibility that interindividual differences in stress sensitivity and in the functioning of the circadian system are related. At 2 months of age, corticosterone secretion in response to a 20-min restraint stress was assessed in 9 Sprague-Dawley rats for which running wheel activity was recorded as a rhythmic behavioral marker of the circadian clock. Two weeks later, the adaptive response of the circadian system to an abrupt shift in the light:dark (LD) cycle was assessed in those rats using a jet-lag paradigm. Finally, after resynchronization to the new LD cycle, rats were transferred to constant darkness to assess the free-running period of their circadian rhythm of running-wheel activity. Results indicate that stress-induced corticosterone secretion was (1) positively correlated with the number of days to resynchronize the circadian activity rhythm to the new LD cycle, and with the value of its free-running period, and (2) negatively correlated with the intensity of daily locomotor activity. Those data, emphasizing the interactions between the stress response of an organism and the functioning of its circadian system, could explain interindividual differences in humans' susceptibility to shift work or other circadian-related disorders. PMID:12375620

  20. SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability

    PubMed Central

    Li, Lei; Shi, Lan; Yang, Shangda; Yan, Ruorong; Zhang, Di; Yang, Jianguo; He, Lin; Li, Wanjin; Yi, Xia; Sun, Luyang; Liang, Jing; Cheng, Zhongyi; Shi, Lei; Shang, Yongfeng; Yu, Wenhua

    2016-01-01

    Although SIRT7 is a member of sirtuin family proteins that are described as NAD+-dependent class III histone deacetylases, the intrinsic enzymatic activity of this sirtuin protein remains to be investigated and the cellular function of SIRT7 remains to be explored. Here we report that SIRT7 is an NAD+-dependent histone desuccinylase. We show that SIRT7 is recruited to DNA double-strand breaks (DSBs) in a PARP1-dependent manner and catalyses desuccinylation of H3K122 therein, thereby promoting chromatin condensation and DSB repair. We demonstrate that depletion of SIRT7 impairs chromatin compaction during DNA-damage response and sensitizes cells to genotoxic stresses. Our study indicates SIRT7 is a histone desuccinylase, providing a molecular basis for the understanding of epigenetic regulation by this sirtuin protein. Our experiments reveal that SIRT7-catalysed H3K122 desuccinylation is critically implemented in DNA-damage response and cell survival, providing a mechanistic insight into the cellular function of SIRT7. PMID:27436229

  1. Health as normal function: a weak link in Daniels's theory of just health distribution.

    PubMed

    Krag, Erik

    2014-10-01

    Drawing on Christopher Boorse's Biostatistical Theory (BST), Norman Daniels contends that a genuine health need is one which is necessary to restore normal functioning - a supposedly objective notion which he believes can be read from the natural world without reference to potentially controversial normative categories. But despite his claims to the contrary, this conception of health harbors arbitrary evaluative judgments which make room for intractable disagreement as to which conditions should count as genuine health needs and therefore which needs should be met. I begin by offering a brief summary of Boorse's BST, the theory to which Daniels appeals for providing the conception of health as normal functioning upon which his overall distributive scheme rests. Next, I consider what I call practical objections to Daniels's use of Boorse's theory. Finally I recount Elseljin Kingma's theoretical objection to Boorse's BST and discuss its impact on Daniels's overall theory. Though I conclude that Boorse's view, so weakened, will no longer be able to sustain the judgments which Daniels's theory uses it to reach, in the end, I offer Daniels an olive branch by briefly sketching an alternative strategy for reaching suitably objective conclusions regarding the health and/or disease status of various conditions.

  2. SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability.

    PubMed

    Li, Lei; Shi, Lan; Yang, Shangda; Yan, Ruorong; Zhang, Di; Yang, Jianguo; He, Lin; Li, Wanjin; Yi, Xia; Sun, Luyang; Liang, Jing; Cheng, Zhongyi; Shi, Lei; Shang, Yongfeng; Yu, Wenhua

    2016-01-01

    Although SIRT7 is a member of sirtuin family proteins that are described as NAD(+)-dependent class III histone deacetylases, the intrinsic enzymatic activity of this sirtuin protein remains to be investigated and the cellular function of SIRT7 remains to be explored. Here we report that SIRT7 is an NAD(+)-dependent histone desuccinylase. We show that SIRT7 is recruited to DNA double-strand breaks (DSBs) in a PARP1-dependent manner and catalyses desuccinylation of H3K122 therein, thereby promoting chromatin condensation and DSB repair. We demonstrate that depletion of SIRT7 impairs chromatin compaction during DNA-damage response and sensitizes cells to genotoxic stresses. Our study indicates SIRT7 is a histone desuccinylase, providing a molecular basis for the understanding of epigenetic regulation by this sirtuin protein. Our experiments reveal that SIRT7-catalysed H3K122 desuccinylation is critically implemented in DNA-damage response and cell survival, providing a mechanistic insight into the cellular function of SIRT7. PMID:27436229

  3. Balanced translocation linked to psychiatric disorder, glutamate, and cortical structure/function

    PubMed Central

    Thomson, Pippa A; Duff, Barbara; Blackwood, Douglas H R; Romaniuk, Liana; Watson, Andrew; Whalley, Heather C; Li, Xiang; Dauvermann, Maria R; Moorhead, T William J; Bois, Catherine; Ryan, Niamh M; Redpath, Holly; Hall, Lynsey; Morris, Stewart W; van Beek, Edwin J R; Roberts, Neil; Porteous, David J; St. Clair, David; Whitcher, Brandon; Dunlop, John; Brandon, Nicholas J; Hughes, Zoë A; Hall, Jeremy; McIntosh, Andrew; Lawrie, Stephen M

    2016-01-01

    Rare genetic variants of large effect can help elucidate the pathophysiology of brain disorders. Here we expand the clinical and genetic analyses of a family with a (1;11)(q42;q14.3) translocation multiply affected by major psychiatric illness and test the effect of the translocation on the structure and function of prefrontal, and temporal brain regions. The translocation showed significant linkage (LOD score 6.1) with a clinical phenotype that included schizophrenia, schizoaffective disorder, bipolar disorder, and recurrent major depressive disorder. Translocation carriers showed reduced cortical thickness in the left temporal lobe, which correlated with general psychopathology and positive psychotic symptom severity. They showed reduced gyrification in prefrontal cortex, which correlated with general psychopathology severity. Translocation carriers also showed significantly increased activation in the caudate nucleus on increasing verbal working memory load, as well as statistically significant reductions in the right dorsolateral prefrontal cortex glutamate concentrations. These findings confirm that the t(1;11) translocation is associated with a significantly increased risk of major psychiatric disorder and suggest a general vulnerability to psychopathology through altered cortical structure and function, and decreased glutamate levels.

  4. The functional genetic link of NLGN4X knockdown and neurodevelopment in neural stem cells

    PubMed Central

    Shi, Lingling; Chang, Xiao; Zhang, Peilin; Coba, Marcelo P.; Lu, Wange; Wang, Kai

    2013-01-01

    Genetic mutations in NLGN4X (neuroligin 4), including point mutations and copy number variants (CNVs), have been associated with susceptibility to autism spectrum disorders (ASDs). However, it is unclear how mutations in NLGN4X result in neurodevelopmental defects. Here, we used neural stem cells (NSCs) as in vitro models to explore the impacts of NLGN4X knockdown on neurodevelopment. Using two shRNAmir-based vectors targeting NLGN4X and one control shRNAmir vector, we modulated NLGN4X expression and differentiated these NSCs into mature neurons. We monitored the neurodevelopmental process at Weeks 0, 0.5, 1, 2, 4 and 6, based on morphological analysis and whole-genome gene expression profiling. At the cellular level, in NSCs with NLGN4X knockdown, we observed increasingly delayed neuronal development and compromised neurite formation, starting from Week 2 through Week 6 post differentiation. At the molecular level, we identified multiple pathways, such as neurogenesis, neuron differentiation and muscle development, which are increasingly disturbed in cells with NLGN4X knockdown. Notably, several postsynaptic genes, including DLG4, NLGN1 and NLGN3, also have decreased expression. Based on in vitro models, NLGN4X knockdown directly impacts neurodevelopmental process during the formation of neurons and their connections. Our functional genomics study highlights the utility of NSCs models in understanding the functional roles of CNVs in affecting neurodevelopment and conferring susceptibility to neurodevelopmental diseases. PMID:23710042

  5. MELAS syndrome and cardiomyopathy: linking mitochondrial function to heart failure pathogenesis.

    PubMed

    Hsu, Ying-Han R; Yogasundaram, Haran; Parajuli, Nirmal; Valtuille, Lucas; Sergi, Consolato; Oudit, Gavin Y

    2016-01-01

    Heart failure remains an important clinical burden, and mitochondrial dysfunction plays a key role in its pathogenesis. The heart has a high metabolic demand, and mitochondrial function is a key determinant of myocardial performance. In mitochondrial disorders, hypertrophic remodeling is the early pattern of cardiomyopathy with progression to dilated cardiomyopathy, conduction defects and ventricular pre-excitation occurring in a significant proportion of patients. Cardiac dysfunction occurs in approximately a third of patients with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, a stereotypical example of a mitochondrial disorder leading to a cardiomyopathy. We performed unique comparative ultrastructural and gene expression in a MELAS heart compared with non-failing controls. Our results showed a remarkable increase in mitochondrial inclusions and increased abnormal mitochondria in MELAS cardiomyopathy coupled with variable sarcomere thickening, heterogeneous distribution of affected cardiomyocytes and a greater elevation in the expression of disease markers. Investigation and management of patients with mitochondrial cardiomyopathy should follow the well-described contemporary heart failure clinical practice guidelines and include an important role of medical and device therapies. Directed metabolic therapy is lacking, but current research strategies are dedicated toward improving mitochondrial function in patients with mitochondrial disorders. PMID:26712328

  6. MELAS syndrome and cardiomyopathy: linking mitochondrial function to heart failure pathogenesis.

    PubMed

    Hsu, Ying-Han R; Yogasundaram, Haran; Parajuli, Nirmal; Valtuille, Lucas; Sergi, Consolato; Oudit, Gavin Y

    2016-01-01

    Heart failure remains an important clinical burden, and mitochondrial dysfunction plays a key role in its pathogenesis. The heart has a high metabolic demand, and mitochondrial function is a key determinant of myocardial performance. In mitochondrial disorders, hypertrophic remodeling is the early pattern of cardiomyopathy with progression to dilated cardiomyopathy, conduction defects and ventricular pre-excitation occurring in a significant proportion of patients. Cardiac dysfunction occurs in approximately a third of patients with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, a stereotypical example of a mitochondrial disorder leading to a cardiomyopathy. We performed unique comparative ultrastructural and gene expression in a MELAS heart compared with non-failing controls. Our results showed a remarkable increase in mitochondrial inclusions and increased abnormal mitochondria in MELAS cardiomyopathy coupled with variable sarcomere thickening, heterogeneous distribution of affected cardiomyocytes and a greater elevation in the expression of disease markers. Investigation and management of patients with mitochondrial cardiomyopathy should follow the well-described contemporary heart failure clinical practice guidelines and include an important role of medical and device therapies. Directed metabolic therapy is lacking, but current research strategies are dedicated toward improving mitochondrial function in patients with mitochondrial disorders.

  7. Isolation of N-linked glycopeptides by hydrazine-functionalized magnetic particles.

    PubMed

    Sun, Shisheng; Yang, Ganglong; Wang, Ting; Wang, Qinzhe; Chen, Chao; Li, Zheng

    2010-04-01

    We introduce a novel combination of magnetic particles with hydrazine chemistry, dubbed as hydrazine-functionalized magnetic particles (HFMP) for isolation of glycopeptides. Four methods have been developed and compared for the production of HFMP by hydrazine modification of the surface of the carboxyl and epoxy-silanized magnetic particles, respectively. The evaluation of the capability and specificity of HFMP as well as the optimization of the coupling condition for capturing of glycoproteins were systematically investigated. The results showed that HFMP prepared by adipic dihydrazide functionalization from carboxyl-silanized magnetic particles (HFCA) displayed the maximum capture capacity and isolated efficiency for glycoprotein. When measured with glycoproteins, the capacity of the HFCA (1 g) for coupling bovine fetuin was 130 +/- 5.3 mg. The capability of this method was also confirmed by successful isolation of all formerly glycosylated peptides from standard glycoproteins and identification of their glycosylation sites, which demonstrated the feasibility of the HFCA as an alternative solid support for isolation of glycoproteins/glycopeptides. PMID:20169334

  8. Balanced translocation linked to psychiatric disorder, glutamate, and cortical structure/function

    PubMed Central

    Thomson, Pippa A; Duff, Barbara; Blackwood, Douglas H R; Romaniuk, Liana; Watson, Andrew; Whalley, Heather C; Li, Xiang; Dauvermann, Maria R; Moorhead, T William J; Bois, Catherine; Ryan, Niamh M; Redpath, Holly; Hall, Lynsey; Morris, Stewart W; van Beek, Edwin J R; Roberts, Neil; Porteous, David J; St. Clair, David; Whitcher, Brandon; Dunlop, John; Brandon, Nicholas J; Hughes, Zoë A; Hall, Jeremy; McIntosh, Andrew; Lawrie, Stephen M

    2016-01-01

    Rare genetic variants of large effect can help elucidate the pathophysiology of brain disorders. Here we expand the clinical and genetic analyses of a family with a (1;11)(q42;q14.3) translocation multiply affected by major psychiatric illness and test the effect of the translocation on the structure and function of prefrontal, and temporal brain regions. The translocation showed significant linkage (LOD score 6.1) with a clinical phenotype that included schizophrenia, schizoaffective disorder, bipolar disorder, and recurrent major depressive disorder. Translocation carriers showed reduced cortical thickness in the left temporal lobe, which correlated with general psychopathology and positive psychotic symptom severity. They showed reduced gyrification in prefrontal cortex, which correlated with general psychopathology severity. Translocation carriers also showed significantly increased activation in the caudate nucleus on increasing verbal working memory load, as well as statistically significant reductions in the right dorsolateral prefrontal cortex glutamate concentrations. These findings confirm that the t(1;11) translocation is associated with a significantly increased risk of major psychiatric disorder and suggest a general vulnerability to psychopathology through altered cortical structure and function, and decreased glutamate levels. PMID:27602385

  9. Balanced translocation linked to psychiatric disorder, glutamate, and cortical structure/function.

    PubMed

    Thomson, Pippa A; Duff, Barbara; Blackwood, Douglas H R; Romaniuk, Liana; Watson, Andrew; Whalley, Heather C; Li, Xiang; Dauvermann, Maria R; Moorhead, T William J; Bois, Catherine; Ryan, Niamh M; Redpath, Holly; Hall, Lynsey; Morris, Stewart W; van Beek, Edwin J R; Roberts, Neil; Porteous, David J; St Clair, David; Whitcher, Brandon; Dunlop, John; Brandon, Nicholas J; Hughes, Zoë A; Hall, Jeremy; McIntosh, Andrew; Lawrie, Stephen M

    2016-01-01

    Rare genetic variants of large effect can help elucidate the pathophysiology of brain disorders. Here we expand the clinical and genetic analyses of a family with a (1;11)(q42;q14.3) translocation multiply affected by major psychiatric illness and test the effect of the translocation on the structure and function of prefrontal, and temporal brain regions. The translocation showed significant linkage (LOD score 6.1) with a clinical phenotype that included schizophrenia, schizoaffective disorder, bipolar disorder, and recurrent major depressive disorder. Translocation carriers showed reduced cortical thickness in the left temporal lobe, which correlated with general psychopathology and positive psychotic symptom severity. They showed reduced gyrification in prefrontal cortex, which correlated with general psychopathology severity. Translocation carriers also showed significantly increased activation in the caudate nucleus on increasing verbal working memory load, as well as statistically significant reductions in the right dorsolateral prefrontal cortex glutamate concentrations. These findings confirm that the t(1;11) translocation is associated with a significantly increased risk of major psychiatric disorder and suggest a general vulnerability to psychopathology through altered cortical structure and function, and decreased glutamate levels. PMID:27602385

  10. A Kinase-Independent Function of CDK6 Links the Cell Cycle to Tumor Angiogenesis

    PubMed Central

    Kollmann, Karoline; Heller, Gerwin; Schneckenleithner, Christine; Warsch, Wolfgang; Scheicher, Ruth; Ott, Rene G.; Schäfer, Markus; Fajmann, Sabine; Schlederer, Michaela; Schiefer, Ana-Iris; Reichart, Ursula; Mayerhofer, Matthias; Hoeller, Christoph; Zöchbauer-Müller, Sabine; Kerjaschki, Dontscho; Bock, Christoph; Kenner, Lukas; Hoefler, Gerald; Freissmuth, Michael; Green, Anthony R.; Moriggl, Richard; Busslinger, Meinrad; Malumbres, Marcos; Sexl, Veronika

    2013-01-01

    Summary In contrast to its close homolog CDK4, the cell cycle kinase CDK6 is expressed at high levels in lymphoid malignancies. In a model for p185BCR-ABL+ B-acute lymphoid leukemia, we show that CDK6 is part of a transcription complex that induces the expression of the tumor suppressor p16INK4a and the pro-angiogenic factor VEGF-A. This function is independent of CDK6’s kinase activity. High CDK6 expression thus suppresses proliferation by upregulating p16INK4a, providing an internal safeguard. However, in the absence of p16INK4a, CDK6 can exert its full tumor-promoting function by enhancing proliferation and stimulating angiogenesis. The finding that CDK6 connects cell-cycle progression to angiogenesis confirms CDK6’s central role in hematopoietic malignancies and could underlie the selection pressure to upregulate CDK6 and silence p16INK4a. PMID:23948297

  11. The Fanconi Anaemia Components UBE2T and FANCM Are Functionally Linked to Nucleotide Excision Repair

    PubMed Central

    Kelsall, Ian R.; Langenick, Judith; MacKay, Craig; Patel, Ketan J.; Alpi, Arno F.

    2012-01-01

    The many proteins that function in the Fanconi anaemia (FA) monoubiquitylation pathway initiate replicative DNA crosslink repair. However, it is not clear whether individual FA genes participate in DNA repair pathways other than homologous recombination and translesion bypass. Here we show that avian DT40 cell knockouts of two integral FA genes – UBE2T and FANCM are unexpectedly sensitive to UV-induced DNA damage. Comprehensive genetic dissection experiments indicate that both of these FA genes collaborate to promote nucleotide excision repair rather than translesion bypass to protect cells form UV genotoxicity. Furthermore, UBE2T deficiency impacts on the efficient removal of the UV-induced photolesion cyclobutane pyrimidine dimer. Therefore, this work reveals that the FA pathway shares two components with nucleotide excision repair, intimating not only crosstalk between the two major repair pathways, but also potentially identifying a UBE2T-mediated ubiquitin-signalling response pathway that contributes to nucleotide excision repair. PMID:22615860

  12. Incorporating Data Link Messaging into a Multi-function Display for General Aviation Aircraft

    NASA Technical Reports Server (NTRS)

    Adams, Catherine A.; Murdoch, Jennifer L.

    2006-01-01

    One objective of the Small Aircraft Transportation System (SATS) Project is to increase the capacity and utilization of small non-towered, non-radar equipped airports by transferring traffic management activities to an automated system and separation responsibilities to general aviation (GA) pilots. This paper describes the development of a research multi-function display (MFD) to support the interaction between pilots and an automated Airport Management Module (AMM). Preliminary results of simulation and flight tests indicate that adding the responsibility of monitoring other traffic for self-separation does not increase pilots subjective workload levels. Pilots preferred using the enhanced MFD to execute flight procedures, reporting improved situation awareness over conventional instrument flight rules (IFR) procedures.

  13. Molecular Mechanisms Underlying the Link between Nuclear Receptor Function and Cholesterol Gallstone Formation

    PubMed Central

    Vázquez, Mary Carmen; Rigotti, Attilio; Zanlungo, Silvana

    2012-01-01

    Cholesterol gallstone disease is highly prevalent in western countries, particularly in women and some specific ethnic groups. The formation of water-insoluble cholesterol crystals is due to a misbalance between the three major lipids present in the bile: cholesterol, bile salts, and phospholipids. Many proteins implicated in biliary lipid secretion in the liver are regulated by several transcription factors, including nuclear receptors LXR and FXR. Human and murine genetic, physiological, pathophysiological, and pharmacological evidence is consistent with the relevance of these nuclear receptors in gallstone formation. In addition, there is emerging data that also suggests a role for estrogen receptor ESR1 in abnormal cholesterol metabolism leading to gallstone disease. A better comprehension of the role of nuclear receptor function in gallstone formation may help to design new and more effective therapeutic strategies for this highly prevalent disease condition. PMID:22132343

  14. Gamma oscillations in the midbrain spatial attention network: linking circuits to function.

    PubMed

    Sridharan, Devarajan; Knudsen, Eric I

    2015-04-01

    Gamma-band (25-140Hz) oscillations are ubiquitous in mammalian forebrain structures involved in sensory processing, attention, learning and memory. The optic tectum (OT) is the central structure in a midbrain network that participates critically in controlling spatial attention. In this review, we summarize recent advances in characterizing a neural circuit in this midbrain network that generates large amplitude, space-specific, gamma oscillations in the avian OT, both in vivo and in vitro. We describe key physiological and pharmacological mechanisms that produce and regulate the structure of these oscillations. The extensive similarities between midbrain gamma oscillations in birds and those in the neocortex and hippocampus of mammals, offer important insights into the functional significance of a midbrain gamma oscillatory code.

  15. Impacts of warming revealed by linking resource growth rates with consumer functional responses.

    PubMed

    West, Derek C; Post, David M

    2016-05-01

    Warming global temperatures are driving changes in species distributions, growth and timing, but much uncertainty remains regarding how climate change will alter species interactions. Consumer-Resource interactions in particular can be strongly impacted by changes to the relative performance of interacting species. While consumers generally gain an advantage over their resources with increasing temperatures, nonlinearities can change this relation near temperature extremes. We use an experimental approach to determine how temperature changes between 5 and 30 °C will alter the growth of the algae Scenedesmus obliquus and the functional responses of the small-bodied Daphnia ambigua and the larger Daphnia pulicaria. The impact of warming generally followed expectations, making both Daphnia species more effective grazers, with the increase in feeding rates outpacing the increases in algal growth rate. At the extremes of our temperature range, however, warming resulted in a decrease in Daphnia grazing effectiveness. Between 25 and 30 °C, both species of Daphnia experienced a precipitous drop in feeding rates, while algal growth rates remained high, increasing the likelihood of algal blooms in warming summer temperatures. Daphnia pulicaria performed significantly better at cold temperatures than D. ambigua, but by 20 °C, there was no significant difference between the two species, and at 25 °C, D. ambigua outperformed D. pulicaria. Warming summer temperatures will favour the smaller D. ambigua, but only over a narrow temperature range, and warming beyond 25 °C could open D. ambigua to invasion from tropical species. By fitting our results to temperature-dependent functions, we develop a temperature- and density-dependent model, which produces a metric of grazing effectiveness, quantifying the grazer density necessary to halt algal growth. This approach should prove useful for tracking the transient dynamics of other density-dependent consumer

  16. Crystal Structure of Human Senescence Marker Protein 30: Insights Linking Structural, Enzymatic, and Physiological Functions

    SciTech Connect

    Chakraborti, Subhendu; Bahnson, Brian J.

    2010-05-25

    Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. SMP30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. SMP30 is also referred to as regucalcin and has been suggested to have functions in calcium homeostasis. The crystal structure of the human enzyme has been solved from X-ray diffraction data collected to a resolution of 1.4 {angstrom}. The protein has a 6-bladed {beta}-propeller fold, and it contains a single metal ion. Crystal structures have been solved with the metal site bound with either a Ca{sup 2+} or a Zn{sup 2+} atom. The catalytic role of the metal ion has been confirmed by mutagenesis of the metal coordinating residues. Kinetic studies using the substrate gluconolactone showed a k{sub cat} preference of divalent cations in the order Zn{sup 2+} > Mn{sup 2+} > Ca{sup 2+} > Mg{sup 2+}. Notably, the Ca{sup 2+} had a significantly higher value of K{sub d} compared to those of the other metal ions tested (566, 82, 7, and 0.6 {micro}m for Ca{sup 2+}, Mg{sup 2+}, Zn{sup 2+}, and Mn{sup 2+}, respectively), suggesting that the Ca{sup 2+}-bound form may be physiologically relevant for stressed cells with an elevated free calcium level.

  17. Hydrologic Storage Functions of an Alpine Talus: Linking Field Observations with Numerical Simulations

    NASA Astrophysics Data System (ADS)

    Kurylyk, B.; Hayashi, M.

    2015-12-01

    Alpine watersheds source major rivers in many regions of the world and thereby supply essential water for irrigation, human consumption, and hydroelectricity. Coarse depositional units in alpine catchments, such as taluses and proglacial moraines, are thought to store and transmit significant volumes of groundwater and thus buffer flooding during snowmelt and augment stream discharge during the dry season when water supply is critical. This study focuses on the hydrologic functions of an alpine talus unit within the Lake O'Hara watershed in the Canadian Rockies of British Columbia. Previous field investigations indicate that the talus exhibits very high hydraulic conductivity, low storage capacity, and a fast hydrograph recession with an exponential decay of approximately 1 d-1. Despite the low storage and flashy response to snowmelt input, the isotopic signature of the stream fed by the talus indicates that the discharging water is predominantly pre-event water. Herein we investigate internal processes controlling the bulk hydrologic functioning of this talus unit using a finite element model of coupled subsurface water flow and transport. The hydrologic parameters of the model are calibrated to achieve congruence between the simulated and observed response (lag time) to the snowmelt input. The transport equation is employed to simulate the age of discharging water and investigate how the mean transit time is influenced by hydraulic conductivity, boundary conditions, and talus geometry (e.g., step features in the bedrock plane beneath the talus). The hydraulic properties and talus boundaries are adjusted within the model to see how other talus units with differing geologic composition and geometry may store and transmit water and thus attenuate flood stage or enhance baseflow in other alpine catchments. Also, earlier snowmelt infiltration is considered to examine how a warming climate may influence the timing and magnitude of talus discharge to alpine streams.

  18. The cognitive nature of action - functional links between cognitive psychology, movement science, and robotics.

    PubMed

    Schack, Thomas; Ritter, Helge

    2009-01-01

    This paper examines the cognitive architecture of human action, showing how it is organized over several levels and how it is built up. Basic action concepts (BACs) are identified as major building blocks on a representation level. These BACs are cognitive tools for mastering the functional demands of movement tasks. Results from different lines of research showed that not only the structure formation of mental representations in long-term memory but also chunk formation in working memory are built up on BACs and relate systematically to movement structures. It is concluded that such movement representations might provide the basis for action implementation and action control in skilled voluntary movements in the form of cognitive reference structures. To simulate action implementation we discuss challenges and issues that arise when we try to replicate complex movement abilities in robots. Among the key issues to be addressed is the question how structured representations can arise during skill acquisition and how the underlying processes can be understood sufficiently succinctly to replicate them on robot platforms. Working towards this goal, we translate our findings in studies of motor control in humans into models that can guide the implementation of cognitive robot architectures. Focusing on the issue of manual action control, we illustrate some results in the context of grasping with a five-fingered anthropomorphic robot hand.

  19. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism

    PubMed Central

    Darnell, Jennifer C.; Van Driesche, Sarah J.; Zhang, Chaolin; Hung, Ka Ying Sharon; Mele, Aldo; Fraser, Claire E.; Stone, Elizabeth F.; Chen, Cynthia; Fak, John J.; Chi, Sung Wook; Licatalosi, Donny D.; Richter, Joel D.; Darnell, Robert B.

    2011-01-01

    Summary FMRP loss-of-function causes Fragile X Syndrome (FXS) and autistic features. FMRP is a polyribosome-associated neuronal RNA-binding protein, suggesting that it plays a key role in regulating neuronal translation, but there has been little consensus regarding either its RNA targets or mechanism of action. Here we use high throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify FMRP interactions with mouse brain polyribosomal mRNAs. FMRP interacts with the coding region of transcripts encoding pre- and postsynaptic proteins, and transcripts implicated in autism spectrum disorders (ASD). We developed a brain polyribosome-programmed translation system, revealing that FMRP reversibly stalls ribosomes specifically on its target mRNAs. Our results indicate that loss of a translational brake on the synthesis of a subset of synaptic proteins may contribute to FXS. In addition, they provide insight into the molecular basis of the cognitive and allied defects in FXS and ASD, and suggest multiple targets for clinical intervention. PMID:21784246

  20. Microplastic moves pollutants and additives to worms, reducing functions linked to health and biodiversity.

    PubMed

    Browne, Mark Anthony; Niven, Stewart J; Galloway, Tamara S; Rowland, Steve J; Thompson, Richard C

    2013-12-01

    Inadequate products, waste management, and policy are struggling to prevent plastic waste from infiltrating ecosystems [1, 2]. Disintegration into smaller pieces means that the abundance of micrometer-sized plastic (microplastic) in habitats has increased [3] and outnumbers larger debris [2, 4]. When ingested by animals, plastic provides a feasible pathway to transfer attached pollutants and additive chemicals into their tissues [5-15]. Despite positive correlations between concentrations of ingested plastic and pollutants in tissues of animals, few, if any, controlled experiments have examined whether ingested plastic transfers pollutants and additives to animals. We exposed lugworms (Arenicola marina) to sand with 5% microplastic that was presorbed with pollutants (nonylphenol and phenanthrene) and additive chemicals (Triclosan and PBDE-47). Microplastic transferred pollutants and additive chemicals into gut tissues of lugworms, causing some biological effects, although clean sand transferred larger concentrations of pollutants into their tissues. Uptake of nonylphenol from PVC or sand reduced the ability of coelomocytes to remove pathogenic bacteria by >60%. Uptake of Triclosan from PVC diminished the ability of worms to engineer sediments and caused mortality, each by >55%, while PVC alone made worms >30% more susceptible to oxidative stress. As global microplastic contamination accelerates, our findings indicate that large concentrations of microplastic and additives can harm ecophysiological functions performed by organisms. PMID:24309271

  1. Daily parental knowledge of youth activities is linked to youth physical symptoms and HPA functioning.

    PubMed

    Lippold, Melissa A; Davis, Kelly D; McHale, Susan M; Almeida, David M

    2016-03-01

    Considerable evidence documents linkages between parental knowledge of youth activities and youth risky behavior. We extended this research to determine whether parental knowledge was associated with youth physical health, including reports of physical symptoms (e.g., headaches, stomachaches) and a biomarker of hypothalamic pituitary adrenocortical (HPA) axis functioning (i.e., salivary cortisol levels). Participants were children of employees in the Information Technology division of a Fortune 500 company (N = 132, mean age youth = 13.39 years, 55% female) who participated in a daily diary study. Data were collected via telephone calls on 8 consecutive evenings. On 4 study days, cortisol samples were collected at 4 time points (waking, 30 min after waking, before dinner, bedtime). Multilevel models revealed that, at the between-person level, youth whose parents had higher average knowledge about their activities, exhibited lower bedtime cortisol levels. Furthermore, at the within-person level, on days when parents displayed more knowledge than usual (relative to their own 8-day average), youth had lower before-dinner cortisol than usual. Linkages between average parental knowledge and physical health symptoms were moderated by youth age: Younger but not older adolescents whose parents were more knowledgeable had fewer physical health symptoms, on average. A next step is to identify the processes that underlie these associations. PMID:26751757

  2. Functional Characterization of IPSC-Derived Brain Cells as a Model for X-Linked Adrenoleukodystrophy

    PubMed Central

    Baarine, Mauhamad; Khan, Mushfiquddin; Singh, Avtar; Singh, Inderjit

    2015-01-01

    X-ALD is an inherited neurodegenerative disorder where mutations in the ABCD1 gene result in clinically diverse phenotypes: the fatal disorder of cerebral childhood ALD (cALD) or a milder disorder of adrenomyeloneuropathy (AMN). The various models used to study the pathobiology of X-ALD disease lack the appropriate presentation for different phenotypes of cALD vs AMN. This study demonstrates that induced pluripotent stem cells (IPSC) derived brain cells astrocytes (Ast), neurons and oligodendrocytes (OLs) express morphological and functional activities of the respective brain cell types. The excessive accumulation of saturated VLCFA, a “hallmark” of X-ALD, was observed in both AMN OLs and cALD OLs with higher levels observed in cALD OLs than AMN OLs. The levels of ELOVL1 (ELOVL Fatty Acid Elongase 1) mRNA parallel the VLCFA load in AMN and cALD OLs. Furthermore, cALD Ast expressed higher levels of proinflammatory cytokines than AMN Ast and control Ast with or without stimulation with lipopolysaccharide. These results document that IPSC-derived Ast and OLs from cALD and AMN fibroblasts mimic the respective biochemical disease phenotypes and thus provide an ideal platform to investigate the mechanism of VLCFA load in cALD OLs and VLCFA-induced inflammatory disease mechanisms of cALD Ast and thus for testing of new therapeutics for AMN and cALD disease of X-ALD. PMID:26581106

  3. Trip report: pilot studies of factors linking watershed function and coastal ecosystem health in American Samoa

    USGS Publications Warehouse

    Atkinson, Carter T.; Medeiros, Arthur C.

    2010-01-01

    Coral reef resources in the territory of American Samoa face significant problems from overfishing, non-point source pollution, global warming, and continuing population growth and development. The islands are still relatively isolated relative to other parts of the Pacific and have managed to avoid some of the more devastating invasive species that have reached other archipelagoes. As a result, there are opportunities for collaborative and integrative research and monitoring programs to help restore and maintain biodiversity and functioning natural ecosystem in the archipelago. We found that the 'Ridge to Reef' paradigm already exists in American Samoa, with a high degree of interagency cooperation and efficient use of limited resources already taking place in the Territory. USGS may be able to make contributions as a partner organization in the Coral Reef Advisory Group (CRAG) through deployment of sediment monitoring instrumentation to supplement stream monitoring by the American Samoa Environmental Protection Agency, by providing high resolution vegetation and land-use maps of main islands, by providing additional support to the American Samoa Department of Marine and Wildlife Resources and the National Park Service for monitoring of invasive species, by working with members of CRAG to initiate sediment transport studies on Samoan reefs, and by developing new projects on the effects of bacterial contamination and pollutants on coral reef physiology and demography.

  4. Discs-Large and Strabismus are functionally linked to plasma membrane formation.

    PubMed

    Lee, Ok-Kyung; Frese, Kristopher K; James, Jennifer S; Chadda, Darshana; Chen, Zhi-Hong; Javier, Ronald T; Cho, Kyung-Ok

    2003-11-01

    During early embryogenesis in Drosophila melanogaster, extensive vesicle transport occurs to build cell boundaries for 6,000 nuclei. Here we show that this important process depends on a functional complex formed between the tumour suppressor and adaptor protein Discs-Large (Dlg) and the integral membrane protein Strabismus (Stbm)/Van Gogh (Vang). In support of this idea, embryos with mutations in either dlg or stbm displayed severe defects in plasma membrane formation. Conversely, overexpression of Dlg and Stbm synergistically induced excessive plasma membrane formation. In addition, ectopic co-expression of Stbm (which associated with post-Golgi vesicles) and the mammalian Dlg homologue SAP97/hDlg promoted translocation of SAP97 from the cytoplasm to both post-Golgi vesicles and the plasma membrane. This effect was dependent on the interaction between Stbm and SAP97. These findings suggest that the Dlg-Stbm complex recruits membrane-associated proteins and lipids from internal membranes to sites of new plasma membrane formation.

  5. A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration

    PubMed Central

    Lobo, Daniel; Feldman, Erica B.; Shah, Michelle; Malone, Taylor J.

    2014-01-01

    Abstract Amphibians and molting arthropods have the remarkable capacity to regenerate amputated limbs, as described by an extensive literature of experimental cuts, amputations, grafts, and molecular techniques. Despite a rich history of experimental effort, no comprehensive mechanistic model exists that can account for the pattern regulation observed in these experiments. While bioinformatics algorithms have revolutionized the study of signaling pathways, no such tools have heretofore been available to assist scientists in formulating testable models of large‐scale morphogenesis that match published data in the limb regeneration field. Major barriers to preventing an algorithmic approach are the lack of formal descriptions for experimental regenerative information and a repository to centralize storage and mining of functional data on limb regeneration. Establishing a new bioinformatics of shape would significantly accelerate the discovery of key insights into the mechanisms that implement complex regeneration. Here, we describe a novel mathematical ontology for limb regeneration to unambiguously encode phenotype, manipulation, and experiment data. Based on this formalism, we present the first centralized formal database of published limb regeneration experiments together with a user‐friendly expert system tool to facilitate its access and mining. These resources are freely available for the community and will assist both human biologists and artificial intelligence systems to discover testable, mechanistic models of limb regeneration. PMID:25729585

  6. Microplastic moves pollutants and additives to worms, reducing functions linked to health and biodiversity.

    PubMed

    Browne, Mark Anthony; Niven, Stewart J; Galloway, Tamara S; Rowland, Steve J; Thompson, Richard C

    2013-12-01

    Inadequate products, waste management, and policy are struggling to prevent plastic waste from infiltrating ecosystems [1, 2]. Disintegration into smaller pieces means that the abundance of micrometer-sized plastic (microplastic) in habitats has increased [3] and outnumbers larger debris [2, 4]. When ingested by animals, plastic provides a feasible pathway to transfer attached pollutants and additive chemicals into their tissues [5-15]. Despite positive correlations between concentrations of ingested plastic and pollutants in tissues of animals, few, if any, controlled experiments have examined whether ingested plastic transfers pollutants and additives to animals. We exposed lugworms (Arenicola marina) to sand with 5% microplastic that was presorbed with pollutants (nonylphenol and phenanthrene) and additive chemicals (Triclosan and PBDE-47). Microplastic transferred pollutants and additive chemicals into gut tissues of lugworms, causing some biological effects, although clean sand transferred larger concentrations of pollutants into their tissues. Uptake of nonylphenol from PVC or sand reduced the ability of coelomocytes to remove pathogenic bacteria by >60%. Uptake of Triclosan from PVC diminished the ability of worms to engineer sediments and caused mortality, each by >55%, while PVC alone made worms >30% more susceptible to oxidative stress. As global microplastic contamination accelerates, our findings indicate that large concentrations of microplastic and additives can harm ecophysiological functions performed by organisms.

  7. In Vivo Evaluation of Vena Caval Filters: Can Function Be Linked to Design Characteristics?

    SciTech Connect

    Proctor, Mary C.; Cho, Kyung J.; Greenfield, Lazar J.

    2000-11-15

    Purpose: To compare the five vena caval filters marketed in the United States and one investigational vena caval filter and to determine whether there is an association between their design and their in vivo function.Methods: Four of each type of filter-Simon Nitinol (SN), Bird's Nest (BN), Vena Tech (VT), Greenfield stainless steel (PSGF), Greenfield titanium (TGF), and the investigational stent cone filter (NGF)-were studied for 60 days in 12 sheep. Radiographic and pathologic outcomes to be assessed included clot capture and resolution, vena caval penetration, position of the filter, thrombogenicity, and vessel wall reaction.Results: Filters differed with respect to the number of clot-trapping levels and the interdependence of the legs. All devices were successfully placed. Intentionally embolized clot was captured. One VT and two SN filters migrated in response to clot capture. Resolution of thrombus was variable, and related to the design of the device. Fibrin webbing was widely present with the VT, BN, and SN filters but limited in the others. The VT and NGF filters demonstrated the most stable filter base diameter.Conclusions: The performance of vena caval filters differs with respect to clot resolution and mechanical stability. Interdependent filter limbs and single-stage conical capture sites appear to result in more favorable performance in in vivo studies.

  8. Linking the fate of massive black hole binaries to the active galactic nuclei luminosity function

    NASA Astrophysics Data System (ADS)

    Dotti, M.; Merloni, A.; Montuori, C.

    2015-04-01

    Massive black hole binaries are naturally predicted in the context of the hierarchical model of structure formation. The binaries that manage to lose most of their angular momentum can coalesce to form a single remnant. In the last stages of this process, the holes undergo an extremely loud phase of gravitational wave emission, possibly detectable by current and future probes. The theoretical effort towards obtaining a coherent physical picture of the binary path down to coalescence is still underway. In this paper, for the first time, we take advantage of observational studies of active galactic nuclei evolution to constrain the efficiency of gas-driven binary decay. Under conservative assumptions we find that gas accretion towards the nuclear black holes can efficiently lead binaries of any mass forming at high redshift (≳2) to coalescence within the current time. The observed `downsizing' trend of the accreting black hole luminosity function further implies that the gas inflow is sufficient to drive light black holes down to coalescence, even if they bind in binaries at lower redshifts, down to z ≈ 0.5 for binaries of ˜107 M⊙, and z ≈ 0.2 for binaries of ˜106 M⊙. This has strong implications for the detection rates of coalescing black hole binaries of future space-based gravitational wave experiments.

  9. Identification and functional characterization of three novel alleles for the serotonin transporter-linked polymorphic region.

    PubMed

    Ehli, E A; Hu, Y; Lengyel-Nelson, T; Hudziak, J J; Davies, G E

    2012-02-01

    A promoter polymorphism in the serotonin transporter gene (5-HTTLPR) has been reported to confer relative risk for phenotypes (depression/anxiety) and endophenotypes (amygdala reactivity). In this report, we identify and characterize three rare 5-HTTLPR alleles not previously described in the human literature. The three novel alleles were identified while genotyping 5-HTTLPR in a family-based attention deficit hyperactivity disorder clinical population. Two of the novel alleles are longer than the common 16-repeat long (L) allele (17 and 18 repeats) and the third is significantly smaller than the 14-repeat short (S) allele (11 repeats). The sequence and genetic architecture of each novel allele is described in detail. We report a significant decrease in the expression between the XL₁₇ (17r) allele and the L(A) (16r) allele. The XS₁₁ (11r) allele showed similar expression with the S (14r) allele. A 1.8-fold increase in expression was observed with the L(A)(16r) allele compared with the L(G) (16r) allele, which replicates results from earlier 5-HTTLPR expression experiments. In addition, transcription factor binding site (TFBS) analysis was performed using MatInspector (Genomatix) that showed the presence or absence of different putative TFBSs between the novel alleles and the common L (16r) and S (14r) alleles. The identification of rare variants and elucidation of their functional impact could potentially lead to understanding the contribution that the rare variant may have on the inheritance/susceptibility of multifactorial common diseases.

  10. Establishing a Functional Link Between African Dust and Region-wide Coral Reef Decline

    NASA Astrophysics Data System (ADS)

    Hayes, M. L.; Barber, R. T.

    2003-12-01

    For nearly thirty years, coral reefs in the Western Atlantic and Caribbean basin have experienced historically unprecedented declines. Algal blooms, mass coral bleaching, disease outbreaks and shifts in the dominance of benthic coral-competitors were first documented in the 1970s and have increased in frequency, intensity, variety and range over the past two decades. Recent studies of decreasing coral cover document regional losses averaging nearly 80% over this period. Here, we provide experimental evidence that increased supplies of iron-rich eolian dust from Africa to typically iron-poor marine environments throughout the region could have played a key role in these profound changes. Atmospheric inputs of "new" micronutrients, especially iron, have the potential to overcome limitations to the growth of opportunistic coral-competitors and the virulence of coral pathogens. Microcosm and mesocosm experiments with a putative bacterial pathogen of stony corals, Aurantimonas coralicida, and a temperate stony coral, Oculina arbuscula, provide a means to test the functional relationship between iron availability, microbial growth and coral health. Iron limitation of A. coralicida growth rates is readily induced by the addition of synthetic chelators such as 2,2' Dipyridyl to bacterial cultures at relatively low concentrations (e.g. 10 μ M). This growth limitation is reversed by 100 nM over-enrichments of pure reagent-grade iron as well as iron-rich "synthetic dust" derived from African lake-bed sediments. The Chrome-azurol S assay demonstrates that A. coralicida also synthesizes high-affinity iron-capture mechanisms (i.e. siderophores) that may serve as critical determinants of virulence. Finally, our experimental mesocosms are based on oligotrophic Mediterranean seawater and permit controlled experimentation under relatively low iron ( ˜5 nM) conditions. Using this system, denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified ribosomal DNA

  11. Bicarbonate and functional CFTR channel are required for proper mucin secretion and link cystic fibrosis with its mucus phenotype

    PubMed Central

    Gustafsson, Jenny K.; Ermund, Anna; Ambort, Daniel; Johansson, Malin E.V.; Nilsson, Harriet E.; Thorell, Kaisa; Hebert, Hans; Sjövall, Henrik

    2012-01-01

    Cystic fibrosis (CF) is caused by a nonfunctional chloride and bicarbonate ion channel (CF transmembrane regulator [CFTR]), but the link to the phenomenon of stagnant mucus is not well understood. Mice lacking functional CFTR (CftrΔ508) have no lung phenotype but show similar ileal problems to humans. We show that the ileal mucosa in CF have a mucus that adhered to the epithelium, was denser, and was less penetrable than that of wild-type mice. The properties of the ileal mucus of CF mice were normalized by secretion into a high concentration sodium bicarbonate buffer (∼100 mM). In addition, bicarbonate added to already formed CF mucus almost completely restored the mucus properties. This knowledge may provide novel therapeutic options for CF. PMID:22711878

  12. Generation of functional neutrophils from a mouse model of X-linked chronic granulomatous disorder using induced pluripotent stem cells.

    PubMed

    Mukherjee, Sayandip; Santilli, Giorgia; Blundell, Michael P; Navarro, Susana; Bueren, Juan A; Thrasher, Adrian J

    2011-01-01

    Murine models of human genetic disorders provide a valuable tool for investigating the scope for application of induced pluripotent stem cells (iPSC). Here we present a proof-of-concept study to demonstrate generation of iPSC from a mouse model of X-linked chronic granulomatous disease (X-CGD), and their successful differentiation into haematopoietic progenitors of the myeloid lineage. We further demonstrate that additive gene transfer using lentiviral vectors encoding gp91(phox) is capable of restoring NADPH-oxidase activity in mature neutrophils derived from X-CGD iPSC. In the longer term, correction of iPSC from human patients with CGD has therapeutic potential not only through generation of transplantable haematopoietic stem cells, but also through production of large numbers of autologous functional neutrophils.

  13. Loss of FANCC function is associated with failure to inhibit late firing replication origins after DNA cross-linking

    SciTech Connect

    Phelps, Randall A.; Gingras, Helene; Hockenbery, David M. . E-mail: dhockenb@fhcrc.org

    2007-07-01

    Fanconi anemia (FA) cells are abnormally sensitive to DNA cross-linking agents with increased levels of apoptosis and chromosomal instability. Defects in eight FA complementation groups inhibit monoubiquitination of FANCD2, and subsequent recruitment of FANCD2 to DNA damage and S-phase-associated nuclear foci. The specific functional defect in repair or response to DNA damage in FA cells remains unknown. Damage-resistant DNA synthesis is present 2.5-5 h after cross-linker treatment of FANCC, FANCA and FANCD2-deficient cells. Analysis of the size distribution of labeled DNA replication strands revealed that diepoxybutane treatment suppressed labeling of early but not late-firing replicons in FANCC-deficient cells. In contrast, normal responses to ionizing radiation were observed in FANCC-deficient cells. Absence of this late S-phase response in FANCC-deficient cells leads to activation of secondary checkpoint responses.

  14. Influence of the linking spacer length and type on the enantioseparation ability of β-cyclodextrin functionalized monoliths.

    PubMed

    Guo, Jialiang; Xiao, Yuan; Lin, Yuanjing; Zhang, Qiaoxuan; Chang, Yiqun; Crommen, Jacques; Jiang, Zhengjin

    2016-05-15

    In order to investigate the effect of the linking spacer on the enantioseparation ability of β-cyclodextrin (β-CD) functionalized polymeric monoliths, three β-CD-functionalized organic polymeric monoliths with different spacer lengths were prepared by using three amino-β-CDs, i.e. mono-6-amino-6-deoxy-β-CD, mono-6-ethylenediamine-6-deoxy-β-CD, mono-6-hexamethylenediamine-6-deoxy-β-CD, as starting materials. These amino-β-CDs reacted with glycidyl methacrylate to produce functional monomers which were then copolymerized with ethylene dimethacrylate. The enantioseparation ability of the three monoliths was evaluated using 14 chiral acidic compounds, including mandelic acid derivatives, nonsteroidal anti-inflammatory drugs, N-derivatized amino acids, and chiral herbicides under optimum chromatographic conditions. Notably, the poly(GMA-NH2-β-CD-co-EDMA) column provides higher enantioresolution and enantioselectivity than the poly(GMA-EDA-β-CD-co-EDMA) and poly(GMA-HDA-β-CD-co-EDMA) columns for most tested chiral analytes. Furthermore, the enantioseparation performance of triazole-linker containing monoliths was compared to that of ethylenediamine-linker containing monoliths. The results indicate that the enantioselectivity of β-CD monolithic columns is strongly related to the length and type of spacer tethering β-CD to the polymeric support. PMID:26992519

  15. Impact of physicochemical environment on the super disintegrant functionality of cross-linked carboxymethyl sodium starch: insight on formulation precautions.

    PubMed

    Delalonde, Michèle; Fitouri, Raja; Ruiz, Emilie; Bataille, Bernard; Sharkawi, Tahmer

    2015-04-01

    The aim of this work is to improve the understanding of the physicochemical mechanisms involved in the functionality of cross-linked carboxymethyl sodium starch (CCSS) as a tablet super disintegrant (SD). The behavior and properties of this SD (medium uptake, disintegration times, particle size, and rheology) was investigated in a wetting medium of different physicochemical properties. In particular, the relative permittivity (dielectric constant) of these media was intentionally modified for evaluating its effect on CCSS properties. Results showed different swelling behaviors of CCSS particles according to the relative permittivity of the tested media and allow to propose two underlying mechanisms that explain CCSS functionality. Both the intra-particular swelling and the inter-particular repulsion are affected by the relative permittivity of the media. Finally, disintegration test performed on tablets specially formulated with mannitol (used commonly as an excipient and known to modify relative permittivity) confirmed that the functionality of CCSS and therefore the disintegration of the tablet can be altered according to the mannitol content.

  16. An apomixis-linked ORC3-like pseudogene is associated with silencing of its functional homolog in apomictic Paspalum simplex.

    PubMed

    Siena, Lorena A; Ortiz, Juan Pablo A; Calderini, Ornella; Paolocci, Francesco; Cáceres, Maria E; Kaushal, Pankaj; Grisan, Simone; Pessino, Silvina C; Pupilli, Fulvio

    2016-03-01

    Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio. PMID:26842983

  17. An apomixis-linked ORC3-like pseudogene is associated with silencing of its functional homolog in apomictic Paspalum simplex.

    PubMed

    Siena, Lorena A; Ortiz, Juan Pablo A; Calderini, Ornella; Paolocci, Francesco; Cáceres, Maria E; Kaushal, Pankaj; Grisan, Simone; Pessino, Silvina C; Pupilli, Fulvio

    2016-03-01

    Apomixis in plants consists of asexual reproduction by seeds. Here we characterized at structural and functional levels an apomixis-linked sequence of Paspalum simplex homologous to subunit 3 of the ORIGIN RECOGNITION COMPLEX (ORC3). ORC is a multiprotein complex which controls DNA replication and cell differentiation in eukaryotes. Three PsORC3 copies were identified, each one characterized by a specific expression profile. Of these, PsORC3a, specific for apomictic genotypes, is a pseudogene that was poorly and constitutively expressed in all developmental stages of apomictic flowers, whereas PsORC3b, the putative functional gene in sexual flowers, showed a precise time-related regulation. Sense transcripts of PsORC3 were expressed in the female cell lineage of both apomictic and sexual reproductive phenotypes, and in aposporous initials. Although strong expression was detected in sexual early endosperm, no expression was present in the apomictic endosperm. Antisense PsORC3 transcripts were revealed exclusively in apomictic germ cell lineages. Defective orc3 mutants of rice and Arabidopsis showed normal female gametophytes although the embryo and endosperm were arrested at early phases of development. We hypothesize that PsORC3a is associated with the down-regulation of its functional homolog and with the development of apomictic endosperm which deviates from the canonical 2(maternal):1(paternal) genome ratio.

  18. Impact of physicochemical environment on the super disintegrant functionality of cross-linked carboxymethyl sodium starch: insight on formulation precautions.

    PubMed

    Delalonde, Michèle; Fitouri, Raja; Ruiz, Emilie; Bataille, Bernard; Sharkawi, Tahmer

    2015-04-01

    The aim of this work is to improve the understanding of the physicochemical mechanisms involved in the functionality of cross-linked carboxymethyl sodium starch (CCSS) as a tablet super disintegrant (SD). The behavior and properties of this SD (medium uptake, disintegration times, particle size, and rheology) was investigated in a wetting medium of different physicochemical properties. In particular, the relative permittivity (dielectric constant) of these media was intentionally modified for evaluating its effect on CCSS properties. Results showed different swelling behaviors of CCSS particles according to the relative permittivity of the tested media and allow to propose two underlying mechanisms that explain CCSS functionality. Both the intra-particular swelling and the inter-particular repulsion are affected by the relative permittivity of the media. Finally, disintegration test performed on tablets specially formulated with mannitol (used commonly as an excipient and known to modify relative permittivity) confirmed that the functionality of CCSS and therefore the disintegration of the tablet can be altered according to the mannitol content. PMID:25348810

  19. Dissociable deficits of executive function caused by gestational adversity are linked to specific transcriptional changes in the prefrontal cortex.

    PubMed

    Grissom, Nicola M; Herdt, Christopher T; Desilets, Jeffery; Lidsky-Everson, Jordan; Reyes, Teresa M

    2015-05-01

    Poor-quality maternal diet during pregnancy, and subsequent gestational growth disturbances in the offspring, have been implicated in the etiology of multiple neurodevelopmental disorders, including ADHD, schizophrenia, and autism. These disorders are characterized, in part, by abnormalities in responses to reward and errors of executive function. Here, we demonstrate dissociable deficits in reward processing and executive function in male and female mice, solely due to maternal malnutrition via high-fat or low-protein diets. Gestational exposure to a high-fat diet delayed acquisition of a fixed ratio response, and decreased motivation as assessed by progressive ratio. In contrast, offspring of a low-protein diet displayed no deficits in operant learning, but were more prone to assign salience to a cue that predicts reward (sign-tracking) in a Pavlovian-conditioned approach task. In the 5-choice serial reaction time task (5-CSRTT), gestational exposure to a high-fat diet promoted impulsivity, whereas exposure to a low-protein diet led to marked inattention. These dissociable executive function deficits are known to be mediated by the medial prefrontal cortex (PFC), which displays markers of epigenetic dysregulation in neurodevelopmental disorders. Following behavioral characterization, we assayed PFC gene expression using a targeted PCR array and found that both maternal diets increased overall transcription in PFC. Cluster analysis of the relationships between individual transcripts and behavioral outcomes revealed a cluster of primarily epigenetic modulators, whose overexpression was linked to executive function deficits. The overexpression of four genes, DNA methyltransferase 1 (DNMT1), δ-opioid receptor (OPRD1), cannabinoid receptor 1 (CNR1), and catechol-o-methyltransferase (COMT), was strongly associated with overall poor performance. All 5-CSRTT deficits were associated with DNMT1 upregulation, whereas impulsive behavior could be dissociated from

  20. Dissociable Deficits of Executive Function Caused by Gestational Adversity are Linked to Specific Transcriptional Changes in the Prefrontal Cortex

    PubMed Central

    Grissom, Nicola M; Herdt, Christopher T; Desilets, Jeffery; Lidsky-Everson, Jordan; Reyes, Teresa M

    2015-01-01

    Poor-quality maternal diet during pregnancy, and subsequent gestational growth disturbances in the offspring, have been implicated in the etiology of multiple neurodevelopmental disorders, including ADHD, schizophrenia, and autism. These disorders are characterized, in part, by abnormalities in responses to reward and errors of executive function. Here, we demonstrate dissociable deficits in reward processing and executive function in male and female mice, solely due to maternal malnutrition via high-fat or low-protein diets. Gestational exposure to a high-fat diet delayed acquisition of a fixed ratio response, and decreased motivation as assessed by progressive ratio. In contrast, offspring of a low-protein diet displayed no deficits in operant learning, but were more prone to assign salience to a cue that predicts reward (sign-tracking) in a Pavlovian-conditioned approach task. In the 5-choice serial reaction time task (5-CSRTT), gestational exposure to a high-fat diet promoted impulsivity, whereas exposure to a low-protein diet led to marked inattention. These dissociable executive function deficits are known to be mediated by the medial prefrontal cortex (PFC), which displays markers of epigenetic dysregulation in neurodevelopmental disorders. Following behavioral characterization, we assayed PFC gene expression using a targeted PCR array and found that both maternal diets increased overall transcription in PFC. Cluster analysis of the relationships between individual transcripts and behavioral outcomes revealed a cluster of primarily epigenetic modulators, whose overexpression was linked to executive function deficits. The overexpression of four genes, DNA methyltransferase 1 (DNMT1), δ-opioid receptor (OPRD1), cannabinoid receptor 1 (CNR1), and catechol-o-methyltransferase (COMT), was strongly associated with overall poor performance. All 5-CSRTT deficits were associated with DNMT1 upregulation, whereas impulsive behavior could be dissociated from

  1. The superficial white matter in temporal lobe epilepsy: a key link between structural and functional network disruptions.

    PubMed

    Liu, Min; Bernhardt, Boris C; Hong, Seok-Jun; Caldairou, Benoit; Bernasconi, Andrea; Bernasconi, Neda

    2016-09-01

    Drug-resistant temporal lobe epilepsy is increasingly recognized as a system-level disorder affecting the structure and function of large-scale grey matter networks. While diffusion magnetic resonance imaging studies have demonstrated deep fibre tract alterations, the superficial white matter immediately below the cortex has so far been neglected despite its proximity to neocortical regions and key role in maintaining cortico-cortical connectivity. Using multi-modal 3 T magnetic resonance imaging, we mapped the topography of superficial white matter diffusion alterations in 61 consecutive temporal lobe epilepsy patients relative to 38 healthy controls and studied the relationship to large-scale structural as well as functional networks. Our approach continuously sampled mean diffusivity and fractional anisotropy along surfaces running 2 mm below the cortex. Multivariate statistics mapped superficial white matter diffusion anomalies in patients relative to controls, while correlation and mediation analyses evaluated their relationship to structural (cortical thickness, mesiotemporal volumetry) and functional parameters (resting state functional magnetic resonance imaging amplitude) and clinical variables. Patients presented with overlapping anomalies in mean diffusivity and anisotropy, particularly in ipsilateral temporo-limbic regions. Diffusion anomalies did not relate to cortical thinning; conversely, they mediated large-scale functional amplitude decreases in patients relative to controls in default mode hub regions (i.e. anterior and posterior midline regions, lateral temporo-parietal cortices), and were themselves mediated by hippocampal atrophy. With respect to clinical variables, we observed more marked diffusion anomalies in patients with a history of febrile convulsions and those with longer disease duration. Similarly, more marked diffusion alterations were associated with seizure-free outcome. Bootstrap analyses indicated high reproducibility of our

  2. New insights into ferritin synthesis and function highlight a link between iron homeostasis and oxidative stress in plants

    PubMed Central

    Briat, Jean-Francois; Ravet, Karl; Arnaud, Nicolas; Duc, Céline; Boucherez, Jossia; Touraine, Brigitte; Cellier, Francoise; Gaymard, Frederic

    2010-01-01

    Background Iron is an essential element for both plant productivity and nutritional quality. Improving plant iron content was attempted through genetic engineering of plants overexpressing ferritins. However, both the roles of these proteins in plant physiology, and the mechanisms involved in the regulation of their expression are largely unknown. Although the structure of ferritins is highly conserved between plants and animals, their cellular localization differs. Furthermore, regulation of ferritin gene expression in response to iron excess occurs at the transcriptional level in plants, in contrast to animals which regulate ferritin expression at the translational level. Scope In this review, an overview of our knowledge of bacterial and mammalian ferritin synthesis and functions is presented. Then the following will be reviewed: (a) the specific features of plant ferritins; (b) the regulation of their synthesis during development and in response to various environmental cues; and (c) their function in plant physiology, with special emphasis on the role that both bacterial and plant ferritins play during plant–bacteria interactions. Arabidopsis ferritins are encoded by a small nuclear gene family of four members which are differentially expressed. Recent results obtained by using this model plant enabled progress to be made in our understanding of the regulation of the synthesis and the in planta function of these various ferritins. Conclusions Studies on plant ferritin functions and regulation of their synthesis revealed strong links between these proteins and protection against oxidative stress. In contrast, their putative iron-storage function to furnish iron during various development processes is unlikely to be essential. Ferritins, by buffering iron, exert a fine tuning of the quantity of metal required for metabolic purposes, and help plants to cope with adverse situations, the deleterious effects of which would be amplified if no system had evolved to

  3. The superficial white matter in temporal lobe epilepsy: a key link between structural and functional network disruptions.

    PubMed

    Liu, Min; Bernhardt, Boris C; Hong, Seok-Jun; Caldairou, Benoit; Bernasconi, Andrea; Bernasconi, Neda

    2016-09-01

    Drug-resistant temporal lobe epilepsy is increasingly recognized as a system-level disorder affecting the structure and function of large-scale grey matter networks. While diffusion magnetic resonance imaging studies have demonstrated deep fibre tract alterations, the superficial white matter immediately below the cortex has so far been neglected despite its proximity to neocortical regions and key role in maintaining cortico-cortical connectivity. Using multi-modal 3 T magnetic resonance imaging, we mapped the topography of superficial white matter diffusion alterations in 61 consecutive temporal lobe epilepsy patients relative to 38 healthy controls and studied the relationship to large-scale structural as well as functional networks. Our approach continuously sampled mean diffusivity and fractional anisotropy along surfaces running 2 mm below the cortex. Multivariate statistics mapped superficial white matter diffusion anomalies in patients relative to controls, while correlation and mediation analyses evaluated their relationship to structural (cortical thickness, mesiotemporal volumetry) and functional parameters (resting state functional magnetic resonance imaging amplitude) and clinical variables. Patients presented with overlapping anomalies in mean diffusivity and anisotropy, particularly in ipsilateral temporo-limbic regions. Diffusion anomalies did not relate to cortical thinning; conversely, they mediated large-scale functional amplitude decreases in patients relative to controls in default mode hub regions (i.e. anterior and posterior midline regions, lateral temporo-parietal cortices), and were themselves mediated by hippocampal atrophy. With respect to clinical variables, we observed more marked diffusion anomalies in patients with a history of febrile convulsions and those with longer disease duration. Similarly, more marked diffusion alterations were associated with seizure-free outcome. Bootstrap analyses indicated high reproducibility of our

  4. Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

    PubMed

    Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

    2013-04-22

    For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

  5. Linking functional diversity and social actor strategies in a framework for interdisciplinary analysis of nature's benefits to society

    PubMed Central

    Díaz, Sandra; Cáceres, Daniel M.; Trainor, Sarah F.; Pérez-Harguindeguy, Natalia; Bret-Harte, M. Syndonia; Finegan, Bryan; Peña-Claros, Marielos; Poorter, Lourens

    2011-01-01

    The crucial role of biodiversity in the links between ecosystems and societies has been repeatedly highlighted both as source of wellbeing and as a target of human actions, but not all aspects of biodiversity are equally important to different ecosystem services. Similarly, different social actors have different perceptions of and access to ecosystem services, and therefore, they have different wants and capacities to select directly or indirectly for particular biodiversity and ecosystem characteristics. Their choices feed back onto the ecosystem services provided to all parties involved and in turn, affect future decisions. Despite this recognition, the research communities addressing biodiversity, ecosystem services, and human outcomes have yet to develop frameworks that adequately treat the multiple dimensions and interactions in the relationship. Here, we present an interdisciplinary framework for the analysis of relationships between functional diversity, ecosystem services, and human actions that is applicable to specific social environmental systems at local scales. We connect the mechanistic understanding of the ecological role of diversity with its social relevance: ecosystem services. The framework permits connections between functional diversity components and priorities of social actors using land use decisions and ecosystem services as the main links between these ecological and social components. We propose a matrix-based method that provides a transparent and flexible platform for quantifying and integrating social and ecological information and negotiating potentially conflicting land uses among multiple social actors. We illustrate the applicability of our framework by way of land use examples from temperate to subtropical South America, an area of rapid social and ecological change. PMID:21220325

  6. Analyzing swine sera for functional antibody titers against influenza A neuraminidase proteins using an enzyme-linked lectin assay (ELLA).

    PubMed

    Sandbulte, Matthew R; Eichelberger, Maryna C

    2014-01-01

    Neuraminidase (NA) is an envelope glycoprotein of influenza viruses, including swine-lineage influenza A viruses. NA possesses sialidase activity, which is functionally important at multiple points in viral replication, counter-balancing the sialic acid receptor binding activity of the hemagglutinin (HA), the other major envelope glycoprotein. The NA proteins of influenza A viruses have been classified into nine serological subtypes, and they undergo antigenic drift variation similar to that of HA. Antibodies to NA are analyzed much less often than antibodies to HA. The conventional assay for NA inhibition (NI) antibody titration, established decades ago, is widely considered unwieldy and inefficient for routine use. In recent years, a few new formats have been developed which still measure inhibition of NA enzymatic function, but more efficiently and with less chemical waste produced. Described here is the enzyme-linked lectin assay (ELLA), which is performed in 96-well plates and analyzed on a spectrophotometric plate reader. An important factor in adoption of the ELLA technique for animal studies, such as swine, is the choice of NA antigen, which may be purified protein or whole virus containing an antigenically irrelevant HA protein. This NI assay, in conjunction with the hemagglutination inhibiting (HI) antibody assay, offers a practical way to characterize viral isolates more fully and to quantify antibodies induced by infection or vaccination.

  7. Stereotyped subset #1 chronic lymphocytic leukemia: a direct link between B-cell receptor structure, function, and patients' prognosis.

    PubMed

    Del Giudice, Ilaria; Chiaretti, Sabina; Santangelo, Simona; Tavolaro, Simona; Peragine, Nadia; Marinelli, Marilisa; Ilari, Caterina; Raponi, Sara; Messina, Monica; Nanni, Mauro; Mauro, Francesca Romana; Piciocchi, Alfonso; Bontempi, Katia; Rossi, Davide; Gaidano, Gianluca; Guarini, Anna; Foà, Robin

    2014-01-01

    Chronic lymphocytic leukemia (CLL) with stereotyped B-cell receptor (BCR) belonging to subset #1 (IGHV1-5-7/ IGKV1-39) display a poor outcome. To characterize their genetic and genomic features and BCR function, we selected 20 subset #1 CLL from a series of 579 cases. Subset #1 CLL, all showing unmutated IGHV, were associated with the presence of del(11q) (50%) in comparison with unmutated CLL, unmutated stereotyped CLL other than subset #1 and with cases using the same IGHV genes but a heterogeneous VH CDR3 (non-subset #1 CLL). There were no distinctive features regarding CD38, ZAP-70, and TP53 disruption. NOTCH1, SF3B1, and BIRC3 were mutated in 15%, 0%, and 5% of cases, respectively, while BIRC3 was deleted in 22% of cases. Microarray unsupervised analysis on 80 unmutated/mutated/stereotyped/non-stereotyped CLL showed a tight clustering of subset #1 cases. Their genomic signature exhibited several differentially expressed transcripts involved in BCR signal transduction, apoptosis regulation, cell proliferation, and oxidative processes, regardless of del(11q). Accordingly, BCR ligation with anti-IgM revealed a significant higher proliferation of subset #1 versus unmutated non-subset #1 CLL, both at baseline and after 24–48 hr stimulation. Subset #1 CLL represent a paradigmatic example of the direct link between BCR structure, function, and patients prognosis.

  8. Different neural pathways linking personality traits and eudaimonic well-being: a resting-state functional magnetic resonance imaging study.

    PubMed

    Kong, Feng; Liu, Ling; Wang, Xu; Hu, Siyuan; Song, Yiying; Liu, Jia

    2015-06-01

    Eudaimonic well-being (EWB) is the fulfillment of human potential and a meaningful life. Previous studies have shown that personality traits, especially extraversion, neuroticism, and conscientiousness, significantly contribute to EWB. However, the neurobiological pathways linking personality and EWB are not understood. Here, we used resting-state functional magnetic resonance imaging (rs-fMRI) to investigate this issue. Specifically, we correlated individuals' EWB scores with the regional fractional amplitude of low-frequency fluctuations (fALFF) of the brain, and then examined how personality traits predicted EWB-related spontaneous brain activity. We found that EWB was positively correlated with the fALFF in the right posterior superior temporal gyrus (pSTG) and thalamus, and negatively correlated with the strength of the thalamic-insular connectivity. More importantly, we found that personality traits influenced EWB in different ways. At the regional level, the fALFF in the pSTG and thalamus mediated the effects of neuroticism and extraversion on EWB, whereas the thalamus mediated the effect of conscientiousness on EWB. At the functional connectivity level, the thalamic-insular connectivity only mediated the effect of neuroticism on EWB. Taken together, our study provides the first evidence that EWB is associated with personality traits through different neural substrates.

  9. Midbrain functional connectivity and ventral striatal dopamine D2-type receptors: Link to impulsivity in methamphetamine users

    PubMed Central

    Kohno, Milky; Okita, Kyoji; Morales, Angelica M.; Robertson, Chelsea; Dean, Andy C.; Ghahremani, Dara G.; Sabb, Fred; Mandelkern, Mark A.; Bilder, Robert M.; London, Edythe D.

    2015-01-01

    Stimulant use disorders are associated with deficits in striatal dopamine receptor availability, abnormalities in mesocorticolimbic resting-state functional connectivity (RSFC), and impulsivity. In methamphetamine-dependent research participants, impulsivity is correlated negatively with striatal D2-type receptor availability, and mesocorticolimbic RSFC is stronger than in controls. The extent to which these features of methamphetamine dependence are interrelated, however, is unknown. This question was addressed in two studies. In Study 1, 19 methamphetamine-dependent and 26 healthy control subjects underwent [18F]fallypride positron emission tomography to measure ventral striatal dopamine D2-type receptor availability, indexed by binding potential (BPND), and functional magnetic resonance imaging (fMRI) to assess mesocorticolimbic RSFC, using a midbrain seed. In Study 2, an independent sample of 20 methamphetamine-dependent and 18 control subjects completed the Barratt Impulsiveness Scale in addition to fMRI. Study 1 showed a significant group by ventral striatal BPND interaction effect on RSFC, reflecting a negative relationship between ventral striatal BPND and RSFC between midbrain and striatum, orbitofrontal cortex, and insula in methamphetamine-dependent participants but a positive relationship in the control group. In Study 2, an interaction of group with RSFC on impulsivity was observed. Methamphetamine-dependent participants users exhibited a positive relationship of midbrain RSFC to the left ventral striatum with cognitive impulsivity, whereas a negative relationship was observed in healthy controls. The results indicate that ventral striatal D2-type receptor signaling may affect system-level activity within the mesocorticolimbic system, providing a functional link that may help explain high impulsivity in methamphetamine-dependent individuals. PMID:26830141

  10. The structural and functional effects of the familial hypertrophic cardiomyopathy-linked cardiac troponin C mutation, L29Q

    PubMed Central

    Robertson, Ian M.; Sevrieva, Ivanka; Li, Monica X.; Irving, Malcolm; Sun, Yin-Biao; Sykes, Brian D.

    2015-01-01

    Familial hypertrophic cardiomyopathy (FHC) is characterized by severe abnormal cardiac muscle growth. The traditional view of disease progression in FHC is that an increase in the Ca2 +-sensitivity of cardiac muscle contraction ultimately leads to pathogenic myocardial remodeling, though recent studies suggest this may be an oversimplification. For example, FHC may be developed through altered signaling that prevents downstream regulation of contraction. The mutation L29Q, found in the Ca2 +-binding regulatory protein in heart muscle, cardiac troponin C (cTnC), has been linked to cardiac hypertrophy. However, reports on the functional effects of this mutation are conflicting, and our goal was to combine in vitro and in situ structural and functional data to elucidate its mechanism of action. We used nuclear magnetic resonance and circular dichroism to solve the structure and characterize the backbone dynamics and stability of the regulatory domain of cTnC with the L29Q mutation. The overall structure and dynamics of cTnC were unperturbed, although a slight rearrangement of site 1, an increase in backbone flexibility, and a small decrease in protein stability were observed. The structure and function of cTnC was also assessed in demembranated ventricular trabeculae using fluorescence for in situ structure. L29Q reduced the cooperativity of the Ca2 +-dependent structural change in cTnC in trabeculae under basal conditions and abolished the effect of force-generating myosin cross-bridges on this structural change. These effects could contribute to the pathogenesis of this mutation. PMID:26341255

  11. Nature of functional links in valuation networks differentiates impulsive behaviors between abstinent heroin-dependent subjects and nondrug-using subjects.

    PubMed

    Zhai, Tianye; Shao, Yongcong; Chen, Gang; Ye, Enmao; Ma, Lin; Wang, Lubin; Lei, Yu; Chen, Guangyu; Li, Wenjun; Zou, Feng; Jin, Xiao; Li, Shi-Jiang; Yang, Zheng

    2015-07-15

    Advanced neuroimaging studies have identified brain correlates of pathological impulsivity in a variety of neuropsychiatric disorders. However, whether and how these spatially separate and functionally integrated neural correlates collectively contribute to aberrant impulsive behaviors remains unclear. Building on recent progress in neuroeconomics toward determining a biological account of human behaviors, we employed resting-state functional MRI to characterize the nature of the links between these neural correlates and to investigate their impact on impulsivity. We demonstrated that through functional connectivity with the ventral medial prefrontal cortex, the δ-network (regions of the executive control system, such as the dorsolateral prefrontal cortex) and the β-network (regions of the reward system involved in the mesocorticolimbic pathway), jointly influence impulsivity measured by the Barratt impulsiveness scale scores. In control nondrug-using subjects, the functional link between the β- and δ-networks is balanced, and the δ-network competitively controls impulsivity. However, in abstinent heroin-dependent subjects, the link is imbalanced, with stronger β-network connectivity and weaker δ-network connectivity. The imbalanced link is associated with impulsivity, indicating that the β- and δ-networks may mutually reinforce each other in abstinent heroin-dependent subjects. These findings of an aberrant link between the β- and δ-networks in abstinent heroin-dependent subjects may shed light on the mechanism of aberrant behaviors of drug addiction and may serve as an endophenotype to mark individual subjects' self-control capacity. PMID:25944613

  12. Tapping linked to function and structure in premanifest and symptomatic Huntington disease(e–Pub ahead of print)

    PubMed Central

    Bechtel, N.; Scahill, R.I.; Rosas, H.D.; Acharya, T.; van den Bogaard, S.J.A.; Jauffret, C.; Say, M.J.; Sturrock, A.; Johnson, H.; Onorato, C.E.; Salat, D.H.; Durr, A.; Leavitt, B.R.; Roos, R.A.C.; Landwehrmeyer, G.B.; Langbehn, D.R.; Stout, J.C.; Tabrizi, S.J.; Reilmann, R.

    2010-01-01

    Objective: Motor signs are functionally disabling features of Huntington disease. Characteristic motor signs define disease manifestation. Their severity and onset are assessed by the Total Motor Score of the Unified Huntington's Disease Rating Scale, a categorical scale limited by interrater variability and insensitivity in premanifest subjects. More objective, reliable, and precise measures are needed which permit clinical trials in premanifest populations. We hypothesized that motor deficits can be objectively quantified by force-transducer-based tapping and correlate with disease burden and brain atrophy. Methods: A total of 123 controls, 120 premanifest, and 123 early symptomatic gene carriers performed a speeded and a metronome tapping task in the multicenter study TRACK-HD. Total Motor Score, CAG repeat length, and MRIs were obtained. The premanifest group was subdivided into A and B, based on the proximity to estimated disease onset, the manifest group into stages 1 and 2, according to their Total Functional Capacity scores. Analyses were performed centrally and blinded. Results: Tapping variability distinguished between all groups and subgroups in both tasks and correlated with 1) disease burden, 2) clinical motor phenotype, 3) gray and white matter atrophy, and 4) cortical thinning. Speeded tapping was more sensitive to the detection of early changes. Conclusion: Tapping deficits are evident throughout manifest and premanifest stages. Deficits are more pronounced in later stages and correlate with clinical scores as well as regional brain atrophy, which implies a link between structure and function. The ability to track motor phenotype progression with force-transducer-based tapping measures will be tested prospectively in the TRACK-HD study. GLOSSARY CoV = coefficient of variation; DBS = disease burden score; Freq = frequency; HD = Huntington disease; ICV = intracranial volume; IOI = interonset interval; ΔIOI = deviation from interonset interval; IPI

  13. SAP gene transfer restores cellular and humoral immune function in a murine model of X-linked lymphoproliferative disease.

    PubMed

    Rivat, Christine; Booth, Claire; Alonso-Ferrero, Maria; Blundell, Michael; Sebire, Neil J; Thrasher, Adrian J; Gaspar, H Bobby

    2013-02-14

    X-linked lymphoproliferative disease (XLP1) arises from mutations in the gene encoding SLAM-associated protein (SAP) and leads to abnormalities of NKT-cell development, NK-cell cytotoxicity, and T-dependent humoral function. Curative treatment is limited to allogeneic hematopoietic stem cell (HSC) transplantation. We tested whether HSC gene therapy could correct the multilineage defects seen in SAP(-/-) mice. SAP(-/-) murine HSCs were transduced with lentiviral vectors containing either SAP or reporter gene before transplantation into irradiated recipients. NKT-cell development was significantly higher and NK-cell cytotoxicity restored to wild-type levels in mice receiving the SAP vector in comparison to control mice. Baseline immunoglobulin levels were significantly increased and T-dependent humoral responses to NP-CGG, including germinal center formation, were restored in SAP-transduced mice.We demonstrate for the first time that HSC gene transfer corrects the cellular and humoral defects in SAP(-/-) mice providing proof of concept for gene therapy in XLP1.

  14. Enzymatically Regulated Peptide Pairing and Catalysis for the Bioanalysis of Extracellular Prometastatic Activities of Functionally Linked Enzymes.

    PubMed

    Li, Hao; Huang, Yue; Yu, Yue; Li, Tianqi; Li, Genxi; Anzai, Jun-Ichi

    2016-05-03

    Diseases such as cancer arise from systematical reconfiguration of interactions of exceedingly large numbers of proteins in cell signaling. The study of such complicated molecular mechanisms requires multiplexed detection of the inter-connected activities of several proteins in a disease-associated context. However, the existing methods are generally not well-equipped for this kind of application. Here a method for analyzing functionally linked protein activities is developed based on enzyme controlled pairing between complementary peptide helix strands, which simultaneously enables elaborate regulation of catalytic activity of the paired peptides. This method has been used to detect three different types of protein modification enzymes that participate in the modification of extracellular matrix and the formation of invasion front in tumour. In detecting breast cancer tissue samples using this method, up-regulated activity can be observed for two of the assessed enzymes, while the third enzyme is found to have a subtle fluctuation of activity. These results may point to the application of this method in evaluating prometastatic activities of proteins in tumour.

  15. Enzymatically Regulated Peptide Pairing and Catalysis for the Bioanalysis of Extracellular Prometastatic Activities of Functionally Linked Enzymes

    PubMed Central

    Li, Hao; Huang, Yue; Yu, Yue; Li, Tianqi; Li, Genxi; Anzai, Jun-ichi

    2016-01-01

    Diseases such as cancer arise from systematical reconfiguration of interactions of exceedingly large numbers of proteins in cell signaling. The study of such complicated molecular mechanisms requires multiplexed detection of the inter-connected activities of several proteins in a disease-associated context. However, the existing methods are generally not well-equipped for this kind of application. Here a method for analyzing functionally linked protein activities is developed based on enzyme controlled pairing between complementary peptide helix strands, which simultaneously enables elaborate regulation of catalytic activity of the paired peptides. This method has been used to detect three different types of protein modification enzymes that participate in the modification of extracellular matrix and the formation of invasion front in tumour. In detecting breast cancer tissue samples using this method, up-regulated activity can be observed for two of the assessed enzymes, while the third enzyme is found to have a subtle fluctuation of activity. These results may point to the application of this method in evaluating prometastatic activities of proteins in tumour. PMID:27140831

  16. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.

    PubMed

    Schmid, Amy K; Reiss, David J; Pan, Min; Koide, Tie; Baliga, Nitin S

    2009-01-01

    During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in response to changes in carbon source availability. Specifically, during nutritional limitation, TrmB binds a cis-regulatory element to activate or repress 113 promoters of genes encoding enzymes in diverse metabolic pathways. By this mechanism, TrmB coordinates the expression of glycolysis, TCA cycle, and amino-acid biosynthesis pathways with the biosynthesis of their cognate cofactors (e.g. purine and thiamine). Notably, the TrmB-regulated metabolic network includes enzyme-coding genes that are uniquely archaeal as well as those that are conserved across all three domains of life. Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins.

  17. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

    PubMed Central

    Schmid, Amy K; Reiss, David J; Pan, Min; Koide, Tie; Baliga, Nitin S

    2009-01-01

    During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in response to changes in carbon source availability. Specifically, during nutritional limitation, TrmB binds a cis-regulatory element to activate or repress 113 promoters of genes encoding enzymes in diverse metabolic pathways. By this mechanism, TrmB coordinates the expression of glycolysis, TCA cycle, and amino-acid biosynthesis pathways with the biosynthesis of their cognate cofactors (e.g. purine and thiamine). Notably, the TrmB-regulated metabolic network includes enzyme-coding genes that are uniquely archaeal as well as those that are conserved across all three domains of life. Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins. PMID:19536205

  18. Structural and Functional Characteristics in Carriers of X-Linked Retinitis Pigmentosa with a Tapetal-Like Reflex

    PubMed Central

    Genead, Mohamed A.; Fishman, Gerald A.; Lindeman, Martin; affiliation, COMT Institute

    2010-01-01

    Purpose to identify the functional and structural characteristics in three female obligate carriers of X-linked retinitis pigmentosa (XLRP) from the same family by using spectral-domain OCT (SD-OCT), fundus autofluorescence (FAF), and microperimetry (MP). Methods Three female obligate carriers with a tapetal-like reflex (TLR), 21, 49, and 57 years of age, from a single family of XLRP that was seen in the ophthalmology department at the University of Illinois at Chicago, were enrolled in the study. All carriers underwent a complete ophthalmic examination. SD-OCT measurements, a macular MP exam, and FAF testing were performed. Results The SD-OCT exam in all three carriers showed a normal retinal micro-structure and thickness. Microperimeter testing showed subnormal retinal sensitivity in the areas of the TLR. FAF exam showed the presence of speckled areas of enhanced AF. Conclusions Our study demonstrates that the carriers of XLRP with a TLR can show an enhanced reflectance on infrared images, abnormal autofluorescence properties, elevated retinal thresholds, and a normal retinal morphology within the posterior pole on SD-OCT testing PMID:20829740

  19. Intracoronary Transplantation of Mesenchymal Stem Cells with Overexpressed Integrin-Linked Kinase Improves Cardiac Function in Porcine Myocardial Infarction

    PubMed Central

    Mu, Dan; Zhang, Xin-Lin; Xie, Jun; Yuan, Hui-Hua; Wang, Kun; Huang, Wei; Li, Guan-Nan; Lu, Jian-Rong; Mao, Li-Juan; Wang, Lian; Cheng, Le; Mai, Xiao-Li; Yang, Jun; Tian, Chuan-Shuai; Kang, Li-Na; Gu, Rong; Zhu, Bin; Xu, Biao

    2016-01-01

    The effect of mesenchymal stem cell (MSCs)-based therapy on treating acute myocardial infarction (MI) is limited due to poor engraftment and limited regenerative potential. Here we engineered MSCs with integrin-linked kinase (ILK), a pleiotropic protein critically regulating cell survival, proliferation, differentiation, and angiogenesis. We firstly combined ferumoxytol with poly-L-lysine (PLL), and found this combination promisingly enabled MRI visualization of MSCs in vitro and in vivo with good safety. We provided visually direct evidence that intracoronary ILK-MSCs had substantially enhanced homing capacity to infarct myocardium in porcine following cardiac catheterization induced MI. Intracoronary transplantation of allogeneic ILK-MSCs, but not vector-MSCs, significantly enhanced global left ventricular ejection fraction (LVEF) by 7.8% compared with baseline, by 10.3% compared with vehicles, and inhibited myocardial remodeling compared with vehicles at 15-day follow-up. Compared with vector-MSCs, ILK-MSCs significantly improved regional LV contractile function, reduced scar size, fibrosis, cell apoptosis, and increased regional myocardial perfusion and cell proliferation. This preclinical study indicates that ILK-engineered MSCs might promote the clinical translation of MSC-based therapy in post-MI patients, and provides evidence that ferumoxytol labeling of cells combined with PLL is feasible in in vivo cell tracking. PMID:26750752

  20. Biologically compatible, phosphorescent dimetallic rhenium complexes linked through functionalized alkyl chains: syntheses, spectroscopic properties, and applications in imaging microscopy.

    PubMed

    Balasingham, Rebeca G; Thorp-Greenwood, Flora L; Williams, Catrin F; Coogan, Michael P; Pope, Simon J A

    2012-02-01

    A range of luminescent, dimetallic complexes based upon the rhenium fac-tricarbonyl diimine core, linked by aliphatic chains of varying lengths and functionality, have been synthesized and their photophysical properties examined. Each complex displays characteristic (3)M(Re)L(diimine)CT emission in aerated acetonitrile solution, with long lifetimes in the range of 129-248 ns and corresponding quantum yields in the range 3.2-8.0%. In aqueous solution, as opposed to acetonitrile, the complexes generally show a small hypsochromic shift in λ(em) and an extension of the (3)MLCT lifetime, attributed to a hydrophobically driven association of the alkyl chains with the rhenium-bound diimine units. In live cell imaging experiments using MCF7 cells the complexes all show good uptake by non-energy dependent mechanisms without endosomal entrainment, and with varying propensity to localize in organelles. The degrees of uptake and localization properties are discussed in terms of the length and chemical nature of the linkers, and in terms of the likely interactions between these and the various cellular components encountered.

  1. The Florence Nightingale Effect: Organizational Identification Explains the Peculiar Link Between Others' Suffering and Workplace Functioning in the Homelessness Sector.

    PubMed

    Ferris, Laura J; Jetten, Jolanda; Johnstone, Melissa; Girdham, Elise; Parsell, Cameron; Walter, Zoe C

    2016-01-01

    Frontline employees in the helping professions often perform their duties against a difficult backdrop, including a complex client base and ongoing themes of crisis, suffering, and distress. These factors combine to create an environment in which workers are vulnerable to workplace stress and burnout. The present study tested two models to understand how frontline workers in the homelessness sector deal with the suffering of their clients. First, we examined whether relationships between suffering and workplace functioning (job satisfaction and burnout) would be mediated by organizational identification. Second, we examined whether emotional distance from clients (i.e., infrahumanization, measured as reduced attribution of secondary emotions) would predict improved workplace functioning (less burnout and greater job satisfaction), particularly when client contact is high. The study involved a mixed-methods design comprising interview (N = 26) and cross-sectional survey data (N = 60) with a sample of frontline staff working in the homelessness sector. Participants were asked to rate the level of client suffering and attribute emotions in a hypothetical client task, and to complete questionnaire measures of burnout, job satisfaction, and organizational identification. We found no relationships between secondary emotion attribution and burnout or satisfaction. Instead, we found that perceiving higher client suffering was linked with higher job satisfaction and lower burnout. Mediation analyses revealed a mediating role for identification, such that recognizing suffering predicted greater identification with the organization, which fully mediated the relationship between suffering and job satisfaction, and also between suffering and burnout. Qualitative analysis of interview data also resonated with this conceptualization. We introduce this novel finding as the 'Florence Nightingale effect'. With this sample drawn from the homelessness sector, we provide preliminary

  2. Impaired Hippocampal Neuroligin-2 Function by Chronic Stress or Synthetic Peptide Treatment is Linked to Social Deficits and Increased Aggression

    PubMed Central

    van der Kooij, Michael A; Fantin, Martina; Kraev, Igor; Korshunova, Irina; Grosse, Jocelyn; Zanoletti, Olivia; Guirado, Ramon; Garcia-Mompó, Clara; Nacher, Juan; Stewart, Michael G; Berezin, Vladimir; Sandi, Carmen

    2014-01-01

    Neuroligins (NLGNs) are cell adhesion molecules that are important for proper synaptic formation and functioning, and are critical regulators of the balance between neural excitation/inhibition (E/I). Mutations in NLGNs have been linked to psychiatric disorders in humans involving social dysfunction and are related to similar abnormalities in animal models. Chronic stress increases the likelihood for affective disorders and has been shown to induce changes in neural structure and function in different brain regions, with the hippocampus being highly vulnerable to stress. Previous studies have shown evidence of chronic stress-induced changes in the neural E/I balance in the hippocampus. Therefore, we hypothesized that chronic restraint stress would lead to reduced hippocampal NLGN-2 levels, in association with alterations in social behavior. We found that rats submitted to chronic restraint stress in adulthood display reduced sociability and increased aggression. This occurs along with a reduction of NLGN-2, but not NLGN-1 expression (as shown with western blot, immunohistochemistry, and electron microscopy analyses), throughout the hippocampus and detectable in different layers of the CA1, CA3, and DG subfields. Furthermore, using synthetic peptides that comprise sequences in either NLGN-1 (neurolide-1) or NLGN-2 (neurolide-2) involved in the interaction with their presynaptic partner neurexin (NRXN)-1, intra-hippocampal administration of neurolide-2 led also to reduced sociability and increased aggression. These results highlight hippocampal NLGN-2 as a key molecular substrate regulating social behaviors and underscore NLGNs as promising targets for the development of novel drugs for the treatment of dysfunctional social behaviors. PMID:24213355

  3. Linking Tropical Forest Function to Hydraulic Traits in a Size-Structured and Trait-Based Model

    NASA Astrophysics Data System (ADS)

    Christoffersen, B. O.; Gloor, E. U.; Fauset, S.; Fyllas, N.; Galbraith, D.; Baker, T. R.; Rowland, L.; Fisher, R.; Binks, O.; Mencuccini, M.; Malhi, Y.; Stahl, C.; Wagner, F. H.; Bonal, D.; da Costa, A. C. L.; Ferreira, L.; Meir, P.

    2014-12-01

    A major weakness of forest ecosystem models applied to Amazonia is their inability to capture the diversity of responses to changes in water availability commonly observed within and across forest communities, severely hampering efforts to predict the fate of Amazon forests under climate change. Such models often prescribe moisture sensitivity using heuristic response functions which are uniform across all individuals and lack important knowledge about trade-offs in hydraulic traits. We address this weakness by implementing a process representation of plant hydraulics into an individual- and trait-based model (Trait Forest Simulator; TFS) intended for application at discrete sites across Amazonia. The model represents a trade-off in the safety and efficiency of water conduction in xylem tissue through hydraulic traits, which then lead to variation in plant water use and growth dynamics. The model accounts for the buffering effects of leaf and stem capacitance on leaf water potential at short time scales, and cavitation-induced reductions in whole-plant conductance over longer periods of water stress. We explore multiple possible links between this hydraulic trait spectrum and other whole-plant traits, such as maximum photosynthetic capacity and wood density. The model is shown to greatly improve the diversity of tree response to seasonal changes in water availability as well as response to drought, as determined by comparison with sap flux and stem dendrometry measurements. Importantly, this individual- and trait-based framework provides a testbed for identifying both critical processes and functional traits needed for inclusion in coarse-scale Dynamic Global Vegetation Models, which will lead to reduced uncertainty in the future state of Amazon tropical forests.

  4. The Florence Nightingale Effect: Organizational Identification Explains the Peculiar Link Between Others’ Suffering and Workplace Functioning in the Homelessness Sector

    PubMed Central

    Ferris, Laura J.; Jetten, Jolanda; Johnstone, Melissa; Girdham, Elise; Parsell, Cameron; Walter, Zoe C.

    2016-01-01

    Frontline employees in the helping professions often perform their duties against a difficult backdrop, including a complex client base and ongoing themes of crisis, suffering, and distress. These factors combine to create an environment in which workers are vulnerable to workplace stress and burnout. The present study tested two models to understand how frontline workers in the homelessness sector deal with the suffering of their clients. First, we examined whether relationships between suffering and workplace functioning (job satisfaction and burnout) would be mediated by organizational identification. Second, we examined whether emotional distance from clients (i.e., infrahumanization, measured as reduced attribution of secondary emotions) would predict improved workplace functioning (less burnout and greater job satisfaction), particularly when client contact is high. The study involved a mixed-methods design comprising interview (N = 26) and cross-sectional survey data (N = 60) with a sample of frontline staff working in the homelessness sector. Participants were asked to rate the level of client suffering and attribute emotions in a hypothetical client task, and to complete questionnaire measures of burnout, job satisfaction, and organizational identification. We found no relationships between secondary emotion attribution and burnout or satisfaction. Instead, we found that perceiving higher client suffering was linked with higher job satisfaction and lower burnout. Mediation analyses revealed a mediating role for identification, such that recognizing suffering predicted greater identification with the organization, which fully mediated the relationship between suffering and job satisfaction, and also between suffering and burnout. Qualitative analysis of interview data also resonated with this conceptualization. We introduce this novel finding as the ‘Florence Nightingale effect’. With this sample drawn from the homelessness sector, we provide

  5. Mandibular corpus strain in primates: further evidence for a functional link between symphyseal fusion and jaw-adductor muscle force.

    PubMed

    Hylander, W L; Ravosa, M J; Ross, C F; Johnson, K R

    1998-11-01

    Previous work indicates that compared to adult thick-tailed galagos, adult long-tailed macaques have much more bone strain on the balancing-side mandibular corpus during unilateral isometric molar biting (Hylander [1979a] J. Morphol. 159:253-296). Recently we have confirmed in these same two species the presence of similar differences in bone-strain patterns during forceful mastication. Moreover, we have also recorded mandibular bone strain patterns in adult owl monkeys, which are slightly smaller than the galago subjects. The owl monkey data indicate the presence of a strain pattern very similar to that recorded for macaques, and quite unlike that recorded for galagos. We interpret these bone-strain pattern differences to be importantly related to differences in balancing-side jaw-adductor muscle force recruitment patterns. That is, compared to galagos, macaques and owl monkeys recruit relatively more balancing-side jaw-adductor muscle force during forceful mastication. Unlike an earlier study (Hylander [1979b] J. Morphol. 160:223-240), we are unable to estimate the actual amount of working-side muscle force relative to balancing-side muscle force (i.e., the W/B muscle force ratio) in these species because we have no reliable estimate of magnitude, direction, and precise location of the bite force during mastication. A comparison of the mastication data with the earlier data recorded during isometric molar biting, however, supports the hypothesis that the two anthropoids have a small W/B jaw-adductor muscle force ratio in comparison to thick-tailed galagos. These data also support the hypothesis that increased recruitment of balancing-side jaw-adductor muscle force in anthropoids is functionally linked to the evolution of symphyseal fusion or strengthening. Moreover, these data refute the hypothesis that the recruitment pattern differences between macaques and thick-tailed galagos are due to allometric factors. Finally, although the evolution of symphyseal fusion

  6. N-linked glycosylation of N48 is required for equilibrative nucleoside transporter 1 (ENT1) function.

    PubMed

    Bicket, Alex; Coe, Imogen R

    2016-08-01

    Human equilibrative nucleoside transporter 1 (hENT1) transports nucleosides and nucleoside analogue drugs across cellular membranes and is necessary for the uptake of many anti-cancer, anti-parasitic and anti-viral drugs. Previous work, and in silico prediction, suggest that hENT1 is glycosylated at Asn(48) in the first extracellular loop of the protein and that glycosylation plays a role in correct localization and function of hENT1. Site-directed mutagenesis of wild-type (wt) hENT1 removed potential glycosylation sites. Constructs (wt 3xFLAG-hENT1, N48Q-3xFLAG-hENT1 or N288Q-3xFLAG-hENT2) were transiently transfected into HEK293 cells and cell lysates were treated with or without peptide-N-glycosidase F (PNGase-F), followed by immunoblotting analysis. Substitution of N48 prevents hENT1 glycosylation, confirming a single N-linked glycosylation site. N48Q-hENT1 protein is found at the plasma membrane in HEK293 cells but at lower levels compared with wt hENT1 based on S-(4-nitrobenzyl)-6-thioinosine (NBTI) binding analysis (wt 3xFLAG-ENT1 Bmax, 41.5±2.9 pmol/mg protein; N48Q-3xFLAG-ENT1 Bmax, 13.5±0.45 pmol/mg protein) and immunofluorescence microscopy. Although present at the membrane, chloroadenosine transport assays suggest that N48Q-hENT1 is non-functional (wt 3xFLAG-ENT1, 170.80±44.01 pmol/mg protein; N48Q-3xFLAG-ENT1, 57.91±17.06 pmol/mg protein; mock-transfected 74.31±19.65 pmol/mg protein). Co-immunoprecipitation analyses suggest that N48Q ENT1 is unable to interact with self or with wt hENT1. Based on these data we propose that glycosylation at N48 is critical for the localization, function and oligomerization of hENT1. PMID:27480168

  7. N-linked glycosylation of N48 is required for equilibrative nucleoside transporter 1 (ENT1) function

    PubMed Central

    Bicket, Alex; Coe, Imogen R.

    2016-01-01

    Human equilibrative nucleoside transporter 1 (hENT1) transports nucleosides and nucleoside analogue drugs across cellular membranes and is necessary for the uptake of many anti-cancer, anti-parasitic and anti-viral drugs. Previous work, and in silico prediction, suggest that hENT1 is glycosylated at Asn48 in the first extracellular loop of the protein and that glycosylation plays a role in correct localization and function of hENT1. Site-directed mutagenesis of wild-type (wt) hENT1 removed potential glycosylation sites. Constructs (wt 3xFLAG-hENT1, N48Q-3xFLAG-hENT1 or N288Q-3xFLAG-hENT2) were transiently transfected into HEK293 cells and cell lysates were treated with or without peptide–N-glycosidase F (PNGase-F), followed by immunoblotting analysis. Substitution of N48 prevents hENT1 glycosylation, confirming a single N-linked glycosylation site. N48Q-hENT1 protein is found at the plasma membrane in HEK293 cells but at lower levels compared with wt hENT1 based on S-(4-nitrobenzyl)-6-thioinosine (NBTI) binding analysis (wt 3xFLAG-ENT1 Bmax, 41.5±2.9 pmol/mg protein; N48Q-3xFLAG-ENT1 Bmax, 13.5±0.45 pmol/mg protein) and immunofluorescence microscopy. Although present at the membrane, chloroadenosine transport assays suggest that N48Q-hENT1 is non-functional (wt 3xFLAG-ENT1, 170.80±44.01 pmol/mg protein; N48Q-3xFLAG-ENT1, 57.91±17.06 pmol/mg protein; mock-transfected 74.31±19.65 pmol/mg protein). Co-immunoprecipitation analyses suggest that N48Q ENT1 is unable to interact with self or with wt hENT1. Based on these data we propose that glycosylation at N48 is critical for the localization, function and oligomerization of hENT1. PMID:27480168

  8. Robust Cross-Linked Stereocomplexes and C60 Inclusion Complexes of Vinyl-Functionalized Stereoregular Polymers Derived from Chemo/Stereoselective Coordination Polymerization.

    PubMed

    Vidal, Fernando; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Chen, Eugene Y-X

    2016-08-01

    The successful synthesis of highly syndiotactic polar vinyl polymers bearing the reactive pendant vinyl group on each repeat unit, which is enabled by perfectly chemoselective and highly syndiospecific coordination polymerization of divinyl polar monomers developed through this work, has allowed the construction of robust cross-linked supramolecular stereocomplexes and C60 inclusion complexes. The metal-mediated coordination polymerization of three representative polar divinyl monomers, including vinyl methacrylate (VMA), allyl methacrylate (AMA), and N,N-diallyl acrylamide (DAA) by Cs-ligated zirconocenium ester enolate catalysts under ambient conditions exhibits complete chemoselectivity and high stereoselectivity, thus producing the corresponding vinyl-functionalized polymers with high (92% rr) to quantitative (>99% rr) syndiotacticity. A combined experimental (synthetic, kinetic, and mechanistic) and theoretical (DFT) investigation has yielded a unimetallic, enantiomorphic-site-controlled propagation mechanism. Postfunctionalization of the obtained syndiotactic vinyl-functionalized polymers via the thiol-ene click and photocuring reactions readily produced the corresponding thiolated polymers and flexible cross-linked thin-film materials, respectively. Complexation of such syndiotactic vinyl-functionalized polymers with isotactic poly(methyl methacrylate) and fullerene C60 generates supramolecular crystalline helical stereocomplexes and inclusion complexes, respectively. Cross-linking of such complexes affords robust cross-linked stereocomplexes that are solvent-resistant and also exhibit considerably enhanced thermal and mechanical properties compared with the un-cross-linked stereocomplexes. PMID:27388024

  9. Molecular mechanisms linking diabetes mellitus and Alzheimer disease: beta-amyloid peptide, insulin signaling, and neuronal function.

    PubMed

    Takeda, Shuko; Sato, Naoyuki; Rakugi, Hiromi; Morishita, Ryuichi

    2011-06-01

    The incidence of Alzheimer disease (AD) and diabetes mellitus (DM) is increasing at an alarming rate and has become a major public health concern worldwide. Recent epidemiological studies have provided direct evidence that DM is a strong risk factor for AD; this finding is now attracting attention. However, the underlying mechanisms for this association remain largely unknown. Previous in vitro and in vivo studies reported that diabetic conditions could cause an increase in the beta-amyloid peptide (Aβ) levels, which exhibits neurotoxic properties and plays a causative role in AD. However, unexpectedly, recent clinicopathological studies have shown no evidence that the pathological hallmarks of AD, including amyloid plaque, were increased in the brains of diabetic patients, suggesting that DM could affect the pathogenesis of AD through mechanisms other than modulation of Aβ metabolism. One possible mechanism is the alteration in brain insulin signaling. It has been shown that insulin signaling is involved in a variety of neuronal functions, and that it also plays a significant role in the pathophysiology of AD. Thus, the modification of neuronal insulin signaling by diabetic conditions may contribute to AD progression. Another possible mechanism is cerebrovascular alteration, a common pathological change observed in both diseases. Accumulating evidence has suggested the importance of Aβ-induced cerebrovascular dysfunction in AD, and indicated that pathological interactions between the receptor for advanced glycation end products (RAGE) and Aβ peptides may play a role in this dysfunction. Our study has provided a further understanding of the potential underlying mechanisms linking DM and AD by establishing novel mouse models showing pathological manifestations of both diseases. The current review summarizes the results from recent studies on the pathological relationship between DM and AD while focusing on brain insulin signaling and cerebrovascular alteration

  10. Amelioration of altered antioxidant status and membrane linked functions by vanadium and Trigonella in alloxan diabetic rat brains.

    PubMed

    Siddiqui, Mohammad Rizwan; Taha, Asia; Moorthy, K; Hussain, Mohd Ejaz; Basir, S F; Baquer, Najma Zaheer

    2005-09-01

    Trigonella foenum graecum seed powder (TSP) and sodium orthovanadate (SOV) have been reported to have antidiabetic effects. However, SOV exerts hypoglycemic effects at relatively high doses with several toxic effects. We used low doses of vanadate in combination with TSP and evaluated their antidiabetic effects on anti-oxidant enzymes and membrane-linked functions in diabetic rat brains. In rats, diabetes was induced by alloxan monohydrate (15 mg/100 g body wt.) and they were treated with 2 IU insulin, 0.6 mg/ml SOV, 5% TSP and a combination of 0.2 mg/ml SOV with 5% TSP for 21 days. Blood glucose levels, activity of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), Na+/K+ ATPase, membrane lipid peroxidation and fluidity were determined in different fractions of whole brain after 21 days of treatment. Diabetic rats showed high blood glucose (P less than 0.001), decreased activities of SOD, catalase and Na+/K+ ATPase (P less than 0.01, P less than 0.001 and P less than 0.01), increased levels of GPx and MDA (P less than 0.01 and P less than 0.001) and decreased membrane fluidity (P less than 0.01). Treatment with different antidiabetic compounds restored the above-altered parameters. Combined dose of Trigonella and vanadate was found to be the most effective treatment in normalizing these alterations. Lower doses of vanadate could be used in combination with TSP to effectively counter diabetic alterations without any toxic effects.

  11. Functional link between bone morphogenetic proteins and insulin-like peptide 3 signaling in modulating ovarian androgen production

    PubMed Central

    Glister, Claire; Satchell, Leanne; Bathgate, Ross A. D.; Wade, John D.; Dai, Yanzhenzi; Ivell, Richard; Anand-Ivell, Ravinder; Rodgers, Raymond J.; Knight, Philip G.

    2013-01-01

    Bone morphogenetic proteins (BMPs) are firmly implicated as intra-ovarian regulators of follicle development and steroidogenesis. Here we report a microarray analysis showing that treatment of cultured bovine theca cells (TC) with BMP6 significantly (>twofold; P < 0.01) up- or down-regulated expression of 445 genes. Insulin-like peptide 3 (INSL3) was the most heavily down-regulated gene (−43-fold) with cytochrome P450, subfamily XVII (CYP17A1) and other key steroidogenic transcripts including steroidogenic acute regulatory protein (STAR), cytochrome P450 family 11, subfamily A1 (CYP11A1) and 3 beta-hydroxysteroid dehydrogenase type 1 (HSD3B1) also down-regulated. BMP6 also reduced expression of nuclear receptor subfamily 5A1 (NR5A1) known to target the promoter regions of the aforementioned genes. Real-time PCR confirmed these findings and also revealed a marked reduction in expression of INSL3 receptor, relaxin/insulin-like family peptide receptor 2 (RXFP2). Secretion of INSL3 protein and androstenedione were also suppressed suggesting a functional link between BMP and INSL3 pathways in controlling androgen synthesis. RNAi-mediated knockdown of INSL3 reduced INSL3 mRNA (75%) and protein (94%) level and elicited a 77% reduction in CYP17A1 mRNA and 83% reduction in androstenedione secretion. Knockdown of RXFP2 also reduced CYP17A1 expression (81%) and androstenedione secretion (88%). Conversely, treatment with exogenous (human) INSL3 increased androstenedione secretion ∼twofold. The CYP17A1 inhibitor abiraterone abolished androgen secretion and reduced expression of both INSL3 and RXFP2. Collectively, these findings indicate a positive autoregulatory role for INSL3 signaling in maintaining thecal androgen production, and visa versa. Moreover, BMP6-induced suppression of thecal androgen synthesis may be mediated, at least in part, by reduced INSL3-RXFP2 signaling. PMID:23530236

  12. Processing Semblances Induced through Inter-Postsynaptic Functional LINKs, Presumed Biological Parallels of K-Lines Proposed for Building Artificial Intelligence

    PubMed Central

    Vadakkan, Kunjumon I.

    2011-01-01

    The internal sensation of memory, which is available only to the owner of an individual nervous system, is difficult to analyze for its basic elements of operation. We hypothesize that associative learning induces the formation of functional LINK between the postsynapses. During memory retrieval, the activation of either postsynapse re-activates the functional LINK evoking a semblance of sensory activity arriving at its opposite postsynapse, nature of which defines the basic unit of internal sensation – namely, the semblion. In neuronal networks that undergo continuous oscillatory activity at certain levels of their organization re-activation of functional LINKs is expected to induce semblions, enabling the system to continuously learn, self-organize, and demonstrate instantiation, features that can be utilized for developing artificial intelligence (AI). This paper also explains suitability of the inter-postsynaptic functional LINKs to meet the expectations of Minsky’s K-lines, basic elements of a memory theory generated to develop AI and methods to replicate semblances outside the nervous system. PMID:21845180

  13. PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links

    PubMed Central

    Carroll, Adam J.; Zhang, Peng; Whitehead, Lynne; Kaines, Sarah; Tcherkez, Guillaume; Badger, Murray R.

    2015-01-01

    This article describes PhenoMeter (PM), a new type of metabolomics database search that accepts metabolite response patterns as queries and searches the MetaPhen database of reference patterns for responses that are statistically significantly similar or inverse for the purposes of detecting functional links. To identify a similarity measure that would detect functional links as reliably as possible, we compared the performance of four statistics in correctly top-matching metabolic phenotypes of Arabidopsis thaliana metabolism mutants affected in different steps of the photorespiration metabolic pathway to reference phenotypes of mutants affected in the same enzymes by independent mutations. The best performing statistic, the PM score, was a function of both Pearson correlation and Fisher’s Exact Test of directional overlap. This statistic outperformed Pearson correlation, biweight midcorrelation and Fisher’s Exact Test used alone. To demonstrate general applicability, we show that the PM reliably retrieved the most closely functionally linked response in the database when queried with responses to a wide variety of environmental and genetic perturbations. Attempts to match metabolic phenotypes between independent studies were met with varying success and possible reasons for this are discussed. Overall, our results suggest that integration of pattern-based search tools into metabolomics databases will aid functional annotation of newly recorded metabolic phenotypes analogously to the way sequence similarity search algorithms have aided the functional annotation of genes and proteins. PM is freely available at MetabolomeExpress (https://www.metabolome-express.org/phenometer.php). PMID:26284240

  14. CO2/light gas separation performance of cross-linked poly(vinylimidazolium) gel membranes as a function of ionic liquid loading and cross-linker content

    SciTech Connect

    Carlisle, TK; Nicodemus, GD; Gin, DL; Noble, RD

    2012-04-15

    A series of cross-linked poly(vinylimidazolium)-RTIL gel membranes was synthesized and evaluated for room-temperature, ideal CO2/N-2, CO2/CH4, and CO2/H-2 separation performance. The membranes were formed by photo-polymerization of oligo(ethylene glycol)-functionalized cross-linking (i.e., di-functional) and non-cross-linking (i.e., mono-functional) vinylimidazolium RTIL monomers with nonpolymerizable, "free RTIL." The effect of free RTIL ([emim][Tf2N]) loading on CO2 separation performance was evaluated by varying RTIL loading at three levels (45, 65, and 75 wt.%). The effect of cross-linker content on CO2 separation performance was also evaluated by varying the copolymer composition of cross-linked membranes from 5 to 100 mol% di-functional monomer. The substituent on the monofunctional RTIL monomer was also varied to investigate the effect of substituent structure and chemistry on CO2 separation performance. CO2 permeability was dramatically increased with higher loading of free RTIL. Increased RTIL loading had no effect on CO2/N-2 or CO2/CH4 permeability selectivity, but significantly improved CO2/H-2 permeability selectivity. Reducing the cross-linking monomer concentration generally improved CO2 permeability. However, anomalous permeability and selectivity behavior was observed below critical concentrations of cross-linker. The effect of the substituent on the monofunctional monomer on CO2 separation performance was minimal compared to the effects of RTIL loading and copolymer composition. (C) 2012 Elsevier B.V. All rights reserved.

  15. Functional Analysis of the Glucuronyltransferases GlcAT-P and GlcAT-S of Drosophila melanogaster: Distinct Activities towards the O-linked T-antigen.

    PubMed

    Breloy, Isabelle; Schwientek, Tilo; Althoff, Deborah; Holz, Marvin; Koppen, Tim; Krupa, Angelika; Hanisch, Franz-Georg

    2016-01-01

    The Drosophila melanogaster glucuronyltransferases dGlcAT-S and dGlcAT-P were reported to be expressed ubiquitously and results of in vitro activity assays indicate a functional redundancy. We analyzed both transferases in vivo and in vitro and could show significant differences in their activity towards N-and O-glycoproteins in vivo. While GlcAT-P is able to use N-linked N-acetyllactosamine chains and the O-linked T-antigen as a substrate to form non-sulfated HNK1- (GlcAβ1-3Galβ1-4GlcNAcβ1-) and glucuronyl-T-antigens in vivo, GlcAT-S adds glucuronic acid only to N-linked chains, thereby synthesizing only the non-sulfated HNK1-antigen. PMID:26751495

  16. Functional Analysis of the Glucuronyltransferases GlcAT-P and GlcAT-S of Drosophila melanogaster: Distinct Activities towards the O-linked T-antigen

    PubMed Central

    Breloy, Isabelle; Schwientek, Tilo; Althoff, Deborah; Holz, Marvin; Koppen, Tim; Krupa, Angelika; Hanisch, Franz-Georg

    2016-01-01

    The Drosophila melanogaster glucuronyltransferases dGlcAT-S and dGlcAT-P were reported to be expressed ubiquitously and results of in vitro activity assays indicate a functional redundancy. We analyzed both transferases in vivo and in vitro and could show significant differences in their activity towards N-and O-glycoproteins in vivo. While GlcAT-P is able to use N-linked N-acetyllactosamine chains and the O-linked T-antigen as a substrate to form non-sulfated HNK1- (GlcAβ1-3Galβ1-4GlcNAcβ1-) and glucuronyl-T-antigens in vivo, GlcAT-S adds glucuronic acid only to N-linked chains, thereby synthesizing only the non-sulfated HNK1-antigen. PMID:26751495

  17. In situ infrared spectroscopic and density-functional studies of the cross-linked structure of one-dimensional C{sub 60} polymer

    SciTech Connect

    Takashima, A.; Onoe, J.; Nishii, T.

    2010-08-15

    We have examined the infrared (IR) spectra of electron-beam (EB) irradiated C{sub 60} films, using in situ IR spectroscopy in the temperature range of 60-300 K. The irradiation-time evolution of the IR spectra shows that two highly intense new peaks finally appear around 565 and 1340 cm{sup -1} when the EB-induced C{sub 60} polymerization was saturated. To determine the cross-linked structure of the polymer explicitly, we have compared the IR spectra with theoretical spectra obtained from the cross-linked structure of all C{sub 120} stable isomers derived from the general Stone-Wales (GSW) rearrangement, using first-principles density-functional calculations. Since each C{sub 120} isomer has the same cross-linked structure as that of its corresponding one-dimensional (1D) C{sub 60} polymer, the IR modes obtained from the cross-linked structure of C{sub 120} are close to those obtained from the corresponding 1D polymer. Comparison between the experimental and theoretical IR spectra suggests that the 1D peanut-shaped C{sub 60} polymer has a cross-linked structure roughly similar to that of the P08 peanut-shaped C{sub 120} isomer.

  18. The link in Linking

    PubMed Central

    Caldwell, Jane C; Chiale, Pablo A; Gonzalez, Mario D; Baranchuk, Adrian

    2013-01-01

    We present 2 cases of the slow-fast form of AVNRT with initially narrow QRS complexes followed by sudden unexpected transition to persistently wide QRS complexes due to aberrant intraventricular conduction. Introduction of a properly timed extrastimulus in one case and critical oscillations in cycle length due to short-long coupling in the second case set the stage for the initial bundle branch block. However, persistence of the aberrancy pattern once the initial event abated was maintained by the "linking" phenomenon. Delayed, retrograde concealed activation from the contralateral bundle branch perpetuated the initial bundle branch block. PMID:23840106

  19. Biocomposites from Natural Rubber: Synergistic Effects of Functionalized Cellulose Nanocrystals as Both Reinforcing and Cross-Linking Agents via Free-Radical Thiol-ene Chemistry.

    PubMed

    Parambath Kanoth, Bipinbal; Claudino, Mauro; Johansson, Mats; Berglund, Lars A; Zhou, Qi

    2015-08-01

    Natural rubber/cellulose nanocrystals (NR/CNCs) form true biocomposites from renewable resources and are demonstrated to show significantly improved thermo-mechanical properties and reduced stress-softening. The nanocomposites were prepared from chemically functionalized CNCs bearing thiols. CNCs served as both reinforcing and cross-linking agents in the NR matrix, and the study was designed to prove the cross-linking function of modified CNCs. CNCs were prepared from cotton, and the cross-linkable mercapto-groups were introduced onto the surface of CNCs by esterification. Nanocomposite films were prepared by dispersing the modified CNCs (m-CNCs) in NR matrix by solution casting. The cross-links at the filler-matrix (m-CNCs-NR) interface were generated by photochemically initiated thiol-ene reactions as monitored by real-time FTIR analysis. The synergistic effects of reinforcement and chemical cross-linking at the m-CNCs-NR interface on structure, thermo-mechanical, and stress-softening behavior were investigated. Methods included field emission scanning electron microscopy (FE-SEM), swelling tests, dynamic mechanical analysis, and tensile tests. Compared to biocomposites from NR with unmodified CNCs, the NR/m-CNCs nanocomposites showed 2.4-fold increase in tensile strength, 1.6-fold increase in strain-to-failure, and 2.9-fold increase in work-of-fracture at 10 wt % of m-CNCs in NR. PMID:26151647

  20. Children’s Patterns of Emotional Reactivity to Conflict as Explanatory Mechanisms in Links Between Interpartner Aggression and Child Physiological Functioning

    PubMed Central

    Davies, Patrick T.; Sturge-Apple, Melissa L.; Cicchetti, Dante; Manning, Liviah G.; Zale, Emily

    2009-01-01

    Background This paper examined children’s fearful, sad, and angry reactivity to interparental conflict as mediators of associations between their exposure to interparental aggression and physiological functioning. Methods Participants included 200 toddlers and their mothers. Assessments of interparental aggression and children’s emotional reactivity were derived from maternal surveys and a semi-structured interview. Cortisol levels and cardiac indices of sympathetic nervous system (SNS) and parasympathetic nervous system (PNS) activity were used to assess toddler physiological functioning. Results Results indicated that toddler exposure to interparental aggression was associated with greater cortisol levels and PNS activity and diminished SNS activity. Toddler angry emotional reactivity mediated associations between interparental aggression and cortisol and PNS functioning. Fearful emotional reactivity was a mediator of the link between interparental aggression and SNS functioning. Conclusions The results are interpreted within conceptualizations of how exposure and reactivity to family risk organizing individual differences in physiological functioning. PMID:19744183

  1. Elucidating the functional relationship between working memory capacity and psychometric intelligence: a fixed-links modeling approach for experimental repeated-measures designs.

    PubMed

    Thomas, Philipp; Rammsayer, Thomas; Schweizer, Karl; Troche, Stefan

    2015-01-01

    Numerous studies reported a strong link between working memory capacity (WMC) and fluid intelligence (Gf), although views differ in respect to how close these two constructs are related to each other. In the present study, we used a WMC task with five levels of task demands to assess the relationship between WMC and Gf by means of a new methodological approach referred to as fixed-links modeling. Fixed-links models belong to the family of confirmatory factor analysis (CFA) and are of particular interest for experimental, repeated-measures designs. With this technique, processes systematically varying across task conditions can be disentangled from processes unaffected by the experimental manipulation. Proceeding from the assumption that experimental manipulation in a WMC task leads to increasing demands on WMC, the processes systematically varying across task conditions can be assumed to be WMC-specific. Processes not varying across task conditions, on the other hand, are probably independent of WMC. Fixed-links models allow for representing these two kinds of processes by two independent latent variables. In contrast to traditional CFA where a common latent variable is derived from the different task conditions, fixed-links models facilitate a more precise or purified representation of the WMC-related processes of interest. By using fixed-links modeling to analyze data of 200 participants, we identified a non-experimental latent variable, representing processes that remained constant irrespective of the WMC task conditions, and an experimental latent variable which reflected processes that varied as a function of experimental manipulation. This latter variable represents the increasing demands on WMC and, hence, was considered a purified measure of WMC controlled for the constant processes. Fixed-links modeling showed that both the purified measure of WMC (β = .48) as well as the constant processes involved in the task (β = .45) were related to Gf. Taken

  2. Functional analysis of N-linked glycosylation mutants of the measles virus fusion protein synthesized by recombinant vaccinia virus vectors.

    PubMed Central

    Alkhatib, G; Shen, S H; Briedis, D; Richardson, C; Massie, B; Weinberg, R; Smith, D; Taylor, J; Paoletti, E; Roder, J

    1994-01-01

    The role of N-linked glycosylation in the biological activity of the measles virus (MV) fusion (F) protein was analyzed by expressing glycosylation mutants with recombinant vaccinia virus vectors. There are three potential N-linked glycosylation sites located on the F2 subunit polypeptide of MV F, at asparagine residues 29, 61, and 67. Each of the three potential glycosylation sites was mutated separately as well as in combination with the other sites. Expression of mutant proteins in mammalian cells showed that all three sites are used for the addition of N-linked oligosaccharides. Cell surface expression of mutant proteins was reduced by 50% relative to the wild-type level when glycosylation at either Asn-29 or Asn-61 was abolished. Despite the similar levels of cell surface expression, the Asn-29 and Asn-61 mutant proteins had different biological activities. While the Asn-61 mutant was capable of inducing syncytium formation, the Asn-29 mutant protein did not exhibit any significant cell fusion activity. Inactivation of the Asn-67 glycosylation site also reduced cell surface transport of mutant protein but had little effect on its ability to cause cell fusion. However, when the Asn-67 mutation was combined with mutations at either of the other two sites, cleavage-dependent activation, cell surface expression, and cell fusion activity were completely abolished. Our data show that the loss of N-linked oligosaccharides markedly impaired the proteolytic cleavage, stability, and biological activity of the MV F protein. The oligosaccharide side chains in MV F are thus essential for optimum conformation of the extracellular F2 subunit that is presumed to bind cellular membranes. Images PMID:8107215

  3. Mimicking the hierarchical functions of dentin collagen cross-links with plant derived phenols and phenolic acids.

    PubMed

    Vidal, Cristina M P; Leme, Ariene A; Aguiar, Thaiane R; Phansalkar, Rasika; Nam, Joo-Won; Bisson, Jonathan; McAlpine, James B; Chen, Shao-Nong; Pauli, Guido F; Bedran-Russo, Ana

    2014-12-16

    Proanthocyanidins (PACs) are secondary plant metabolites that mediate nonenzymatic collagen cross-linking and enhance the properties of collagen based tissue, such as dentin. The extent and nature of cross-linking is influenced by the composition and specific chemical structure of the bioactive compounds present in certain PAC-rich extracts. This study investigated the effect of the molecular weight and stereochemistry of polyphenol compounds on two important properties of dentin, biomechanics, and biostability. For that, purified phenols, a phenolic acid, and some of its derivatives were selected: PAC dimers (A1, A2, B1, and B2) and a trimer (C1), gallic acid (Ga), its esters methyl-gallate (MGa) and propyl-gallate (PGa), and a pentagalloyl ester of glucose (PGG). Synergism was assessed by combining the most active PAC and gallic acid derivative. Mechanical properties of dentin organic matrix were determined by the modulus of elasticity obtained in a flexural test. Biostability was evaluated by the resistance to collagenase degradation. PACs significantly enhanced dentin mechanical properties and decreased collagen digestion. Among the gallic acid derivatives, only PGG had a significant enhancing effect. The lack of observed C1:PGG synergy indicates that both compounds have similar mechanisms of interaction with the dentin matrix. These findings reveal that the molecular weight of polyphenols have a determinant effect on their interaction with type I collagen and modulates the mechanism of cross-linking at the molecular, intermolecular, and inter-microfibrillar levels. PMID:25379878

  4. Genomic Analysis Reveals That Immune Function Genes Are Strongly Linked to Clinical Outcome in the North Central Cancer Treatment Group N9831 Adjuvant Trastuzumab Trial

    PubMed Central

    Perez, Edith A.; Thompson, E. Aubrey; Ballman, Karla V.; Anderson, S. Keith; Asmann, Yan W.; Kalari, Krishna R.; Eckel-Passow, Jeanette E.; Dueck, Amylou C.; Tenner, Kathleen S.; Jen, Jin; Fan, Jian-Bing; Geiger, Xochiquetzal J.; McCullough, Ann E.; Chen, Beiyun; Jenkins, Robert B.; Sledge, George W.; Winer, Eric P.; Gralow, Julie R.; Reinholz, Monica M.

    2015-01-01

    Purpose To develop a genomic signature that predicts benefit from trastuzumab in human epidermal growth factor receptor 2–positive breast cancer. Patients and Methods DASL technology was used to quantify mRNA in samples from 1,282 patients enrolled onto the Combination Chemotherapy With or Without Trastuzumab in Treating Women With Breast Cancer (North Central Cancer Treatment Group N9831 [NCCTG-N9831]) adjuvant trastuzumab trial. Cox proportional hazard ratios (HRs), adjusted for significant clinicopathologic risk factors, were used to determine the association of each gene with relapse-free survival (RFS) for 433 patients who received chemotherapy alone (arm A) and 849 patients who received chemotherapy plus trastuzumab (arms B and C). Network and pathway analyses were used to identify key biologic processes linked to RFS. The signature was built by using a voting scheme. Results Network and functional ontology analyses suggested that increased RFS was linked to a subset of immune function genes. A voting scheme model was used to define immune gene enrichment based on the expression of any nine or more of 14 immune function genes at or above the 0.40 quantile for the population. This model was used to identify immune gene–enriched tumors in arm A and arms B and C. Immune gene enrichment was linked to increased RFS in arms B and C (HR, 0.35; 95% CI, 0.22 to 0.55; P < .001), whereas arm B and C patients who did not exhibit immune gene enrichment did not benefit from trastuzumab (HR, 0.89; 95% CI, 0.62 to 1.28; P = .53). Enriched immune function gene expression as defined by our predictive signature was not associated with increased RFS in arm A (HR, 0.90; 95% CI, 0.60 to 1.37; P = .64). Conclusion Increased expression of a subset of immune function genes may provide a means of predicting benefit from adjuvant trastuzumab. PMID:25605861

  5. Cross-linked Composite Gel Polymer Electrolyte using Mesoporous Methacrylate-Functionalized SiO2 Nanoparticles for Lithium-Ion Polymer Batteries

    PubMed Central

    Shin, Won-Kyung; Cho, Jinhyun; Kannan, Aravindaraj G.; Lee, Yoon-Sung; Kim, Dong-Won

    2016-01-01

    Liquid electrolytes composed of lithium salt in a mixture of organic solvents have been widely used for lithium-ion batteries. However, the high flammability of the organic solvents can lead to thermal runaway and explosions if the system is accidentally subjected to a short circuit or experiences local overheating. In this work, a cross-linked composite gel polymer electrolyte was prepared and applied to lithium-ion polymer cells as a safer and more reliable electrolyte. Mesoporous SiO2 nanoparticles containing reactive methacrylate groups as cross-linking sites were synthesized and dispersed into the fibrous polyacrylonitrile membrane. They directly reacted with gel electrolyte precursors containing tri(ethylene glycol) diacrylate, resulting in the formation of a cross-linked composite gel polymer electrolyte with high ionic conductivity and favorable interfacial characteristics. The mesoporous SiO2 particles also served as HF scavengers to reduce the HF content in the electrolyte at high temperature. As a result, the cycling performance of the lithium-ion polymer cells with cross-linked composite gel polymer electrolytes employing methacrylate-functionalized mesoporous SiO2 nanoparticles was remarkably improved at elevated temperatures. PMID:27189842

  6. Cross-linked Composite Gel Polymer Electrolyte using Mesoporous Methacrylate-Functionalized SiO2 Nanoparticles for Lithium-Ion Polymer Batteries

    NASA Astrophysics Data System (ADS)

    Shin, Won-Kyung; Cho, Jinhyun; Kannan, Aravindaraj G.; Lee, Yoon-Sung; Kim, Dong-Won

    2016-05-01

    Liquid electrolytes composed of lithium salt in a mixture of organic solvents have been widely used for lithium-ion batteries. However, the high flammability of the organic solvents can lead to thermal runaway and explosions if the system is accidentally subjected to a short circuit or experiences local overheating. In this work, a cross-linked composite gel polymer electrolyte was prepared and applied to lithium-ion polymer cells as a safer and more reliable electrolyte. Mesoporous SiO2 nanoparticles containing reactive methacrylate groups as cross-linking sites were synthesized and dispersed into the fibrous polyacrylonitrile membrane. They directly reacted with gel electrolyte precursors containing tri(ethylene glycol) diacrylate, resulting in the formation of a cross-linked composite gel polymer electrolyte with high ionic conductivity and favorable interfacial characteristics. The mesoporous SiO2 particles also served as HF scavengers to reduce the HF content in the electrolyte at high temperature. As a result, the cycling performance of the lithium-ion polymer cells with cross-linked composite gel polymer electrolytes employing methacrylate-functionalized mesoporous SiO2 nanoparticles was remarkably improved at elevated temperatures.

  7. Cross-linked Composite Gel Polymer Electrolyte using Mesoporous Methacrylate-Functionalized SiO2 Nanoparticles for Lithium-Ion Polymer Batteries.

    PubMed

    Shin, Won-Kyung; Cho, Jinhyun; Kannan, Aravindaraj G; Lee, Yoon-Sung; Kim, Dong-Won

    2016-01-01

    Liquid electrolytes composed of lithium salt in a mixture of organic solvents have been widely used for lithium-ion batteries. However, the high flammability of the organic solvents can lead to thermal runaway and explosions if the system is accidentally subjected to a short circuit or experiences local overheating. In this work, a cross-linked composite gel polymer electrolyte was prepared and applied to lithium-ion polymer cells as a safer and more reliable electrolyte. Mesoporous SiO2 nanoparticles containing reactive methacrylate groups as cross-linking sites were synthesized and dispersed into the fibrous polyacrylonitrile membrane. They directly reacted with gel electrolyte precursors containing tri(ethylene glycol) diacrylate, resulting in the formation of a cross-linked composite gel polymer electrolyte with high ionic conductivity and favorable interfacial characteristics. The mesoporous SiO2 particles also served as HF scavengers to reduce the HF content in the electrolyte at high temperature. As a result, the cycling performance of the lithium-ion polymer cells with cross-linked composite gel polymer electrolytes employing methacrylate-functionalized mesoporous SiO2 nanoparticles was remarkably improved at elevated temperatures. PMID:27189842

  8. The Fixed-Links Model in Combination with the Polynomial Function as a Tool for Investigating Choice Reaction Time Data

    ERIC Educational Resources Information Center

    Schweizer, Karl

    2006-01-01

    A model with fixed relations between manifest and latent variables is presented for investigating choice reaction time data. The numbers for fixation originate from the polynomial function. Two options are considered: the component-based (1 latent variable for each component of the polynomial function) and composite-based options (1 latent…

  9. Versatile metal-organic framework-functionalized magnetic graphene nanoporous composites: As deft matrix for high-effective extraction and purification of the N-linked glycans.

    PubMed

    Wang, Jiaxi; Wang, Yanan; Gao, Mingxia; Zhang, Xiangmin; Yang, Pengyuan

    2016-08-17

    The highly selective enrichment of N-linked glycans from complex biological sample is still very important but challenging task due to the ultra-low abundance, complicated structures and strong ion suppress effect caused by distractors such as proteins, peptides and salts. Here, we firstly present a novel metal-organic frameworks (MOFs)-functionalized magnetic nanoporous carbon-graphene composites (C-magG@ZIF-8) synthesized through a smart process. The obtained materials enjoy the unique properties including strong magnetic responsiveness, a large sum of graphitized carbon pore, remarkable biocompatibility and large specific surface area. By virtue of these unique properties, the C-magG@ZIF-8 composites displayed excellent selectivity and sensitivity, good recyclability and incredible size exclusion ability (roughly 2000 times) in the N-linked glycans analysis. Furthermore, 48 N-linked glycans were clearly identified from the normal human serum treated with the C-magG@ZIF-8. There is reason to believe that our smart strategy offers new possibilities for preparing the MOFs-functionalized composites for large-scale characterization of glycoproteomics by mass spectrometry analysis.

  10. Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective.

    PubMed

    García-Palacios, Pablo; Vandegehuchte, Martijn L; Shaw, E Ashley; Dam, Marie; Post, Keith H; Ramirez, Kelly S; Sylvain, Zachary A; de Tomasel, Cecilia Milano; Wall, Diana H

    2015-04-01

    In recent years, there has been an increase in research to understand how global changes' impacts on soil biota translate into altered ecosystem functioning. However, results vary between global change effects, soil taxa, and ecosystem processes studied, and a synthesis of relationships is lacking. Therefore, here we initiate such a synthesis to assess whether the effect size of global change drivers (elevated CO2, N deposition, and warming) on soil microbial abundance is related with the effect size of these drivers on ecosystem functioning (plant biomass, soil C cycle, and soil N cycle) using meta-analysis and structural equation modeling. For N deposition and warming, the global change effect size on soil microbes was positively associated with the global change effect size on ecosystem functioning, and these relationships were consistent across taxa and ecosystem processes. However, for elevated CO2, such links were more taxon and ecosystem process specific. For example, fungal abundance responses to elevated CO2 were positively correlated with those of plant biomass but negatively with those of the N cycle. Our results go beyond previous assessments of the sensitivity of soil microbes and ecosystem processes to global change, and demonstrate the existence of general links between the responses of soil microbial abundance and ecosystem functioning. Further we identify critical areas for future research, specifically altered precipitation, soil fauna, soil community composition, and litter decomposition, that are need to better quantify the ecosystem consequences of global change impacts on soil biodiversity.

  11. Ecological Immunology through the Lens of Exercise Immunology: New Perspective on the Links between Physical Activity and Immune Function and Disease Susceptibility in Wild Animals.

    PubMed

    van Dijk, Jacintha G B; Matson, Kevin D

    2016-08-01

    Locomotion and other physical activities by free-living animals may influence immune function and disease susceptibility. This influence may be a consequence of energetic trade-offs or other mechanisms that are often, but not always, inseparably linked to an animal's life history (e.g., flight and migration). Ecological immunology has mainly focused on these life-history trade-offs, overlooking the possible effects of physical activity per se on immune function and disease susceptibility. In this review, we explore the field of exercise immunology, which examines the impact of exercise on immune function and disease susceptibility in humans, with the aim of presenting new perspectives that might be transferable to ecological immunology. First, we explore key concepts in exercise immunology that could be extended to animals. Next, we investigate the concept "exercise" in animals, and propose the use of "physical activity" instead. We briefly discuss methods used in animals to quantify physical activity in terms of energy expenditure and summarize several examples of animals engaging in physical activity. Then, we highlight potential consequences of physical activity on immune function and disease susceptibility in animals, together with an overview of animal studies that examine these links. Finally, we explore and discuss the potential for incorporating perspectives from exercise immunology into ecological immunology. Such integration could help advance our understanding of human and animal health and contribute new ideas to budding "One Health" initiatives.

  12. Functional brain networks: linking thalamic atrophy to clinical disability in multiple sclerosis, a multimodal fMRI and MEG study.

    PubMed

    Tewarie, Prejaas; Schoonheim, Menno M; Schouten, Daphne I; Polman, Chris H; Balk, Lisanne J; Uitdehaag, Bernard M J; Geurts, Jeroen J G; Hillebrand, Arjan; Barkhof, Frederik; Stam, Cornelis J

    2015-02-01

    Thalamic atrophy is known to be one of the most important predictors for clinical dysfunction in multiple sclerosis (MS). As the thalamus is highly connected to many cortical areas, this suggests that thalamic atrophy is associated with disruption of cortical functional networks. We investigated this thalamo-cortical system to explain the presence of physical and cognitive problems in MS. Functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) were performed in 86 MS patients and 21 healthy subjects. We computed cortical functional networks for fMRI and MEG by respectively the Pearson's correlation coefficient and the phase lag index using the same automated anatomical labeling atlas for both modalities. Thalamo-cortical functional connectivity was only estimated using fMRI. We computed conventional network metrics such as clustering coefficient and path length and analyzed the minimum spanning tree (MST), a subnetwork and backbone of the original network. MS patients showed reduced thalamic volumes and increased thalamo-cortical connectivity. MEG cortical functional networks showed a lower level of integration in MS in terms of the MST, whereas fMRI cortical networks did not differ between groups. Lower integration of MEG cortical functional networks was both related to thalamic atrophy as well as to increased thalamo-cortical functional connectivity in fMRI and to worse cognitive and clinical status. This study demonstrated for the first time that thalamic atrophy is associated with global disruption of cortical functional networks in MS and this global disruption of network activity was related to worse cognitive and clinical function in MS. Hum Brain Mapp 36:603-618, 2015. © 2014 Wiley Periodicals, Inc.

  13. Developmental Trajectories of Acculturation: Links with Family Functioning and Mental Health in Recent-Immigrant Hispanic Adolescents

    PubMed Central

    Schwartz, Seth J.; Unger, Jennifer B.; Zamboanga, Byron L.; Córdova, David; Mason, Craig A.; Huang, Shi; Baezconde-Garbanati, Lourdes; Lorenzo-Blanco, Elma I.; Des Rosiers, Sabrina; Soto, Daniel W.; Villamar, Juan A.; Pattarroyo, Monica; Lizzi, Karina M.; Szapocznik, José

    2014-01-01

    The present study was designed to examine acculturative changes, and their effects on mental health and family functioning, in recent-immigrant Hispanic adolescents. A sample of 302 Hispanic adolescents was assessed five times over a 2½-year period. Participants completed measures of Hispanic and U.S. practices, collectivist and individualist values, and ethnic and U.S. identity at each timepoint. Baseline and Time 5 levels of mental health and family functioning were also assessed. Latent class growth analyses produced two-class solutions for practices, values, and identifications. Adolescents who increased over time in practices and values reported the most adaptive mental health and family functioning. Adolescents who did not change in any acculturation domain reported the least favorable mental health and family functioning. PMID:25644262

  14. X-linked retinitis pigmentosa: Report of a large kindred with loss of central vision and preserved peripheral function

    SciTech Connect

    Shastry, B.S.; Trese, M.T.

    1995-11-20

    X-linked retinitis pigmentosa (XLRP) is the most severe form of the inherited forms of retinitis pigmentosa and is clinically variable and genetically heterogeneous. It affects one in 20,000 live births. The affected individuals manifest degeneration of the peripheral retina during the first two decades of life on the basis of night blindness. Central vision usually is preserved until age 50, when the disease advances, affecting central vision and ultimately leading to complete loss of sight. Linkage analysis has shown two loci with a possibility of a third locus on the human X chromosome. The genetic abnormality that causes XLRP is not known at present. Here we describe a large kindred which manifests central loss of field with the preservation of peripheral vision. 5 refs., 1 fig.

  15. Soluble 1D coordination polymers based on dendron-functionalized bispyridine ligand for linking between immobilized molecules on substrates.

    PubMed

    Tokuhisa, Hideo; Kanesato, Masatoshi

    2005-10-11

    As a monomeric ligand for a soluble 1D coordination polymer, a benzyl-ether based dendrimer having a rigid 4,4'-bispyridine ligand at the focal point has been synthesized and the coordination chemistry with Pd(II) investigated by nuclear magnetic resonance, ultraviolet-visible and fluorescence spectroscopies, gel permeation chromatography measurement, and X-ray photoelectron spectroscopy. As a result, it was found that the synthesized dendrimer forms a stable, soluble Pd(II) coordination polymer with rough estimation of degree of polymerization of 10 in organic solvents. Furthermore, through the coordination polymer we attempted to link fourth-generation poly(amidoamine) dendrimers (PAMAM) individually immobilized on mica and confirmed the interconnection of the PAMAM through coordination polymers by atomic force microscopy.

  16. Archaeal surface appendages: their function and the critical role of N-linked glycosylation in their assembly

    NASA Astrophysics Data System (ADS)

    Jarrell, Ken F.; Nair, Divya B.; Jones, Gareth M.; Aizawa, S.-I.; Chong, James J. P.; Stark, Meg; Logan, Susan M.; Vinogradov, Evgeny; Kelly, John F.

    2011-10-01

    Many cultivated archaea are extremophiles and, as such, various archaea inhabit some of the most inhospitable niches on the planet in terms of temperature, pH, salinity and anaerobiosis. Different archaeal species have been shown to produce a number of unusual and sometimes unique surface structures. The best studied of these are flagella which are fundamentally different from bacterial flagella and instead bear numerous similarities to bacterial type IV pili in their structure and likely assembly. The major structural proteins, flagellins, are made as preproteins with type IV pilin-like signal peptides processed by a specific signal peptidase. In addition, the flagellins are glycoproteins with attached N-linked glycans. Both of these posttranslational modifications have been studied in the anaerobic archaeon, Methanococcus maripaludis, an organism which also possesses other surface appendages, an unusual version of type IV pili, whose major constituents are also glycoproteins. Analysis of mutants unable to make either or both of flagella and pili demonstrated that both are essential for attachment to surfaces. A number of mutants defective in the assembly and biosynthesis of the tetrasaccharide N-linked to the flagellins have been isolated. Investigations of these mutants by electron microscopy, mass spectrometry and motility assays have demonstrated that flagellins possessing no attached glycan or a glycan truncated to a single sugar cannot assemble flagella on their surface. Mutants which can attach a glycan of 2 or 3 sugars to flagellins assemble flagella but they are impaired in their swimming compared with wildtype cells which attach the tetrasaccharide to their flagellins.

  17. Redox-sensitive cross-linking enhances albumin nanoparticle function as delivery system for photodynamic cancer therapy

    PubMed Central

    Molina, Anna M.; Morales-Cruz, Moraima; Benítez, Marimar; Berríos, Kiara; Figueroa, Cindy M.; Griebenow, Kai

    2016-01-01

    Photodynamic cancer therapy is still limited in its efficiency because of a lack of targeted methods avoiding non-specific toxicity. To overcome this we developed a system that is solely effective upon cellular uptake and intracellular activation by incorporating redox-sensitive chemistry. We used a nanoprecipitation method to obtain human serum albumin nanoparticles (HSA NP) with a diameter of 295 ± 5 nm and decorated them with the photosensitizer (PS) chlorin e6 (Ce6). The NP were stabilized using a redox-sensitive cross-linker to create a smart drug delivery system that is activated only upon NP disintegration in the reducing intracellular environment. Indeed, our drug delivery NP broke down in an environment emulating the reducing intracellular environment with 10 mM glutathione, but not under extracellular conditions. In contrast, the control cross-linked with glutaraldehyde did not break down in the reducing environment. Upon NP disintegration Ce6 fluorescence doubled as the result of diminished self-quenching. While the Ce6-HSA NP did not produce a significant amount of singlet oxygen upon irradiation, NP disintegration restored singlet oxygen production to about half of the value generated by the free Ce6. In vitro experiments with HeLa cells showed that the smart system was able to kill up to 81% of the cells while the glutaraldehyde cross-linked control only killed 56% of them at a drug concentration of 10 ng/ml. Also, Ce6 immobilization in HSA NP prevented dark toxicity in three different cell lines. For the first time, we demonstrate that it is possible to design a smart NP drug delivery system delivering a PS drug to cancer cells while avoiding toxicity prior to the uptake and irradiation. This finding may provide a means of designing more efficient PDT in cancer treatment. PMID:27088048

  18. Altered functional connectivity links in neuroleptic-naïve and neuroleptic-treated patients with schizophrenia, and their relation to symptoms including volition

    PubMed Central

    Pu, Weidan; Rolls, Edmund T.; Guo, Shuixia; Liu, Haihong; Yu, Yun; Xue, Zhimin; Feng, Jianfeng; Liu, Zhening

    2014-01-01

    In order to analyze functional connectivity in untreated and treated patients with schizophrenia, resting-state fMRI data were obtained for whole-brain functional connectivity analysis from 22 first-episode neuroleptic-naïve schizophrenia (NNS), 61 first-episode neuroleptic-treated schizophrenia (NTS) patients, and 60 healthy controls (HC). Reductions were found in untreated and treated patients in the functional connectivity between the posterior cingulate gyrus and precuneus, and this was correlated with the reduction in volition from the Positive and Negative Symptoms Scale (PANSS), that is in the willful initiation, sustenance, and control of thoughts, behavior, movements, and speech, and with the general and negative symptoms. In addition in both patient groups interhemispheric functional connectivity was weaker between the orbitofrontal cortex, amygdala and temporal pole. These functional connectivity changes and the related symptoms were not treated by the neuroleptics. Differences between the patient groups were that there were more strong functional connectivity links in the NNS patients (including in hippocampal, frontal, and striatal circuits) than in the NTS patients. These findings with a whole brain analysis in untreated and treated patients with schizophrenia provide evidence on some of the brain regions implicated in the volitional, other general, and negative symptoms, of schizophrenia that are not treated by neuroleptics so have implications for the development of other treatments; and provide evidence on some brain systems in which neuroleptics do alter the functional connectivity. PMID:25389520

  19. Altered functional connectivity links in neuroleptic-naïve and neuroleptic-treated patients with schizophrenia, and their relation to symptoms including volition.

    PubMed

    Pu, Weidan; Rolls, Edmund T; Guo, Shuixia; Liu, Haihong; Yu, Yun; Xue, Zhimin; Feng, Jianfeng; Liu, Zhening

    2014-01-01

    In order to analyze functional connectivity in untreated and treated patients with schizophrenia, resting-state fMRI data were obtained for whole-brain functional connectivity analysis from 22 first-episode neuroleptic-naïve schizophrenia (NNS), 61 first-episode neuroleptic-treated schizophrenia (NTS) patients, and 60 healthy controls (HC). Reductions were found in untreated and treated patients in the functional connectivity between the posterior cingulate gyrus and precuneus, and this was correlated with the reduction in volition from the Positive and Negative Symptoms Scale (PANSS), that is in the willful initiation, sustenance, and control of thoughts, behavior, movements, and speech, and with the general and negative symptoms. In addition in both patient groups interhemispheric functional connectivity was weaker between the orbitofrontal cortex, amygdala and temporal pole. These functional connectivity changes and the related symptoms were not treated by the neuroleptics. Differences between the patient groups were that there were more strong functional connectivity links in the NNS patients (including in hippocampal, frontal, and striatal circuits) than in the NTS patients. These findings with a whole brain analysis in untreated and treated patients with schizophrenia provide evidence on some of the brain regions implicated in the volitional, other general, and negative symptoms, of schizophrenia that are not treated by neuroleptics so have implications for the development of other treatments; and provide evidence on some brain systems in which neuroleptics do alter the functional connectivity.

  20. 14-3-3ζ regulates the mitochondrial respiratory reserve linked to platelet phosphatidylserine exposure and procoagulant function

    PubMed Central

    Schoenwaelder, Simone M.; Darbousset, Roxane; Cranmer, Susan L.; Ramshaw, Hayley S.; Orive, Stephanie L.; Sturgeon, Sharelle; Yuan, Yuping; Yao, Yu; Krycer, James R.; Woodcock, Joanna; Maclean, Jessica; Pitson, Stuart; Zheng, Zhaohua; Henstridge, Darren C.; van der Wal, Dianne; Gardiner, Elizabeth E.; Berndt, Michael C.; Andrews, Robert K.; James, David E.; Lopez, Angel F.; Jackson, Shaun P.

    2016-01-01

    The 14-3-3 family of adaptor proteins regulate diverse cellular functions including cell proliferation, metabolism, adhesion and apoptosis. Platelets express numerous 14-3-3 isoforms, including 14-3-3ζ, which has previously been implicated in regulating GPIbα function. Here we show an important role for 14-3-3ζ in regulating arterial thrombosis. Interestingly, this thrombosis defect is not related to alterations in von Willebrand factor (VWF)–GPIb adhesive function or platelet activation, but instead associated with reduced platelet phosphatidylserine (PS) exposure and procoagulant function. Decreased PS exposure in 14-3-3ζ-deficient platelets is associated with more sustained levels of metabolic ATP and increased mitochondrial respiratory reserve, independent of alterations in cytosolic calcium flux. Reduced platelet PS exposure in 14-3-3ζ-deficient mice does not increase bleeding risk, but results in decreased thrombin generation and protection from pulmonary embolism, leading to prolonged survival. Our studies define an important role for 14-3-3ζ in regulating platelet bioenergetics, leading to decreased platelet PS exposure and procoagulant function. PMID:27670677

  1. Frontal Lobe Function and Risk of Hip Fracture in Patient With Alzheimer Disease: An Analysis of Linked Data.

    PubMed

    Roh, Hyun Woong; Hong, Chang Hyung; Lee, SooJin; Lee, Yunhwan; Lee, Kang Soo; Chang, Ki Jung; Oh, Byoung Hoon; Choi, Seong Hye; Kim, Seong Yoon; Back, Joung Hwan; Chung, Young Ki; Lim, Ki Young; Noh, Jai Sung; Son, Sang Joon

    2015-11-01

    To determine the association between frontal lobe function and risk of hip fracture in patients with Alzheimer disease (AD).Retrospective cohort study using multicenter hospital-based dementia registry and national health insurance claim data was done. Participants who had available data of neuropsychological test, national health insurance claim, and other covariates were included. A total of 1660 patients with AD were included based on Stroop Test results. A total of 1563 patients with AD were included based on the Controlled Oral Word Association Test (COWAT) results. Hip fracture was measured by validated identification criteria using national health insurance claim data. Frontal lobe function was measured by Stroop Test and COWAT at baseline.After adjusting for potential covariates, including cognitive function in other domains (language, verbal and nonverbal memory, and attention), the Cox proportional hazard regression analysis revealed that risk of a hip fracture was decreased with a hazard ratio (HR) of 0.98 per one point of increase in the Stroop Test (adjusted HR = 0.98, 95% confidence interval [CI]: 0.97-1.00) and 0.93 per one point increase in COWAT (adjusted HR = 0.93, 95% CI: 0.88-0.99).The risk of hip fracture in AD patients was associated with baseline frontal lobe function. The result of this research presents evidence of association between frontal lobe function and risk of hip fracture in patients with AD. PMID:26559259

  2. The Architecture of Cross-Hemispheric Communication in the Aging Brain: Linking Behavior to Functional and Structural Connectivity

    PubMed Central

    Kragel, James E.; Madden, David J.; Cabeza, Roberto

    2012-01-01

    Contralateral recruitment remains a controversial phenomenon in both the clinical and normative populations. To investigate the neural correlates of this phenomenon, we explored the tendency for older adults to recruit prefrontal cortex (PFC) regions contralateral to those most active in younger adults. Participants were scanned with diffusion tensor imaging and functional magnetic rresonance imaging during a lateralized word matching task (unilateral vs. bilateral). Cross-hemispheric communication was measured behaviorally as greater accuracy for bilateral than unilateral trials (bilateral processing advantage [BPA]) and at the neural level by functional and structural connectivity between contralateral PFC. Compared with the young, older adults exhibited 1) greater BPAs in the behavioral task, 2) greater compensatory activity in contralateral PFC during the bilateral condition, 3) greater functional connectivity between contralateral PFC during bilateral trials, and 4) a positive correlation between fractional anisotropy in the corpus callosum and both the BPA and the functional connectivity between contralateral PFC, indicating that older adults' ability to distribute processing across hemispheres is constrained by white matter integrity. These results clarify how older adults’ ability to recruit extra regions in response to the demands of aging is mediated by existing structural architecture, and how this architecture engenders corresponding functional changes that allow subjects to meet those task demands. PMID:21653286

  3. Loss-of-function mutation in the X-linked TBX22 promoter disrupts an ETS-1 binding site and leads to cleft palate.

    PubMed

    Fu, Xiazhou; Cheng, Yibin; Yuan, Jia; Huang, Chunhua; Cheng, Hanhua; Zhou, Rongjia

    2015-02-01

    The cleft palate only (CPO) is a common congenital defect with complex etiology in humans. The molecular etiology of the CPO remains unknown. Here, we report a loss-of-function mutation in X-linked TBX22 gene (T-box 22) in a six-generation family of the CPO with obvious phenotypes of both cleft palate and hyper-nasal speech. We identify a functional -73G>A mutation in the promoter of TBX22, which is located at the core-binding site of transcription factor ETS-1 (v-ets avian erythroblastosis virus E26 oncogene homolog 1). Phylogenetic analysis showed that the sequence around the -73G>A mutation site is specific in primates. The mutation was detected in all five affected male members cosegregating with the affected phenotype and heterozygote occurred only in some unaffected females of the family, suggesting an X-linked transmission of the mutation in the family. The -73G>A variant is a novel single nucleotide mutation. Cell co-transfections indicated that ETS-1 could activate the TBX22 promoter. Moreover, EMSA and ChIP assays demonstrated that the allele A disrupts the binding site of ETS-1, thus markedly decreases the activity of the TBX22 promoter, which is likely to lead to the birth defect of the CPO without ankyloglossia. These results suggest that a loss-of-function mutation in the X-linked TBX22 promoter may cause the cleft palate through disruption of TBX22-ETS-1 pathway.

  4. Behavioural Problems in 2-Year-Olds: Links with Individual Differences in Theory of Mind, Executive Function and Harsh Parenting

    ERIC Educational Resources Information Center

    Hughes, Claire; Ensor, Rosie

    2006-01-01

    Background: Cognitive and family factors are implicated in the origins of behavioural problems, but little is known about their independence or interplay. Methods: We present data from 127 two-year-olds from predominantly disadvantaged families who completed tests of "theory of mind" (ToM), executive function (EF) and verbal ability. Researchers'…

  5. Children's Patterns of Emotional Reactivity to Conflict as Explanatory Mechanisms in Links between Interpartner Aggression and Child Physiological Functioning

    ERIC Educational Resources Information Center

    Davies, Patrick T.; Sturge-Apple, Melissa L.; Cicchetti, Dante; Manning, Liviah G.; Zale, Emily

    2009-01-01

    Background: This paper examined children's fearful, sad, and angry reactivity to interparental conflict as mediators of associations between their exposure to interparental aggression and physiological functioning. Methods: Participants included 200 toddlers and their mothers. Assessments of interparental aggression and children's emotional…

  6. Ecodevelopmental Trajectories of Family Functioning: Links with HIV/STI Risk Behaviors and STI among Black Adolescents

    ERIC Educational Resources Information Center

    Córdova, David; Heinze, Justin E.; Mistry, Ritesh; Salas-Wright, Christopher P.; Zimmerman, Marc A.

    2016-01-01

    We examined the effects of family functioning trajectories on sexual risk behaviors and STI in adolescents. A sample of 850 predominantly (80%) Black adolescents from Michigan, United States, was assessed at baseline, 12, 24, and 36 months postbaseline. Adolescents were from working-class families with a mean age of 14.9 years (SD = 0.64, Range =…

  7. Linking food web functioning and habitat diversity for an ecosystem based management: a Mediterranean lagoon case-study.

    PubMed

    Brigolin, D; Facca, C; Franco, A; Franzoi, P; Pastres, R; Sfriso, A; Sigovini, M; Soldatini, C; Tagliapietra, D; Torricelli, P; Zucchetta, M; Pranovi, F

    2014-06-01

    We propose a modelling approach relating the functioning of a transitional ecosystem with the spatial extension of its habitats. A test case is presented for the lagoon of Venice, discussing the results in the context of the application of current EU directives. The effects on food web functioning due to changes related to manageable and unmanageable drivers were investigated. The modelling procedure involved the use of steady-state food web models and network analysis, respectively applied to estimate the fluxes of energy associated with trophic interactions, and to compute indices of food web functioning. On the long term (hundred years) temporal scale, the model indicated that the expected loss of salt marshes will produce further changes at the system level, with a lagoon showing a decrease in the energy processing efficiency. On the short term scale, simulation results indicated that fishery management accompanied by seagrass restoration measures would produce a slight transition towards a more healthy system, with higher energy cycling, and maintaining a good balance between processing efficiency and resilience. Scenarios presented suggest that the effectiveness of short term management strategies can be better evaluated when contextualized in the long term trends of evolution of a system. We also remark the need for further studying the relationship between habitat diversity and indicators of food web functioning.

  8. Executive Functions and Prader-Willi Syndrome: Global Deficit Linked with Intellectual Level and Syndrome-Specific Associations

    ERIC Educational Resources Information Center

    Chevalère, Johann; Postal, Virginie; Jauregui, Joseba; Copet, Pierre; Laurier, Virginie; Thuilleaux, Denise

    2015-01-01

    The aim of this study was to support the growing evidence suggesting that Prader-Willi Syndrome (PWS) might present with an impairment of executive functions (EFs) and to investigate whether this impairment is specific to patients with PWS or due to their intellectual disability (ID). Six tasks were administered to assess EFs (inhibition,…

  9. Ferredoxin-thioredoxin reductase: a catalytically active dithiol group links photoreduced ferredoxin to thioredoxin functional in photosynthetic enzyme regulation

    SciTech Connect

    Droux, M.; Miginiac-Maslow, M.; Jacquot, J.P.; Gadal, P.; Crawford, N.A.; Kosower, N.S.; Buchanan, B.B.

    1987-07-01

    The mechanism by which the ferredoxin-thioredoxin system activates the target enzyme, NADP-malate dehydrogenase, was investigated by analyzing the sulfhydryl status of individual protein components with (/sup 14/C)iodoacetate and monobromobimane. The data indicate that ferredoxin-thioredoxin reductase (FTR)--an iron-sulfur enzyme present in oxygenic photosynthetic organisms--is the first member of a thiol chain that links light to enzyme regulation. FTR possesses a catalytically active dithiol group localized on the 13 kDa (similar) subunit, that occurs in all species investigated and accepts reducing equivalents from photoreduced ferredoxin and transfers them stoichiometrically to the disulfide form of thioredoxin m. The reduced thioredoxin m, in turn, reduces NADP-malate dehydrogenase, thereby converting it from an inactive (S-S) to an active (SH) form. The means by which FTR is able to combine electrons (from photoreduced ferredoxin) with protons (from the medium) to reduce its active disulfide group remains to be determined.

  10. Biochemical characterization of arylsulfatase E and functional analysis of mutations found in patients with X-linked chondrodysplasia punctata.

    PubMed Central

    Daniele, A; Parenti, G; d'Addio, M; Andria, G; Ballabio, A; Meroni, G

    1998-01-01

    X-linked chondrodysplasia punctata (CDPX) is a congenital disorder characterized by abnormalities in cartilage and bone development. Mutations leading to amino acid substitutions were identified recently in CDPX patients, in the coding region of the arylsulfatase E (ARSE) gene, a novel member of the sulfatase gene family. Transfection of the ARSE full-length cDNA, in Cos7 cells, allowed us to establish that its protein product is a 60-kD precursor, which is subject to N-glycosylation, to give a mature 68-kD form that, unique among sulfatases, is localized to the Golgi apparatus. Five missense mutations found in CDPX patients were introduced into wild-type ARSE cDNA by site-directed mutagenesis. These mutants were transfected into Cos7 cells, and the arylsulfatase activity and biochemical properties were determined, to study the effect of these substitutions on the ARSE protein. One of the mutants behaves as the wild-type protein. All four of the other mutations resulted in a complete lack of arylsulfatase activity, although the substitutions do not appear to affect the stability and subcellular localization of the protein. The loss of activity due to these mutations confirms their involvement in the clinical phenotype and points to the importance of these residues in the correct folding of a catalytically active ARSE enzyme. PMID:9497243

  11. Causal Link between the Cortico-Rubral Pathway and Functional Recovery through Forced Impaired Limb Use in Rats with Stroke

    PubMed Central

    Ishida, Akimasa; Isa, Kaoru; Umeda, Tatsuya; Kobayashi, Kazuto; Kobayashi, Kenta; Hida, Hideki

    2016-01-01

    Intensive rehabilitation is believed to induce use-dependent plasticity in the injured nervous system; however, its causal relationship to functional recovery is unclear. Here, we performed systematic analysis of the effects of forced use of an impaired forelimb on the recovery of rats after lesioning the internal capsule with intracerebral hemorrhage (ICH). Forced limb use (FLU) group rats exhibited better recovery of skilled forelimb functions and their cortical motor area with forelimb representation was restored and enlarged on the ipsilesional side. In addition, abundant axonal sprouting from the reemerged forelimb area was found in the ipsilateral red nucleus after FLU. To test the causal relationship between the plasticity in the cortico-rubral pathway and recovery, loss-of-function experiments were conducted using a double-viral vector technique, which induces selective blockade of the target pathway. Blockade of the cortico-rubral tract resulted in deficits of the recovered forelimb function in FLU group rats. These findings suggest that the cortico-rubral pathway is a substrate for recovery induced by intensive rehabilitation after ICH. SIGNIFICANCE STATEMENT The research aimed at determining the causal linkage between reorganization of the motor pathway induced by intensive rehabilitative training and recovery after stroke. We clarified the expansion of the forelimb representation area of the ipsilesional motor cortex by forced impaired forelimb use (FLU) after lesioning the internal capsule with intracerebral hemorrhaging (ICH) in rats. Anterograde tracing showed robust axonal sprouting from the forelimb area to the red nucleus in response to FLU. Selective blockade of the cortico-rubral pathway by the novel double-viral vector technique clearly revealed that the increased cortico-rubral axonal projections had causal linkage to the recovery of reaching movements induced by FLU. Our data demonstrate that the cortico-rubral pathway is responsible for the

  12. The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan

    PubMed Central

    Takemoto, Kazuhiro; Kawakami, Yuko

    2015-01-01

    Metabolic rate and lifespan are important biological parameters that are studied in a wide range of research fields. They are known to correlate with body mass, but their association with gene (protein) functions is poorly understood. In this study, we collected data on the metabolic rate and lifespan of various organisms and investigated the relationship of these parameters with their genomes. We showed that the proportion of genes in a functional category, but not genome size, was correlated with mass-specific metabolic rate and maximal lifespan. In particular, the proportion of genes in oxic reactions (which occur in the presence of oxygen) was significantly associated with these two biological parameters. Additionally, we found that temperature, taxonomy, and mode-of-life traits had little effect on the observed associations. Our findings emphasize the importance of considering the biological functions of genes when investigating the relationships between genome, metabolic rate, and lifespan. Moreover, this provides further insights into these relationships, and may be useful for estimating metabolic rate and lifespan in individuals and the ecosystem using a combination of body mass measurements and genomic data. PMID:25943793

  13. The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan.

    PubMed

    Takemoto, Kazuhiro; Kawakami, Yuko

    2015-05-06

    Metabolic rate and lifespan are important biological parameters that are studied in a wide range of research fields. They are known to correlate with body mass, but their association with gene (protein) functions is poorly understood. In this study, we collected data on the metabolic rate and lifespan of various organisms and investigated the relationship of these parameters with their genomes. We showed that the proportion of genes in a functional category, but not genome size, was correlated with mass-specific metabolic rate and maximal lifespan. In particular, the proportion of genes in oxic reactions (which occur in the presence of oxygen) was significantly associated with these two biological parameters. Additionally, we found that temperature, taxonomy, and mode-of-life traits had little effect on the observed associations. Our findings emphasize the importance of considering the biological functions of genes when investigating the relationships between genome, metabolic rate, and lifespan. Moreover, this provides further insights into these relationships, and may be useful for estimating metabolic rate and lifespan in individuals and the ecosystem using a combination of body mass measurements and genomic data.

  14. The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan.

    PubMed

    Takemoto, Kazuhiro; Kawakami, Yuko

    2015-01-01

    Metabolic rate and lifespan are important biological parameters that are studied in a wide range of research fields. They are known to correlate with body mass, but their association with gene (protein) functions is poorly understood. In this study, we collected data on the metabolic rate and lifespan of various organisms and investigated the relationship of these parameters with their genomes. We showed that the proportion of genes in a functional category, but not genome size, was correlated with mass-specific metabolic rate and maximal lifespan. In particular, the proportion of genes in oxic reactions (which occur in the presence of oxygen) was significantly associated with these two biological parameters. Additionally, we found that temperature, taxonomy, and mode-of-life traits had little effect on the observed associations. Our findings emphasize the importance of considering the biological functions of genes when investigating the relationships between genome, metabolic rate, and lifespan. Moreover, this provides further insights into these relationships, and may be useful for estimating metabolic rate and lifespan in individuals and the ecosystem using a combination of body mass measurements and genomic data. PMID:25943793

  15. Linking trade-offs in habitat selection with the occurrence of functional responses for moose living in two nearby study areas.

    PubMed

    Mabille, Géraldine; Dussault, Christian; Ouellet, Jean-Pierre; Laurian, Catherine

    2012-12-01

    A species may modify its relative habitat use with changing availability, generating functional responses in habitat selection. Functional responses in habitat selection are expected to occur when animals experience trade-offs influencing their habitat selection, but only a few studies to date have explicitly linked functional responses to the underlying trade-offs faced by the animals. We used data from 39 female moose fitted with GPS telemetry collars in two nearby study areas in Canada to investigate if moose (1) were faced with a food/cover trade-off in habitat selection, as typically acknowledged in the literature, and (2) showed a functional response in their use of food/cover-rich habitats. We also examined how habitat selection patterns varied seasonally, and between study areas. The occurrence of functional responses varied strongly between study areas, and could not always be related to a measurable food/cover trade-off. Functional responses were observed more often in the study area where the environmental conditions were more severe (colder temperatures, higher precipitations, and lower food availability). Selection coefficients were also less variable among individuals in that study area, suggesting that severe environmental conditions may constrain individuals to a few selection tactics and promote the development of functional responses. Moose reacted to the availability of different habitat types in different seasons, reflecting the changing trade-offs faced by the animals. We found considerable behavioral differences between individuals from two adjacent study areas, and therefore recommend caution when extrapolating habitat selection results. We advocate for the wider use of functional responses to identify critical habitats for a species from a management or conservation perspective.

  16. Phenotypic and functional characterization of earthworm coelomocyte subsets: Linking light scatter-based cell typing and imaging of the sorted populations.

    PubMed

    Engelmann, Péter; Hayashi, Yuya; Bodó, Kornélia; Ernszt, Dávid; Somogyi, Ildikó; Steib, Anita; Orbán, József; Pollák, Edit; Nyitrai, Miklós; Németh, Péter; Molnár, László

    2016-12-01

    Flow cytometry is a common approach to study invertebrate immune cells including earthworm coelomocytes. However, the link between light-scatter- and microscopy-based phenotyping remains obscured. Here we show, by means of light scatter-based cell sorting, both subpopulations (amoebocytes and eleocytes) can be physically isolated with good sort efficiency and purity confirmed by downstream morphological and cytochemical applications. Immunocytochemical analysis using anti-EFCC monoclonal antibodies combined with phalloidin staining has revealed antigenically distinct, sorted subsets. Screening of lectin binding capacity indicated wheat germ agglutinin (WGA) as the strongest reactor to amoebocytes. This is further evidenced by WGA inhibition assays that suggest high abundance of N-acetyl-d-glucosamine in amoebocytes. Post-sort phagocytosis assays confirmed the functional differences between amoebocytes and eleocytes, with the former being in favor of bacterial engulfment. This study has proved successful in linking flow cytometry and microscopy analysis and provides further experimental evidence of phenotypic and functional heterogeneity in earthworm coelomocyte subsets. PMID:27349970

  17. Mental representation and mental practice: experimental investigation on the functional links between motor memory and motor imagery.

    PubMed

    Frank, Cornelia; Land, William M; Popp, Carmen; Schack, Thomas

    2014-01-01

    Recent research on mental representation of complex action has revealed distinct differences in the structure of representational frameworks between experts and novices. More recently, research on the development of mental representation structure has elicited functional changes in novices' representations as a result of practice. However, research investigating if and how mental practice adds to this adaptation process is lacking. In the present study, we examined the influence of mental practice (i.e., motor imagery rehearsal) on both putting performance and the development of one's representation of the golf putt during early skill acquisition. Novice golfers (N = 52) practiced the task of golf putting under one of four different practice conditions: mental, physical, mental-physical combined, and no practice. Participants were tested prior to and after a practice phase, as well as after a three day retention interval. Mental representation structures of the putt were measured, using the structural dimensional analysis of mental representation. This method provides psychometric data on the distances and groupings of basic action concepts in long-term memory. Additionally, putting accuracy and putting consistency were measured using two-dimensional error scores of each putt. Findings revealed significant performance improvements over the course of practice together with functional adaptations in mental representation structure. Interestingly, after three days of practice, the mental representations of participants who incorporated mental practice into their practice regime displayed representation structures that were more similar to a functional structure than did participants who did not incorporate mental practice. The findings of the present study suggest that mental practice promotes the cognitive adaptation process during motor learning, leading to more elaborate representations than physical practice only. PMID:24743576

  18. Linking Tropical Forest Function to Hydraulic Traits in a Size-Structured and Trait-Based Model

    NASA Astrophysics Data System (ADS)

    Christoffersen, B. O.; Gloor, M.; Fauset, S.; Fyllas, N.; Galbraith, D.; Baker, T. R.; Rowland, L.; Fisher, R.; Binks, O.; Sevanto, S.; Xu, C.; Jansen, S.; Choat, B.; Mencuccini, M.; McDowell, N. G.; Meir, P.

    2015-12-01

    A major weakness of forest ecosystem models is their inability to capture the diversity of responses to changes in water availability, severely hampering efforts to predict the fate of tropical forests under climate change. Such models often prescribe moisture sensitivity using heuristic response functions that are uniform across all individuals and lack important knowledge about trade-offs in hydraulic traits. We address this weakness by implementing a process representation of plant hydraulics into an individual- and trait-based model (Trait Forest Simulator; TFS) intended for application at discrete sites where community-level distributions of stem and leaf trait spectra (wood density, leaf mass per area, leaf nitrogen and phosphorus content) are known. The model represents a trade-off in the safety and efficiency of water conduction in xylem tissue through hydraulic traits, while accounting for the counteracting effects of increasing hydraulic path length and xylem conduit taper on whole-plant hydraulic resistance with increasing tree size. Using existing trait databases and additional meta-analyses from the rich literature on tropical tree ecophysiology, we obtained all necessary hydraulic parameters associated with xylem conductivity, vulnerability curves, pressure-volume curves, and hydraulic architecture (e.g., leaf-to-sapwood area ratios) as a function of the aforementioned traits and tree size. Incorporating these relationships in the model greatly improved the diversity of tree response to seasonal changes in water availability as well as in response to drought, as determined by comparison with field observations and experiments. Importantly, this individual- and trait-based framework provides a testbed for identifying both critical processes and functional traits needed for inclusion in coarse-scale Dynamic Global Vegetation Models, which will lead to reduced uncertainty in the future state of tropical forests.

  19. Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism

    PubMed Central

    Ettema, Thijs J. G.; Makarova, Kira S.; Jellema, Gera L.; Gierman, Hinco J.; Koonin, Eugene V.; Huynen, Martijn A.; de Vos, Willem M.; van der Oost, John

    2004-01-01

    Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been elucidated. Using sensitive sequence comparison methods, we detected a highly conserved, uncharacterized archaeal gene family that is distantly related to the catalytic core of the canonical PEPC. To verify the predicted function of this archaeal gene family, we cloned a representative from the hyperthermophilic acidophile Sulfolobus solfataricus and functionally produced the corresponding enzyme as a fusion with the Escherichia coli maltose-binding protein. The purified fusion protein indeed displayed highly thermostable PEPC activity. The structural and biochemical properties of the characterized archaeal-type PEPC (atPEPC) from S. solfataricus are in good agreement with previously reported biochemical analyses of other archaeal PEPC enzymes. The newly identified atPEPC, with its distinct properties, constitutes yet another example of the versatility of the enzymes of the central carbon metabolic pathways in the archaeal domain. PMID:15516590

  20. Reduced Frontoparietal Activity in Schizophrenia Is Linked to a Specific Deficit in Goal Maintenance: A Multisite Functional Imaging Study.

    PubMed

    Poppe, Andrew B; Barch, Deanna M; Carter, Cameron S; Gold, James M; Ragland, John Daniel; Silverstein, Steven M; MacDonald, Angus W

    2016-09-01

    Patients with schizophrenia (SZ) previously demonstrated specific deficits in an executive function known as goal maintenance, associated with reduced middle frontal gyrus (MFG) activity. This study aimed to validate a new tool-the Dot Pattern Expectancy (DPX) task-developed to facilitate multisite imaging studies of goal maintenance deficits in SZ or other disorders. Additionally, it sought to arrive at recommendations for scan length for future studies using the DPX. Forty-seven SZ and 56 healthy controls (HC) performed the DPX in 3-Tesla functional magnetic resonance imaging (fMRI) scanners at 5 sites. Group differences in DPX-related activity were examined with whole brain voxelwise analyses. SZs showed the hypothesized specific performance deficits with as little as 1 block of data. Reduced activity in SZ compared with HC was observed in bilateral frontal pole/MFG, as well as left posterior parietal lobe. Efficiency analyses found significant group differences in activity using 18 minutes of scan data but not 12 minutes. Several behavioral and imaging findings from the goal maintenance literature were robustly replicated despite the use of different scanners at different sites. We did not replicate a previous correlation with disorganization symptoms among patients. Results were consistent with an executive/attention network dysfunction in the higher levels of a cascading executive system responsible for goal maintenance. Finally, efficiency analyses found that 18 minutes of scanning during the DPX task is sufficient to detect group differences with a similar sample size.

  1. A novel functional link between MAP kinase cascades and the Ras/cAMP pathway that regulates survival.

    PubMed

    Cherkasova, Vera A; McCully, Ryan; Wang, Yunmei; Hinnebusch, Alan; Elion, Elaine A

    2003-07-15

    In mammalian cells, Ras regulates multiple effectors, including activators of mitogen-activated protein kinase (MAPK) cascades, phosphatidylinositol-3-kinase, and guanine nucleotide exchange factors (GEFs) for RalGTPases. In S. cerevisiae, Ras regulates the Kss1 MAPK cascade that promotes filamentous growth and cell integrity, but its major function is to activate adenylyl cyclase and control proliferation and survival ([; see Figure S1 in the Supplemental Data available with this article online). Previous work hints that the mating Fus3/Kss1 MAPK cascade cross-regulates the Ras/cAMP pathway during growth and mating, but direct evidence is lacking. Here, we report that Kss1 and Fus3 act upstream of the Ras/cAMP pathway to regulate survival. Loss of Fus3 increases cAMP and causes poor long-term survival and resistance to stress. These effects are dependent on Kss1 and Ras2. Activation of Kss1 by a hyperactive Ste11 MAPKKK also increases cAMP, but mating receptor/scaffold activation has little effect and may therefore insulate the MAPKs from cross-regulation. Catalytically inactive Fus3 represses cAMP by blocking accumulation of active Kss1 and by another function also shared by Kss1. The conserved RasGEF Cdc25 is a likely control point, because Kss1 and Fus3 complexes associate with and phosphorylate Cdc25. Cross-regulation of Cdc25 may be a general way that MAPKs control Ras signaling networks. PMID:12867033

  2. Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis

    PubMed Central

    Sebastián, David; Hernández-Alvarez, María Isabel; Segalés, Jessica; Sorianello, Eleonora; Muñoz, Juan Pablo; Sala, David; Waget, Aurélie; Liesa, Marc; Paz, José C.; Gopalacharyulu, Peddinti; Orešič, Matej; Pich, Sara; Burcelin, Rémy; Palacín, Manuel; Zorzano, Antonio

    2012-01-01

    Mitochondria are dynamic organelles that play a key role in energy conversion. Optimal mitochondrial function is ensured by a quality-control system tightly coupled to fusion and fission. In this connection, mitofusin 2 (Mfn2) participates in mitochondrial fusion and undergoes repression in muscle from obese or type 2 diabetic patients. Here, we provide in vivo evidence that Mfn2 plays an essential role in metabolic homeostasis. Liver-specific ablation of Mfn2 in mice led to numerous metabolic abnormalities, characterized by glucose intolerance and enhanced hepatic gluconeogenesis. Mfn2 deficiency impaired insulin signaling in liver and muscle. Furthermore, Mfn2 deficiency was associated with endoplasmic reticulum stress, enhanced hydrogen peroxide concentration, altered reactive oxygen species handling, and active JNK. Chemical chaperones or the antioxidant N-acetylcysteine ameliorated glucose tolerance and insulin signaling in liver-specific Mfn2 KO mice. This study provides an important description of a unique unexpected role of Mfn2 coordinating mitochondria and endoplasmic reticulum function, leading to modulation of insulin signaling and glucose homeostasis in vivo. PMID:22427360

  3. Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis.

    PubMed

    Sebastián, David; Hernández-Alvarez, María Isabel; Segalés, Jessica; Sorianello, Eleonora; Muñoz, Juan Pablo; Sala, David; Waget, Aurélie; Liesa, Marc; Paz, José C; Gopalacharyulu, Peddinti; Orešič, Matej; Pich, Sara; Burcelin, Rémy; Palacín, Manuel; Zorzano, Antonio

    2012-04-01

    Mitochondria are dynamic organelles that play a key role in energy conversion. Optimal mitochondrial function is ensured by a quality-control system tightly coupled to fusion and fission. In this connection, mitofusin 2 (Mfn2) participates in mitochondrial fusion and undergoes repression in muscle from obese or type 2 diabetic patients. Here, we provide in vivo evidence that Mfn2 plays an essential role in metabolic homeostasis. Liver-specific ablation of Mfn2 in mice led to numerous metabolic abnormalities, characterized by glucose intolerance and enhanced hepatic gluconeogenesis. Mfn2 deficiency impaired insulin signaling in liver and muscle. Furthermore, Mfn2 deficiency was associated with endoplasmic reticulum stress, enhanced hydrogen peroxide concentration, altered reactive oxygen species handling, and active JNK. Chemical chaperones or the antioxidant N-acetylcysteine ameliorated glucose tolerance and insulin signaling in liver-specific Mfn2 KO mice. This study provides an important description of a unique unexpected role of Mfn2 coordinating mitochondria and endoplasmic reticulum function, leading to modulation of insulin signaling and glucose homeostasis in vivo. PMID:22427360

  4. Longitudinal trajectories of bicultural identity integration in recently immigrated Hispanic adolescents: Links with mental health and family functioning.

    PubMed

    Schwartz, Seth J; Unger, Jennifer B; Baezconde-Garbanati, Lourdes; Benet-Martínez, Verónica; Meca, Alan; Zamboanga, Byron L; Lorenzo-Blanco, Elma I; Des Rosiers, Sabrina E; Oshri, Assaf; Sabet, Raha F; Soto, Daniel W; Pattarroyo, Monica; Huang, Shi; Villamar, Juan A; Lizzi, Karina M; Szapocznik, José

    2015-12-01

    This study examined, in a sample of recently immigrated Hispanic adolescents in Miami and Los Angeles, the extent to which bicultural identity integration (BII; involving the ability to synthesise one's heritage and receiving cultural streams and to identify as a member of both cultures) is best understood as a developmental construct that changes over time or as an individual-difference construct that is largely stable over time. We were also interested in the extent to which these trajectories predicted mental health and family functioning. Recent-immigrant 9th graders (N = 302) were assessed 6 times from 9th to 12th grade. Latent class growth analyses using the first 5 timepoints identified 2 trajectory classes-one with lower BII scores over time and another with higher BII scores over time. Higher heritage and US identity at baseline predicted membership in the higher BII class. At the 6th study timepoint, lower BII adolescents reported significantly poorer self-esteem, optimism, prosocial behaviour and family relationships compared with their higher BII counterparts. These findings are discussed in terms of further research on the over-time trajectory of biculturalism, and on the need to develop interventions to promote BII as a way of facilitating well-being and positive family functioning.

  5. Possible link between the power spectrum of interstellar filaments and the origin of the prestellar core mass function

    NASA Astrophysics Data System (ADS)

    Roy, A.; André, Ph.; Arzoumanian, D.; Peretto, N.; Palmeirim, P.; Könyves, V.; Schneider, N.; Benedettini, M.; Di Francesco, J.; Elia, D.; Hill, T.; Ladjelate, B.; Louvet, F.; Motte, F.; Pezzuto, S.; Schisano, E.; Shimajiri, Y.; Spinoglio, L.; Ward-Thompson, D.; White, G.

    2015-12-01

    A complete understanding of the origin of the prestellar core mass function (CMF) is crucial. Two major features of the prestellar CMF are 1) a broad peak below 1 M⊙, presumably corresponding to a mean gravitational fragmentation scale, and 2) a characteristic power-law slope, very similar to the Salpeter slope of the stellar initial mass function (IMF) at the high-mass end. While recent Herschel observations have shown that the peak of the prestellar CMF is close to the thermal Jeans mass in marginally supercritical filaments, the origin of the power-law tail of the CMF/IMF at the high-mass end is less clear. In 2001, Inutsuka proposed a theoretical scenario in which the origin of the power-law tail can be understood as resulting from the growth of an initial spectrum of density perturbations seeded along the long axis of star-forming filaments by interstellar turbulence. Here, we report the statistical properties of the line-mass fluctuations of filaments in the Pipe, Taurus, and IC 5146 molecular clouds observed with Herschel for a sample of subcritical or marginally supercritical filaments using a 1D power spectrum analysis. The observed filament power spectra were fitted by a power-law function (Ptrue(s) ∝ sα) after removing the effect of beam convolution at small scales. A Gaussian-like distribution of power-spectrum slopes was found, centered at α̅corr = -1.6 ± 0.3. The characteristic index of the observed power spectra is close to that of the 1D velocity power spectrum generated by subsonic Kolomogorov turbulence (-1.67). Given the errors, the measured power-spectrum slope is also marginally consistent with the power spectrum index of -2 expected for supersonic compressible turbulence. With such a power spectrum of initial line-mass fluctuations, Inutsuka's model would yield a mass function of collapsed objects along filaments approaching dN/dM ∝ M- 2.3 ± 0.1 at the high-mass end (very close to the Salpeter power law) after a few free-fall times

  6. On the Link Between Energy Equipartition and Radial Variation in the Stellar Mass Function of Star Clusters

    NASA Astrophysics Data System (ADS)

    Webb, Jeremy J.; Vesperini, Enrico

    2016-10-01

    We make use of N-body simulations to determine the relationship between two observable parameters that are used to quantify mass segregation and energy equipartition in star clusters. Mass segregation can be quantified by measuring how the slope of a cluster's stellar mass function α changes with clustercentric distance r, and then calculating δ _α = d α (r)/d ln(r/r_m) where rm is the cluster's half-mass radius. The degree of energy equipartition in a cluster is quantified by η, which is a measure of how stellar velocity dispersion σ depends on stellar mass m via σ(m)∝m-η. Through a suite of N-body star cluster simulations with a range of initial sizes, binary fractions, orbits, black hole retention fractions, and initial mass functions, we present the co-evolution of δα and η. We find that measurements of the global η are strongly affected by the radial dependence of σ and mean stellar mass and the relationship between η and δα depends mainly on the cluster's initial conditions and the tidal field. Within rm, where these effects are minimized, we find that η and δα initially share a linear relationship. However, once the degree of mass segregation increases such that the radial dependence of σ and mean stellar mass become a factor within rm, or the cluster undergoes core collapse, the relationship breaks down. We propose a method for determining η within rm from an observational measurement of δα. In cases where η and δα can be measured independently, this new method offers a way of measuring the cluster's dynamical state.

  7. Functional Variants in DPYSL2 Sequence Increase Risk of Schizophrenia and Suggest a Link to mTOR Signaling

    PubMed Central

    Liu, Yaping; Pham, Xuan; Zhang, Lilei; Chen, Pei-lung; Burzynski, Grzegorz; McGaughey, David M.; He, Shan; McGrath, John A.; Wolyniec, Paula; Fallin, Margaret D.; Pierce, Megan S.; McCallion, Andrew S.; Pulver, Ann E.; Avramopoulos, Dimitrios; Valle, David

    2014-01-01

    Numerous linkage and association studies by our group and others have implicated DPYSL2 at 8p21.2 in schizophrenia. Here we explore DPYSL2 for functional variation that underlies these associations. We sequenced all 14 exons of DPYSL2 as well as 27 conserved noncoding regions at the locus in 137 cases and 151 controls. We identified 120 variants, eight of which we genotyped in an additional 729 cases and 1542 controls. Several were significantly associated with schizophrenia, including a three single-nucleotide polymorphism (SNP) haplotype in the proximal promoter, two SNPs in intron 1, and a polymorphic dinucleotide repeat in the 5′-untranslated region that alters sequences predicted to be involved in translational regulation by mammalian target of rapamycin signaling. The 3-SNP promoter haplotype and the sequence surrounding one of the intron 1 SNPs direct tissue-specific expression in the nervous systems of Zebrafish in a pattern consistent with the two endogenous dpysl2 paralogs. In addition, two SNP haplotypes over the coding exons and 3′ end of DPYSL2 showed association with opposing sex-specific risks. These data suggest that these polymorphic, schizophrenia-associated sequences function as regulatory elements for DPYSL2 expression. In transient transfection assays, the high risk allele of the polymorphic dinucleotide repeat diminished reporter expression by 3- to 4-fold. Both the high- and low-risk alleles respond to allosteric mTOR inhibition by rapamycin until, at high drug levels, allelic differences are eliminated. Our results suggest that reduced transcription and mTOR-regulated translation of certain DPYSL2 isoforms increase the risk for schizophrenia. PMID:25416705

  8. The high affinity ligand binding conformation of the nuclear 1,25-dihydroxyvitamin D3 receptor is functionally linked to the transactivation domain 2 (AF-2).

    PubMed Central

    Nayeri, S; Kahlen, J P; Carlberg, C

    1996-01-01

    The nuclear receptor for 1,25-dihydroxyvitamin D3 (VD), VDR, is a transcription factor that mediates all genomic actions of the hormone. The activation of VDR by ligand induces a conformational change within its ligand binding domain (LBD). Due to the lack of a crystal structure analysis, biochemical methods have to be applied in order to investigate the details of this receptor-ligand interaction. The limited protease digestion assay can be used as a tool for the determination of a functional dissociation constant (K(df)) of VDR with any potential ligand. This method provided with the natural hormone VD two protease-resistant fragments of the VDR LBD and with the 20-epi conformation of VD, known as MC1288, even an additional fragment of intermediate size. These fragments were interpreted as different receptor conformations and their decreasing size was found to be associated with decreasing ligand binding affinity. A critical amino acid for VDR's high ligand binding conformation has been identified by C-terminal receptor truncations and point mutations as phenylalanine 422. This amino acid appears to directly contact the ligand and belongs to the ligand-inducible activation function-2 (AF-2) domain. Moreover, functional assays supported the observation that high affinity ligand binding is directly linked to transactivation function. PMID:8948643

  9. SOX1 links the function of neural patterning and Notch signalling in the ventral spinal cord during the neuron-glial fate switch

    SciTech Connect

    Genethliou, Nicholas; Panayiotou, Elena; Panayi, Helen; Orford, Michael; Mean, Richard; Lapathitis, George; Gill, Herman; Raoof, Sahir; Gasperi, Rita De; Elder, Gregory; Kessaris, Nicoletta; Richardson, William D.; Malas, Stavros

    2009-12-25

    During neural development the transition from neurogenesis to gliogenesis, known as the neuron-glial ({Nu}/G) fate switch, requires the coordinated function of patterning factors, pro-glial factors and Notch signalling. How this process is coordinated in the embryonic spinal cord is poorly understood. Here, we demonstrate that during the N/G fate switch in the ventral spinal cord (vSC) SOX1 links the function of neural patterning and Notch signalling. We show that, SOX1 expression in the vSC is regulated by PAX6, NKX2.2 and Notch signalling in a domain-specific manner. We further show that SOX1 regulates the expression of Hes1 and that loss of Sox1 leads to enhanced production of oligodendrocyte precursors from the pMN. Finally, we show that Notch signalling functions upstream of SOX1 during this fate switch and is independently required for the acquisition of the glial fate perse by regulating Nuclear Factor I A expression in a PAX6/SOX1/HES1/HES5-independent manner. These data integrate functional roles of neural patterning factors, Notch signalling and SOX1 during gliogenesis.

  10. A Cross-Linking Succinonitrile-Based Composite Polymer Electrolyte with Uniformly Dispersed Vinyl-Functionalized SiO2 Particles for Li-Ion Batteries.

    PubMed

    Liu, Kai; Ding, Fei; Liu, Jiaquan; Zhang, Qingqing; Liu, Xingjiang; Zhang, Jinli; Xu, Qiang

    2016-09-14

    A cross-linking succinonitrile (SN)-based composite polymer electrolyte (referred to as "CLPC-CPE"), in which vinyl-functionalized SiO2 particles connect with trimethylolpropane propoxylate triacrylate (TPPTA) monomers by covalent bonds, was prepared by an ultraviolet irradiation (UV-curing) process successfully. Vinyl-functionalized SiO2 particles may react with TPPTA monomers to form a cross-linking network within the SN-based composite polymer electrolyte under ultraviolet irradiation. Vinyl-functionalized SiO2 particles as the fillers of polymer electrolyte may improve both the thermal stability of CLPC-CPE and interfacial compatibility between CLPC-CPE and electrodes effectively. There is no weight loss for CLPC-CPE until above 230 °C. The ionic conductivity of CLPC-CPE may reach 7.02 × 10(-4) S cm(-1) at 25 °C. CLPC-CPE has no significant oxidation current until up to 4.6 V (vs Li/Li(+)). The cell of LiFePO4/CLPC-CPE/Li has presented superior cycle performance and rate capability. The cell of LiFePO4/CLPC-CPE/Li may deliver a high discharge capacity of 154.4 mAh g(-1) at a rate of 0.1 C after 100 charge-discharge cycles, which is similar than that of the control cell of LiFePO4/liquid electrolyte/Li. Furthermore, the cell of LiFePO4/CLPC-CPE/Li can display a high discharge capacity of 112.7 mAh g(-1) at a rate of 2 C, which is higher than that of the cells assembled with other plastic crystal polymer electrolyte reported before obviously. PMID:27561892

  11. A Cross-Linking Succinonitrile-Based Composite Polymer Electrolyte with Uniformly Dispersed Vinyl-Functionalized SiO2 Particles for Li-Ion Batteries.

    PubMed

    Liu, Kai; Ding, Fei; Liu, Jiaquan; Zhang, Qingqing; Liu, Xingjiang; Zhang, Jinli; Xu, Qiang

    2016-09-14

    A cross-linking succinonitrile (SN)-based composite polymer electrolyte (referred to as "CLPC-CPE"), in which vinyl-functionalized SiO2 particles connect with trimethylolpropane propoxylate triacrylate (TPPTA) monomers by covalent bonds, was prepared by an ultraviolet irradiation (UV-curing) process successfully. Vinyl-functionalized SiO2 particles may react with TPPTA monomers to form a cross-linking network within the SN-based composite polymer electrolyte under ultraviolet irradiation. Vinyl-functionalized SiO2 particles as the fillers of polymer electrolyte may improve both the thermal stability of CLPC-CPE and interfacial compatibility between CLPC-CPE and electrodes effectively. There is no weight loss for CLPC-CPE until above 230 °C. The ionic conductivity of CLPC-CPE may reach 7.02 × 10(-4) S cm(-1) at 25 °C. CLPC-CPE has no significant oxidation current until up to 4.6 V (vs Li/Li(+)). The cell of LiFePO4/CLPC-CPE/Li has presented superior cycle performance and rate capability. The cell of LiFePO4/CLPC-CPE/Li may deliver a high discharge capacity of 154.4 mAh g(-1) at a rate of 0.1 C after 100 charge-discharge cycles, which is similar than that of the control cell of LiFePO4/liquid electrolyte/Li. Furthermore, the cell of LiFePO4/CLPC-CPE/Li can display a high discharge capacity of 112.7 mAh g(-1) at a rate of 2 C, which is higher than that of the cells assembled with other plastic crystal polymer electrolyte reported before obviously.

  12. HESS Opinions: Functional units: a novel framework to explore the link between spatial organization and hydrological functioning of intermediate scale catchments

    NASA Astrophysics Data System (ADS)

    Zehe, E.; Ehret, U.; Pfister, L.; Blume, T.; Schröder, B.; Westhoff, M.; Jackisch, C.; Schymanski, S. J.; Weiler, M.; Schulz, K.; Allroggen, N.; Tronicke, J.; Dietrich, P.; Scherer, U.; Eccard, J.; Wulfmeyer, V.; Kleidon, A.

    2014-03-01

    This opinion paper proposes a novel framework for exploring how spatial organization alongside with spatial heterogeneity controls functioning of intermediate scale catchments of organized complexity. Key idea is that spatial organization in landscapes implies that functioning of intermediate scale catchments is controlled by a hierarchy of functional units: hillslope scale lead topologies and embedded elementary functional units (EFUs). We argue that similar soils and vegetation communities and thus also soil structures "co-developed" within EFUs in an adaptive, self-organizing manner as they have been exposed to similar flows of energy, water and nutrients from the past to the present. Class members of the same EFU (class) are thus deemed to belong to the same ensemble with respect to controls of the energy balance and related vertical flows of capillary bounded soil water and heat. Class members of superordinate lead topologies are characterized by the same spatially organized arrangement of EFUs along the gradient driving lateral flows of free water as well as a similar surface and bedrock topography. We hence postulate that they belong to the same ensemble with respect to controls on rainfall runoff transformation and related vertical and lateral fluxes of free water. We expect class members of these functional units to have a distinct way how their architecture controls the interplay of state dynamics and integral flows, which is typical for all members of one class but dissimilar among the classes. This implies that we might infer on the typical dynamic behavior of the most important classes of EFU and lead topologies in a catchment, by thoroughly characterizing a few members of each class. A major asset of the proposed framework, which steps beyond the concept of hydrological response units, is that it can be tested experimentally. In this respect, we reflect on suitable strategies based on stratified observations drawing from process hydrology, soil

  13. Endoplasmic Reticulum Stress Links Oxidative Stress to Impaired Pancreatic Beta-Cell Function Caused by Human Oxidized LDL.

    PubMed

    Plaisance, Valérie; Brajkovic, Saška; Tenenbaum, Mathie; Favre, Dimitri; Ezanno, Hélène; Bonnefond, Amélie; Bonner, Caroline; Gmyr, Valéry; Kerr-Conte, Julie; Gauthier, Benoit R; Widmann, Christian; Waeber, Gérard; Pattou, François; Froguel, Philippe; Abderrahmani, Amar

    2016-01-01

    Elevated plasma concentration of the pro-atherogenic oxidized low density lipoprotein cholesterol (LDL) triggers adverse effects in pancreatic beta-cells and is associated with type 2 diabetes. Here, we investigated whether the endoplasmic reticulum (ER) stress is a key player coupling oxidative stress to beta-cell dysfunction and death elicited by human oxidized LDL. We found that human oxidized LDL activates ER stress as evidenced by the activation of the inositol requiring 1α, and the elevated expression of both DDIT3 (also called CHOP) and DNAJC3 (also called P58IPK) ER stress markers in isolated human islets and the mouse insulin secreting MIN6 cells. Silencing of Chop and inhibition of ER stress markers by the chemical chaperone phenyl butyric acid (PBA) prevented cell death caused by oxidized LDL. Finally, we found that oxidative stress accounts for activation of ER stress markers induced by oxidized LDL. Induction of Chop/CHOP and p58IPK/P58IPK by oxidized LDL was mimicked by hydrogen peroxide and was blocked by co-treatment with the N-acetylcystein antioxidant. As a conclusion, the harmful effects of oxidized LDL in beta-cells requires ER stress activation in a manner that involves oxidative stress. This mechanism may account for impaired beta-cell function in diabetes and can be reversed by antioxidant treatment. PMID:27636901

  14. A physical and functional link between splicing factors promotes pre-mRNA 3′ end processing

    PubMed Central

    Millevoi, Stefania; Decorsière, Adrien; Loulergue, Clarisse; Iacovoni, Jason; Bernat, Sandra; Antoniou, Michael; Vagner, Stéphan

    2009-01-01

    Polypyrimidine tract-binding protein (PTB) is a splicing regulator that also plays a positive role in pre-mRNA 3′ end processing when bound upstream of the polyadenylation signal (pA signal). Here, we address the mechanism of PTB stimulatory function in mRNA 3′ end formation. We identify PTB as the protein factor whose binding to the human β-globin (HBB) 3′ UTR is abrogated by a 3′ end processing-inactivating mutation. We show that PTB promotes both in vitro 3′ end cleavage and polyadenylation and recruits directly the splicing factor hnRNP H to G-rich sequences associated with several pA signals. Increased binding of hnRNP H results in stimulation of polyadenylation through a direct interaction with poly(A) polymerase. Therefore, our results provide evidence of a concerted regulation of pA signal recognition by splicing factors bound to auxiliary polyadenylation sequence elements. PMID:19506027

  15. Probing the corticospinal link between the motor cortex and motoneurones: some neglected aspects of human motor cortical function.

    PubMed

    Petersen, N C; Butler, J E; Taylor, J L; Gandevia, S C

    2010-04-01

    This review considers the operation of the corticospinal system in primates. There is a relatively widespread cortical area containing corticospinal outputs to a single muscle and thus a motoneurone pool receives corticospinal input from a wide region of the cortex. In addition, corticospinal cells themselves have divergent intraspinal branches which innervate more than one motoneuronal pool but the synergistic couplings involving the many hand muscles are likely to be more diverse than can be accommodated simply by fixed patterns of corticospinal divergence. Many studies using transcranial magnetic stimulation of the human motor cortex have highlighted the capacity of the cortex to modify its apparent excitability in response to altered afferent inputs, training and various pathologies. Studies using cortical stimulation at 'very low' intensities which elicit only short-latency suppression of the discharge of motor units have revealed that the rapidly conducting corticospinal axons (stimulated at higher intensities) drive motoneurones in normal voluntary contractions. There are also major non-linearities generated at a spinal level in the relation between corticospinal output and the output from the motoneurone pool. For example, recent studies have revealed that the efficacy of the human corticospinal connection with motoneurones undergoes activity-dependent changes which influence the size of voluntary contractions. Hence, corticospinal drives must be sculpted continuously to compensate for the changing functional efficacy of the descending systems which activate the motoneurones. This highlights the need for proprioceptive monitoring of movements to ensure their accurate execution. PMID:20003100

  16. Proteomic and functional analysis of proline dehydrogenase 1 link proline catabolism to mitochondrial electron transport in Arabidopsis thaliana.

    PubMed

    Cabassa-Hourton, Cécile; Schertl, Peter; Bordenave-Jacquemin, Marianne; Saadallah, Kaouthar; Guivarc'h, Anne; Lebreton, Sandrine; Planchais, Séverine; Klodmann, Jennifer; Eubel, Holger; Crilat, Emilie; Lefebvre-De Vos, Delphine; Ghelis, Thanos; Richard, Luc; Abdelly, Chedly; Carol, Pierre; Braun, Hans-Peter; Savouré, Arnould

    2016-09-01

    Proline accumulates in many plant species in response to environmental stresses. Upon relief from stress, proline is rapidly oxidized in mitochondria by proline dehydrogenase (ProDH) and then by pyrroline-5-carboxylate dehydrogenase (P5CDH). Two ProDH genes have been identified in the genome of the model plant Arabidopsis thaliana To gain a better understanding of ProDH1 functions in mitochondria, proteomic analysis was performed. ProDH1 polypeptides were identified in Arabidopsis mitochondria by immunoblotting gels after 2D blue native (BN)-SDS/PAGE, probing them with an anti-ProDH antibody and analysing protein spots by MS. The 2D gels showed that ProDH1 forms part of a low-molecular-mass (70-140 kDa) complex in the mitochondrial membrane. To evaluate the contribution of each isoform to proline oxidation, mitochondria were isolated from wild-type (WT) and prodh1, prodh2, prodh1prodh2 and p5cdh mutants. ProDH activity was high for genotypes in which ProDH, most likely ProDH1, was strongly induced by proline. Respiratory measurements indicate that ProDH1 has a role in oxidizing excess proline and transferring electrons to the respiratory chain. PMID:27303048

  17. Altered Cortical Dynamics and Cognitive Function upon Haploinsufficiency of the Autism-Linked Excitatory Synaptic Suppressor MDGA2.

    PubMed

    Connor, Steven A; Ammendrup-Johnsen, Ina; Chan, Allen W; Kishimoto, Yasushi; Murayama, Chiaki; Kurihara, Naokazu; Tada, Atsushi; Ge, Yuan; Lu, Hong; Yan, Ryan; LeDue, Jeffrey M; Matsumoto, Hirotaka; Kiyonari, Hiroshi; Kirino, Yutaka; Matsuzaki, Fumio; Suzuki, Toshiharu; Murphy, Timothy H; Wang, Yu Tian; Yamamoto, Tohru; Craig, Ann Marie

    2016-09-01

    Mutations in a synaptic organizing pathway contribute to autism. Autism-associated mutations in MDGA2 (MAM domain containing glycosylphosphatidylinositol anchor 2) are thought to reduce excitatory/inhibitory transmission. However, we show that mutation of Mdga2 elevates excitatory transmission, and that MDGA2 blocks neuroligin-1 interaction with neurexins and suppresses excitatory synapse development. Mdga2(+/-) mice, modeling autism mutations, demonstrated increased asymmetric synapse density, mEPSC frequency and amplitude, and altered LTP, with no change in measures of inhibitory synapses. Behavioral assays revealed an autism-like phenotype including stereotypy, aberrant social interactions, and impaired memory. In vivo voltage-sensitive dye imaging, facilitating comparison with fMRI studies in autism, revealed widespread increases in cortical spontaneous activity and intracortical functional connectivity. These results suggest that mutations in MDGA2 contribute to altered cortical processing through the dual disadvantages of elevated excitation and hyperconnectivity, and indicate that perturbations of the NRXN-NLGN pathway in either direction from the norm increase risk for autism. PMID:27608760

  18. Testing the link between community structure and function for ectomycorrhizal fungi involved in a global tripartite symbiosis.

    PubMed

    Walker, Jennifer K M; Cohen, Hannah; Higgins, Logan M; Kennedy, Peter G

    2014-04-01

    Alnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria and, although their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts. We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus (P) and nitrogen (N) when compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii. At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than that from P. menziesii, whereas potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites. At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host. Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic P acquisition abilities relative to non-Frankia ECM hosts. This shift, in combination with the chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities. PMID:24320607

  19. Endoplasmic Reticulum Stress Links Oxidative Stress to Impaired Pancreatic Beta-Cell Function Caused by Human Oxidized LDL

    PubMed Central

    Favre, Dimitri; Ezanno, Hélène; Bonnefond, Amélie; Bonner, Caroline; Gmyr, Valéry; Kerr-Conte, Julie; Gauthier, Benoit R.; Widmann, Christian; Waeber, Gérard; Pattou, François; Froguel, Philippe; Abderrahmani, Amar

    2016-01-01

    Elevated plasma concentration of the pro-atherogenic oxidized low density lipoprotein cholesterol (LDL) triggers adverse effects in pancreatic beta-cells and is associated with type 2 diabetes. Here, we investigated whether the endoplasmic reticulum (ER) stress is a key player coupling oxidative stress to beta-cell dysfunction and death elicited by human oxidized LDL. We found that human oxidized LDL activates ER stress as evidenced by the activation of the inositol requiring 1α, and the elevated expression of both DDIT3 (also called CHOP) and DNAJC3 (also called P58IPK) ER stress markers in isolated human islets and the mouse insulin secreting MIN6 cells. Silencing of Chop and inhibition of ER stress markers by the chemical chaperone phenyl butyric acid (PBA) prevented cell death caused by oxidized LDL. Finally, we found that oxidative stress accounts for activation of ER stress markers induced by oxidized LDL. Induction of Chop/CHOP and p58IPK/P58IPK by oxidized LDL was mimicked by hydrogen peroxide and was blocked by co-treatment with the N-acetylcystein antioxidant. As a conclusion, the harmful effects of oxidized LDL in beta-cells requires ER stress activation in a manner that involves oxidative stress. This mechanism may account for impaired beta-cell function in diabetes and can be reversed by antioxidant treatment. PMID:27636901

  20. Evidence for a functional link between Dd-STATa and Dd-PIAS, a Dictyostelium PIAS homologue.

    PubMed

    Kawata, Takefumi; Hirano, Tatsunori; Ogasawara, Shun; Aoshima, Ryota; Yachi, Ayako

    2011-09-01

    Several mammalian protein families inhibit the activity of signal transducer and activator of transcription (STAT) proteins. The protein inhibitor of activated STAT (PIAS) was initially identified through its ability to interact with human STAT proteins. We isolated a gene (pisA) encoding a Dictyostelium orthologue of PIAS, Dd-PIAS, which possesses almost all the representative motifs and domains of mammalian PIAS proteins. A Dd-PIAS null mutant strain displays a normal terminal morphology but with accelerated development once cells are aggregated. In contrast, Dd-PIAS overexpressor strains demonstrate delayed aggregation, almost no slug phototaxis, impaired slug motility, and a prolonged slug migration period. This strain is a near phenocopy of the Dd-STATa null mutant, although it eventually forms a fruiting body, albeit inefficiently. The expression of several Dd-STATa-activated genes is upregulated in the Dd-PIAS null mutant and there is ectopic expression of pstAB makers. The concentration of a PIAS-green fluorescent protein (GFP) fusion protein, expressed under the PIAS promoter, is greatest in the pstO cells and gradually decreases with proximity to the tip of the slug and culminant: a pattern diametrically opposite to that of Dd-STATa. Our results suggest a functional interrelationship between Dd-PIAS and Dd-STATa that influences gene expression and development.

  1. optix functions as a link between the retinal determination network and the dpp pathway to control morphogenetic furrow progression in Drosophila

    PubMed Central

    Li, Yumei; Jiang, Yuwei; Chen, Yiyun; Karandikar, Umesh; Hoffman, Kristi; Chattopadhyay, Abanti; Mardon, Graeme; Chen, Rui

    2013-01-01

    optix, the Drosophila ortholog of the SIX3/6 gene family in vertebrate, encodes a homeodomain protein with a SIX protein-protein interaction domain. In vertebrates, Six3/6 genes are required for normal eye as well as brain development. However, the normal function of optix in Drosophila remains unknown due to lack of loss-of-function mutation. Previous studies suggest that optix is likely to play important role as part of the retinal determination (RD) network. To elucidate normal optix function during retinal development, multiple null alleles for optix have been generated. Loss-of-function mutations in optix result in lethality at the pupae stage. Surprisingly, close examination of its function during eye development reveals that, unlike other members of the RD network, optix is required only for morphogenetic furrow (MF) progression, but not initiation. The mechanisms by which optix regulates MF progression is likely through regulation of signaling molecules in the furrow. Specifically, although unaffected during MF initiation, expression of dpp in the MF is dramatically reduced in optix mutant clones. In parallel, we find that optix is regulated by sine oculis and eyes absent, key members of the RD network. Furthermore, positive feedback between optix and sine oculis and eyes absent is observed, which is likely mediated through dpp signaling pathway. Together with the observation that optix expression does not depend on hh or dpp, we propose that optix functions together with hh to regulate dpp in the MF, serving as a link between the RD network and the patterning pathways controlling normal retinal development. PMID:23792115

  2. Genetic Screen in Drosophila Larvae Links ird1 Function to Toll Signaling in the Fat Body and Hemocyte Motility

    PubMed Central

    Schmid, Martin R.; Anderl, Ines; Vo, Hoa T. M.; Valanne, Susanna; Yang, Hairu; Kronhamn, Jesper; Rämet, Mika; Rusten, Tor Erik

    2016-01-01

    To understand how Toll signaling controls the activation of a cellular immune response in Drosophila blood cells (hemocytes), we carried out a genetic modifier screen, looking for deletions that suppress or enhance the mobilization of sessile hemocytes by the gain-of-function mutation Toll10b (Tl10b). Here we describe the results from chromosome arm 3R, where five regions strongly suppressed this phenotype. We identified the specific genes immune response deficient 1 (ird1), headcase (hdc) and possibly Rab23 as suppressors, and we studied the role of ird1 in more detail. An ird1 null mutant and a mutant that truncates the N-terminal kinase domain of the encoded Ird1 protein affected the Tl10b phenotype, unlike mutations that affect the C-terminal part of the protein. The ird1 null mutant suppressed mobilization of sessile hemocytes, but enhanced other Tl10b hemocyte phenotypes, like the formation of melanotic nodules and the increased number of circulating hemocytes. ird1 mutants also had blood cell phenotypes on their own. They lacked crystal cells and showed aberrant formation of lamellocytes. ird1 mutant plasmatocytes had a reduced ability to spread on an artificial substrate by forming protrusions, which may explain why they did not go into circulation in response to Toll signaling. The effect of the ird1 mutation depended mainly on ird1 expression in hemocytes, but ird1-dependent effects in other tissues may contribute. Specifically, the Toll receptor was translocated from the cell membrane to intracellular vesicles in the fat body of the ird1 mutant, and Toll signaling was activated in that tissue, partially explaining the Tl10b-like phenotype. As ird1 is otherwise known to control vesicular transport, we conclude that the vesicular transport system may be of particular importance during an immune response. PMID:27467079

  3. Genetic Screen in Drosophila Larvae Links ird1 Function to Toll Signaling in the Fat Body and Hemocyte Motility.

    PubMed

    Schmid, Martin R; Anderl, Ines; Vo, Hoa T M; Valanne, Susanna; Yang, Hairu; Kronhamn, Jesper; Rämet, Mika; Rusten, Tor Erik; Hultmark, Dan

    2016-01-01

    To understand how Toll signaling controls the activation of a cellular immune response in Drosophila blood cells (hemocytes), we carried out a genetic modifier screen, looking for deletions that suppress or enhance the mobilization of sessile hemocytes by the gain-of-function mutation Toll10b (Tl10b). Here we describe the results from chromosome arm 3R, where five regions strongly suppressed this phenotype. We identified the specific genes immune response deficient 1 (ird1), headcase (hdc) and possibly Rab23 as suppressors, and we studied the role of ird1 in more detail. An ird1 null mutant and a mutant that truncates the N-terminal kinase domain of the encoded Ird1 protein affected the Tl10b phenotype, unlike mutations that affect the C-terminal part of the protein. The ird1 null mutant suppressed mobilization of sessile hemocytes, but enhanced other Tl10b hemocyte phenotypes, like the formation of melanotic nodules and the increased number of circulating hemocytes. ird1 mutants also had blood cell phenotypes on their own. They lacked crystal cells and showed aberrant formation of lamellocytes. ird1 mutant plasmatocytes had a reduced ability to spread on an artificial substrate by forming protrusions, which may explain why they did not go into circulation in response to Toll signaling. The effect of the ird1 mutation depended mainly on ird1 expression in hemocytes, but ird1-dependent effects in other tissues may contribute. Specifically, the Toll receptor was translocated from the cell membrane to intracellular vesicles in the fat body of the ird1 mutant, and Toll signaling was activated in that tissue, partially explaining the Tl10b-like phenotype. As ird1 is otherwise known to control vesicular transport, we conclude that the vesicular transport system may be of particular importance during an immune response. PMID:27467079

  4. Nuclear Countermeasure Activity of TP508 Linked to Restoration of Endothelial Function and Acceleration of DNA Repair

    PubMed Central

    Olszewska-Pazdrak, Barbara; McVicar, Scott D.; Rayavara, Kempaiah; Moya, Stephanie M.; Kantara, Carla; Gammarano, Chris; Olszewska, Paulina; Fuller, Gerald M.; Sower, Laurie E.; Carney, Darrell H.

    2016-01-01

    There is increasing evidence that radiation-induced damage to endothelial cells and loss of endothelial function may contribute to both acute radiation syndromes and long-term effects of whole-body nuclear irradiation. Therefore, several drugs are being developed to mitigate the effects of nuclear radiation, most of these drugs will target and protect or regenerate leukocytes and platelets. Our laboratory has demonstrated that TP508, a 23-amino acid thrombin peptide, activates endothelial cells and stem cells to revascularize and regenerate tissues. We now show that TP508 can mitigate radiation-induced damage to endothelial cells in vitro and in vivo. Our in vitro results demonstrate that human endothelial cells irradiation attenuates nitric oxide (NO) signaling, disrupts tube formation and induces DNA double-strand breaks (DSB). TP508 treatment reverses radiation effects on NO signaling, restores tube formation and accelerates the repair of radiation-induced DSB. The radiation-mitigating effects of TP508 on endothelial cells were also seen in CD-1 mice where systemic injection of TP508 stimulated endothelial cell sprouting from aortic explants after 8 Gy irradiation. Systemic doses of TP508 that mitigated radiation-induced endothelial cell damage, also significantly increased survival of CD-1 mice when injected 24 h after 8.5 Gy exposure. These data suggest that increased survival observed with TP508 treatment may be due to its effects on vascular and microvascular endothelial cells. Our study supports the usage of a regenerative drug such as TP508 to activate endothelial cells as a countermeasure for mitigating the effects of nuclear radiation. PMID:27388041

  5. Linking sediment structure, hydrological functioning and biogeochemical cycling in disturbed coastal saltmarshes and implications for vegetation development

    NASA Astrophysics Data System (ADS)

    Spencer, Kate; Harvey, Gemma; James, Tempest; Simon, Carr; Michelle, Morris

    2014-05-01

    Saltmarsh restoration undoubtedly provides environmental enhancement, with vegetation quickly re-establishing following the breach of sea walls and subsequent tidal inundation of previously defended areas. Yet evidence increasingly suggests that the restored saltmarshes do not have the same biological characteristics as their natural counterparts (Mossman et al. 2012) and this may be in part be due to physicochemical parameters at the site including anoxia and poor drainage. Hence, restored saltmarshes may not offer the range and quality of ecosystem services anticipated. These environments will have been 'disturbed' by previous land use and there is little understanding of the impacts of this disturbance on the wider hydrogeomorphic and biogeochemical functioning in restored saltmarshes and the implications for saltmarsh vegetation development. This study examines linkages between physical sediment characteristics, sediment structure (using X-ray microtomography), sub-surface hydrology (using pressure transducers and time series analysis), and sediment and porewater geochemistry (major and trace elements, major anions) in sediment cores collected from undisturbed saltmarshes and those restored by de-embankment. Sub-surface sediments in restored saltmarshes have lower organic matter content, lower moisture content and higher bulk density than undisturbed sites. Using X-ray tomography a clear horizon can be observed which separates relict agricultural soils at depth with less dense and structureless sediments deposited since de-embankment. Ratios of open to closed pore space suggest that while undisturbed saltmarshes have the highest porosity, restored saltmarshes have larger void spaces, but limited pore connectivity. Sub-surface hydrological response to tidal flooding was subdued in the restored compared to the undisturbed site, suggesting that porewater flow may be impeded. Time series analysis indicated that flow pathways differ in restored saltmarsh sediments

  6. Neocortex expansion is linked to size variations in gene families with chemotaxis, cell–cell signalling and immune response functions in mammals

    PubMed Central

    Castillo-Morales, Atahualpa; Monzón-Sandoval, Jimena; de Sousa, Alexandra A.

    2016-01-01

    Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations in the relative size of the neocortex remain unknown. By comparing the genomes of 28 mammalian species, we show that neocortical expansion relative to the rest of the brain is associated with variations in gene family size (GFS) of gene families that are significantly enriched in biological functions associated with chemotaxis, cell–cell signalling and immune response. Importantly, we find that previously reported GFS variations associated with increased brain size are largely accounted for by the stronger link between neocortex expansion and variations in the size of gene families. Moreover, genes within these families are more prominently expressed in the human neocortex during early compared with adult development. These results suggest that changes in GFS underlie morphological adaptations during brain evolution in mammalian lineages. PMID:27707894

  7. Imbalanced functional link between executive control network and reward network explain the online-game seeking behaviors in Internet gaming disorder

    PubMed Central

    Dong, Guangheng; Lin, Xiao; Hu, Yanbo; Xie, Chunming; Du, Xiaoxia

    2015-01-01

    Literatures have shown that Internet gaming disorder (IGD) subjects show impaired executive control and enhanced reward sensitivities than healthy controls. However, how these two networks jointly affect the valuation process and drive IGD subjects' online-game-seeking behaviors remains unknown. Thirty-five IGD and 36 healthy controls underwent a resting-states scan in the MRI scanner. Functional connectivity (FC) was examined within control and reward network seeds regions, respectively. Nucleus accumbens (NAcc) was selected as the node to find the interactions between these two networks. IGD subjects show decreased FC in the executive control network and increased FC in the reward network when comparing with the healthy controls. When examining the correlations between the NAcc and the executive control/reward networks, the link between the NAcc - executive control network is negatively related with the link between NAcc - reward network. The changes (decrease/increase) in IGD subjects' brain synchrony in control/reward networks suggest the inefficient/overly processing within neural circuitry underlying these processes. The inverse proportion between control network and reward network in IGD suggest that impairments in executive control lead to inefficient inhibition of enhanced cravings to excessive online game playing. This might shed light on the mechanistic understanding of IGD. PMID:25779894

  8. Going to the gym or to the movies?: situated decisions as a functional link connecting automatic and reflective evaluations of exercise with exercising behavior.

    PubMed

    Brand, Ralf; Schweizer, Geoffrey

    2015-02-01

    The goal of the present paper is to propose a model for the study of automatic cognition and affect in exercise. We have chosen a dual-system approach to social information processing to investigate the hypothesis that situated decisions between behavioral alternatives form a functional link between automatic and reflective evaluations and the time spent on exercise. A new questionnaire is introduced to operationalize this link. A reaction-time-based evaluative priming task was used to test participants' automatic evaluations. Affective and cognitive reflective evaluations, as well as exercising time, were requested via self-report. Path analyses suggest that the affective reflective (beta = .71) and the automatic evaluation (beta = .15) independently explain situated decisions, which, in turn (beta = .60) explain time spent on exercise. Our findings highlight the concept of contextualized decisions. They can serve as a starting point from which the so far seldom investigations of automatic cognition and affect in exercise can be integrated with multitudinous results from studies on reflective psychological determinants of health behavior.

  9. Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis.

    PubMed

    Tourna, Maria; Maclean, Paul; Condron, Leo; O'Callaghan, Maureen; Wakelin, Steven A

    2014-06-01

    Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry.

  10. Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

    PubMed

    Luker, Gary D

    2002-04-01

    The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

  11. Vitamin D, effects on brain development, adult brain function and the links between low levels of vitamin D and neuropsychiatric disease.

    PubMed

    Eyles, Darryl W; Burne, Thomas H J; McGrath, John J

    2013-01-01

    Increasingly vitamin D deficiency is being associated with a number of psychiatric conditions. In particular for disorders with a developmental basis, such as autistic spectrum disorder and schizophrenia the neurobiological plausibility of this association is strengthened by the preclinical data indicating vitamin D deficiency in early life affects neuronal differentiation, axonal connectivity, dopamine ontogeny and brain structure and function. More recently epidemiological associations have been made between low vitamin D and psychiatric disorders not typically associated with abnormalities in brain development such as depression and Alzheimer's disease. Once again the preclinical findings revealing that vitamin D can regulate catecholamine levels and protect against specific Alzheimer-like pathology increase the plausibility of this link. In this review we have attempted to integrate this clinical epidemiology with potential vitamin D-mediated basic mechanisms. Throughout the review we have highlighted areas where we think future research should focus. PMID:22796576

  12. Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

    PubMed

    Luker, Gary D

    2002-04-01

    The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer. PMID:11929844

  13. Designed synthesis of carbon-functional magnetic graphene mesoporous silica materials using polydopamine as carbon precursor for the selective enrichment of N-linked glycan.

    PubMed

    Sun, Nianrong; Yao, Jizong; Deng, Chunhui

    2016-02-01

    Glycosylation, which has been confirmed to be associated with many diseases, is an important protein post-translation modification. Taking into account the low abundant of glycan, the purification of complex biological samples is considered to be very significant before mass spectrometry detection. In this work, carbon-functionalized magnetic graphene /mesoporous silica materials (C-Mag G@mSiO2 materials) with high content of carbon were designed and synthesized by using polydopamine as carbon precursor. Taking advantage of the special interaction between carbon and glycan, C-Mag G@mSiO2 materials were successfully applied to enrich N-linked glycans in different complex samples, such as standard glycoprotein digestion, the mixture of standard glycoprotein digestion, glycoprotein and non-glycoprotein, and human serum.

  14. Satellite Ecology (SATECO)-linking ecology, remote sensing and micrometeorology, from plot to regional scale, for the study of ecosystem structure and function.

    PubMed

    Muraoka, Hiroyuki; Koizumi, Hiroshi

    2009-01-01

    There is a growing requirement for ecosystem science to help inform a deeper understanding of the effects of global climate change and land use change on terrestrial ecosystem structure and function, from small area (plot) to landscape, regional and global scales. To meet these requirements, ecologists have investigated plant growth and carbon cycling processes at plot scale, using biometric methods to measure plant carbon accumulation, and gas exchange (chamber) methods to measure soil respiration. Also at the plot scale, micrometeorologists have attempted to measure canopy- or ecosystem-scale CO(2) flux by the eddy covariance technique, which reveals diurnal, seasonal and annual cycles. Mathematical models play an important role in integrating ecological and micrometeorological processes into ecosystem scales, which are further useful in interpreting time-accumulated information derived from biometric methods by comparing with CO(2) flux measurements. For a spatial scaling of such plot-level understanding, remote sensing via satellite is used to measure land use/vegetation type distribution and temporal changes in ecosystem structures such as leaf area index. However, to better utilise such data, there is still a need for investigations that consider the structure and function of ecosystems and their processes, especially in mountainous areas characterized by complex terrain and a mosaic distribution of vegetation. For this purpose, we have established a new interdisciplinary approach named 'Satellite Ecology', which aims to link ecology, remote sensing and micrometeorology to facilitate the study of ecosystem function, at the plot, landscape, and regional scale.

  15. Pupil Dilation and EEG Alpha Frequency Band Power Reveal Load on Executive Functions for Link-Selection Processes during Text Reading

    PubMed Central

    Scharinger, Christian; Kammerer, Yvonne; Gerjets, Peter

    2015-01-01

    Executive working memory functions play a central role in reading comprehension. In the present research we were interested in additional load imposed on executive functions by link-selection processes during computer-based reading. For obtaining process measures, we used a methodology of concurrent electroencephalographic (EEG) and eye-tracking data recording that allowed us to compare epochs of pure text reading with epochs of hyperlink-like selection processes in an online reading situation. Furthermore, this methodology allowed us to directly compare the two physiological load-measures EEG alpha frequency band power and pupil dilation. We observed increased load on executive functions during hyperlink-like selection processes on both measures in terms of decreased alpha frequency band power and increased pupil dilation. Surprisingly however, the two measures did not correlate. Two additional experiments were conducted that excluded potential perceptual, motor, or structural confounds. In sum, EEG alpha frequency band power and pupil dilation both turned out to be sensitive measures for increased load during hyperlink-like selection processes in online text reading. PMID:26076026

  16. Pupil Dilation and EEG Alpha Frequency Band Power Reveal Load on Executive Functions for Link-Selection Processes during Text Reading.

    PubMed

    Scharinger, Christian; Kammerer, Yvonne; Gerjets, Peter

    2015-01-01

    Executive working memory functions play a central role in reading comprehension. In the present research we were interested in additional load imposed on executive functions by link-selection processes during computer-based reading. For obtaining process measures, we used a methodology of concurrent electroencephalographic (EEG) and eye-tracking data recording that allowed us to compare epochs of pure text reading with epochs of hyperlink-like selection processes in an online reading situation. Furthermore, this methodology allowed us to directly compare the two physiological load-measures EEG alpha frequency band power and pupil dilation. We observed increased load on executive functions during hyperlink-like selection processes on both measures in terms of decreased alpha frequency band power and increased pupil dilation. Surprisingly however, the two measures did not correlate. Two additional experiments were conducted that excluded potential perceptual, motor, or structural confounds. In sum, EEG alpha frequency band power and pupil dilation both turned out to be sensitive measures for increased load during hyperlink-like selection processes in online text reading.

  17. Functional Restoration of gp91phox-Oxidase Activity by BAC Transgenesis and Gene Targeting in X-linked Chronic Granulomatous Disease iPSCs

    PubMed Central

    Laugsch, Magdalena; Rostovskaya, Maria; Velychko, Sergiy; Richter, Cornelia; Zimmer, Ariane; Klink, Barbara; Schröck, Evelin; Haase, Michael; Neumann, Katrin; Thieme, Sebastian; Roesler, Joachim; Brenner, Sebastian; Anastassiadis, Konstantinos

    2016-01-01

    Chronic granulomatous disease (CGD) is an inherited immunodeficiency, caused by the inability of neutrophils to produce functional NADPH oxidase required for fighting microbial infections. The X-linked form of CGD (X-CGD), which is due to mutations in the CYBB (gp91phox) gene, a component of NADPH oxidase, accounts for about two-thirds of CGD cases. We derived induced pluripotent stem cells (iPSCs) from X-CGD patient keratinocytes using a Flp recombinase excisable lentiviral reprogramming vector. For restoring gp91phox function, we applied two strategies: transposon-mediated bacterial artificial chromosome (BAC) transgenesis and gene targeting using vectors with a fixed 5′ homology arm (HA) of 8 kb and 3′HA varying in size from 30 to 80 kb. High efficiency of homologous recombination (up to 22%) was observed with increased size of the 3′HA. Both, BAC transgenesis and gene targeting resulted in functional restoration of the gp91phox measured by an oxidase activity assay in X-CGD iPSCs differentiated into the myeloid lineage. In conclusion, we delivered an important milestone towards the use of genetically corrected autologous cells for the treatment of X-CGD and monogenic diseases in general. PMID:26316390

  18. Satellite Ecology (SATECO)-linking ecology, remote sensing and micrometeorology, from plot to regional scale, for the study of ecosystem structure and function.

    PubMed

    Muraoka, Hiroyuki; Koizumi, Hiroshi

    2009-01-01

    There is a growing requirement for ecosystem science to help inform a deeper understanding of the effects of global climate change and land use change on terrestrial ecosystem structure and function, from small area (plot) to landscape, regional and global scales. To meet these requirements, ecologists have investigated plant growth and carbon cycling processes at plot scale, using biometric methods to measure plant carbon accumulation, and gas exchange (chamber) methods to measure soil respiration. Also at the plot scale, micrometeorologists have attempted to measure canopy- or ecosystem-scale CO(2) flux by the eddy covariance technique, which reveals diurnal, seasonal and annual cycles. Mathematical models play an important role in integrating ecological and micrometeorological processes into ecosystem scales, which are further useful in interpreting time-accumulated information derived from biometric methods by comparing with CO(2) flux measurements. For a spatial scaling of such plot-level understanding, remote sensing via satellite is used to measure land use/vegetation type distribution and temporal changes in ecosystem structures such as leaf area index. However, to better utilise such data, there is still a need for investigations that consider the structure and function of ecosystems and their processes, especially in mountainous areas characterized by complex terrain and a mosaic distribution of vegetation. For this purpose, we have established a new interdisciplinary approach named 'Satellite Ecology', which aims to link ecology, remote sensing and micrometeorology to facilitate the study of ecosystem function, at the plot, landscape, and regional scale. PMID:18958540

  19. Hybrid robust model based on an improved functional link neural network integrating with partial least square (IFLNN-PLS) and its application to predicting key process variables.

    PubMed

    He, Yan-Lin; Xu, Yuan; Geng, Zhi-Qiang; Zhu, Qun-Xiong

    2016-03-01

    In this paper, a hybrid robust model based on an improved functional link neural network integrating with partial least square (IFLNN-PLS) is proposed. Firstly, an improved functional link neural network with small norm of expanded weights and high input-output correlation (SNEWHIOC-FLNN) was proposed for enhancing the generalization performance of FLNN. Unlike the traditional FLNN, the expanded variables of the original inputs are not directly used as the inputs in the proposed SNEWHIOC-FLNN model. The original inputs are attached to some small norm of expanded weights. As a result, the correlation coefficient between some of the expanded variables and the outputs is enhanced. The larger the correlation coefficient is, the more relevant the expanded variables tend to be. In the end, the expanded variables with larger correlation coefficient are selected as the inputs to improve the performance of the traditional FLNN. In order to test the proposed SNEWHIOC-FLNN model, three UCI (University of California, Irvine) regression datasets named Housing, Concrete Compressive Strength (CCS), and Yacht Hydro Dynamics (YHD) are selected. Then a hybrid model based on the improved FLNN integrating with partial least square (IFLNN-PLS) was built. In IFLNN-PLS model, the connection weights are calculated using the partial least square method but not the error back propagation algorithm. Lastly, IFLNN-PLS was developed as an intelligent measurement model for accurately predicting the key variables in the Purified Terephthalic Acid (PTA) process and the High Density Polyethylene (HDPE) process. Simulation results illustrated that the IFLNN-PLS could significant improve the prediction performance. PMID:26685746

  20. Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.

    PubMed

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2012-01-01

    Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.

  1. Community Links

    ERIC Educational Resources Information Center

    Nelson, Mary

    1975-01-01

    At Moraine Valley Community College (Illinois), a chain of events, programs, activities, and services has linked the college and community in such areas as fine arts, ethnic groups, public services, community action, community service, and community education. (Author/NHM)

  2. Link Analysis

    NASA Astrophysics Data System (ADS)

    Donoho, Steve

    Link analysis is a collection of techniques that operate on data that can be represented as nodes and links. This chapter surveys a variety of techniques including subgraph matching, finding cliques and K-plexes, maximizing spread of influence, visualization, finding hubs and authorities, and combining with traditional techniques (classification, clustering, etc). It also surveys applications including social network analysis, viral marketing, Internet search, fraud detection, and crime prevention.

  3. Brief Report: Elastin Microfibril Interface 1 and Integrin-Linked Protein Kinase Are Novel Markers of Islet Regenerative Function in Human Multipotent Mesenchymal Stromal Cells.

    PubMed

    Lavoie, Jessie R; Creskey, Marybeth M; Muradia, Gauri; Bell, Gillian I; Sherman, Stephen E; Gao, Jun; Stewart, Duncan J; Cyr, Terry D; Hess, David A; Rosu-Myles, Michael

    2016-08-01

    Multipotent mesenchymal stromal cell (MSC) transplantation is proposed as a novel therapy for treating diabetes by promoting the regeneration of damaged islets. The clinical promise of such treatments may be hampered by a high degree of donor-related variability in MSC function and a lack of standards for comparing potency. Here, we set out to identify markers of cultured human MSCs directly associated with islet regenerative function. Stromal cultures from nine separate bone marrow donors were demonstrated to have differing capacities to reduce hyperglycemia in the NOD/SCID streptozotocin-induced diabetic model. Regenerative (R) and non-regenerative (NR) MSC cultures were directly compared using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics. A total of 1,410 proteins were quantified resulting in the identification of 612 upregulated proteins and 275 downregulated proteins by ± 1.2-fold in R-MSC cultures. Elastin microfibril interface 1 (EMILIN-1), integrin-linked protein kinase (ILK), and hepatoma-derived growth factor (HDGF) were differentially expressed in R-MSCs, and Ingenuity Pathway Analyses revealed each candidate as known regulators of integrin signaling. Western blot validation of EMILIN-1, ILK, and HDGF not only showed significantly higher abundance levels in R-MSCs, as compared with NR-MSCs, but also correlated with passage-induced loss of islet-regenerative potential. Generalized estimating equation modeling was applied to examine the association between each marker and blood glucose reduction. Both EMILIN-1 and ILK were significantly associated with blood glucose lowering function in vivo. Our study is the first to identify EMILIN-1 and ILK as prospective markers of islet regenerative function in human MSCs. Stem Cells 2016;34:2249-2255. PMID:27090767

  4. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains.

    PubMed

    Ishikawa, Fumihiro; Miyamoto, Kengo; Konno, Sho; Kasai, Shota; Kakeya, Hideaki

    2015-12-18

    A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique

  5. Life Course Pathways of Adversities Linking Adolescent Socioeconomic Circumstances and Functional Somatic Symptoms in Mid-Adulthood: A Path Analysis Study

    PubMed Central

    Jonsson, Frida; San Sebastian, Miguel; Strömsten, Lotta M. J.; Hammarström, Anne; Gustafsson, Per E.

    2016-01-01

    While research examining the health impact of early socioeconomic conditions suggests that effects may exist independently of or jointly with adult socioeconomic position, studies exploring other potential pathways are few. Following a chain of risk life course model, this prospective study seeks to examine whether pathways of occupational class as well as material and social adversities across the life course link socioeconomic disadvantage in adolescent to functional somatic symptoms in mid-adulthood. Applying path analysis, a multiple mediator model was assessed using prospective data collected during 26 years through the Northern Swedish Cohort. The sample contained 987 individuals residing in the municipality of Luleå, Sweden, who participated in questionnaire surveys at age 16, 21, 30 and 42. Socioeconomic conditions (high/low) in adolescence (age 16) were operationalized using the occupation of the parents, while occupational class in adulthood (manual/non-manual) was measured using the participant’s own occupation at age 21 and 30. The adversity measurements were constructed as separate age specific parcels at age 21 and 30. Social adversity included items pertaining to stressful life events that could potentially harm salient relationships, while material adversity was operationalized using items concerning unfavorable financial and material circumstances. Functional somatic symptoms at age 42 was a summary measure of self-reported physical symptoms, palpitation and sleeping difficulties that had occurred during the last 12 months. An association between socioeconomic conditions at age 16 and functional somatic symptoms at age 42 (r = 0.068) which was partially explained by people’s own occupational class at age 21 and then material as well as social adversity at age 30 was revealed. Rather than proposing a direct and independent health effect of the socioeconomic conditions of the family, the present study suggests that growing up in an unfavorable

  6. Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum*

    PubMed Central

    Ostrowski, Adam; Gundogdu, Mehmet; Ferenbach, Andrew T.; Lebedev, Andrey A.; van Aalten, Daan M. F.

    2015-01-01

    Post-translational modification of proteins is a ubiquitous mechanism of signal transduction in all kingdoms of life. One such modification is addition of O-linked N-acetylglucosamine to serine or threonine residues, known as O-GlcNAcylation. This unusual type of glycosylation is thought to be restricted to nucleocytoplasmic proteins of eukaryotes and is mediated by a pair of O-GlcNAc-transferase and O-GlcNAc hydrolase enzymes operating on a large number of substrate proteins. Protein O-GlcNAcylation is responsive to glucose and flux through the hexosamine biosynthetic pathway. Thus, a close relationship is thought to exist between the level of O-GlcNAc proteins within and the general metabolic state of the cell. Although isolated apparent orthologues of these enzymes are present in bacterial genomes, their biological functions remain largely unexplored. It is possible that understanding the function of these proteins will allow development of reductionist models to uncover the principles of O-GlcNAc signaling. Here, we identify orthologues of both O-GlcNAc cycling enzymes in the genome of the thermophilic eubacterium Thermobaculum terrenum. The O-GlcNAcase and O-GlcNAc-transferase are co-expressed and, like their mammalian orthologues, localize to the cytoplasm. The O-GlcNAcase orthologue possesses activity against O-GlcNAc proteins and model substrates. We describe crystal structures of both enzymes, including an O-GlcNAcase·peptide complex, showing conservation of active sites with the human orthologues. Although in vitro activity of the O-GlcNAc-transferase could not be detected, treatment of T. terrenum with an O-GlcNAc-transferase inhibitor led to inhibition of growth. T. terrenum may be the first example of a bacterium possessing a functional O-GlcNAc system. PMID:26491011

  7. Rescue of cytochrome P450 oxidoreductase (Por) mouse mutants reveals functions in vasculogenesis, brain and limb patterning linked to retinoic acid homeostasis.

    PubMed

    Ribes, Vanessa; Otto, Diana M E; Dickmann, Leslie; Schmidt, Katy; Schuhbaur, Brigitte; Henderson, Colin; Blomhoff, Rune; Wolf, C Roland; Tickle, Cheryll; Dollé, Pascal

    2007-03-01

    Cytochrome P450 oxidoreductase (POR) acts as an electron donor for all cytochrome P450 enzymes. Knockout mouse Por(-/-) mutants, which are early embryonic (E9.5) lethal, have been found to have overall elevated retinoic acid (RA) levels, leading to the idea that POR early developmental function is mainly linked to the activity of the CYP26 RA-metabolizing enzymes (Otto et al., Mol. Cell. Biol. 23, 6103-6116). By crossing Por mutants with a RA-reporter lacZ transgene, we show that Por(-/-) embryos exhibit both elevated and ectopic RA signaling activity e.g. in cephalic and caudal tissues. Two strategies were used to functionally demonstrate that decreasing retinoid levels can reverse Por(-/-) phenotypic defects, (i) by culturing Por(-/-) embryos in defined serum-free medium, and (ii) by generating compound mutants defective in RA synthesis due to haploinsufficiency of the retinaldehyde dehydrogenase 2 (Raldh2) gene. Both approaches clearly improved the Por(-/-) early phenotype, the latter allowing mutants to be recovered up until E13.5. Abnormal brain patterning, with posteriorization of hindbrain cell fates and defective mid- and forebrain development and vascular defects were rescued in E9.5 Por(-/-) embryos. E13.5 Por(-/-); Raldh2(+/-) embryos exhibited abdominal/caudal and limb defects that strikingly phenocopy those of Cyp26a1(-/-) and Cyp26b1(-/-) mutants, respectively. Por(-/-); Raldh2(+/-) limb buds were truncated and proximalized and the anterior-posterior patterning system was not established. Thus, POR function is indispensable for the proper regulation of RA levels and tissue distribution not only during early embryonic development but also in later morphogenesis and molecular patterning of the brain, abdominal/caudal region and limbs. PMID:17126317

  8. Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance

    PubMed Central

    Kaiser, Frank J.; Ansari, Morad; Braunholz, Diana; Concepción Gil-Rodríguez, María; Decroos, Christophe; Wilde, Jonathan J.; Fincher, Christopher T.; Kaur, Maninder; Bando, Masashige; Amor, David J.; Atwal, Paldeep S.; Bahlo, Melanie; Bowman, Christine M.; Bradley, Jacquelyn J.; Brunner, Han G.; Clark, Dinah; Del Campo, Miguel; Di Donato, Nataliya; Diakumis, Peter; Dubbs, Holly; Dyment, David A.; Eckhold, Juliane; Ernst, Sarah; Ferreira, Jose C.; Francey, Lauren J.; Gehlken, Ulrike; Guillén-Navarro, Encarna; Gyftodimou, Yolanda; Hall, Bryan D.; Hennekam, Raoul; Hudgins, Louanne; Hullings, Melanie; Hunter, Jennifer M.; Yntema, Helger; Innes, A. Micheil; Kline, Antonie D.; Krumina, Zita; Lee, Hane; Leppig, Kathleen; Lynch, Sally Ann; Mallozzi, Mark B.; Mannini, Linda; Mckee, Shane; Mehta, Sarju G.; Micule, Ieva; Mohammed, Shehla; Moran, Ellen; Mortier, Geert R.; Moser, Joe-Ann S.; Noon, Sarah E.; Nozaki, Naohito; Nunes, Luis; Pappas, John G.; Penney, Lynette S.; Pérez-Aytés, Antonio; Petersen, Michael B.; Puisac, Beatriz; Revencu, Nicole; Roeder, Elizabeth; Saitta, Sulagna; Scheuerle, Angela E.; Schindeler, Karen L.; Siu, Victoria M.; Stark, Zornitza; Strom, Samuel P.; Thiese, Heidi; Vater, Inga; Willems, Patrick; Williamson, Kathleen; Wilson, Louise C.; Hakonarson, Hakon; Quintero-Rivera, Fabiola; Wierzba, Jolanta; Musio, Antonio; Gillessen-Kaesbach, Gabriele; Ramos, Feliciano J.; Jackson, Laird G.; Shirahige, Katsuhiko; Pié, Juan; Christianson, David W.; Krantz, Ian D.; Fitzpatrick, David R.; Deardorff, Matthew A.

    2014-01-01

    Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL, encoding a cohesin regulatory protein, account for >80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A, SMC3 and RAD21 genes, together account for ∼5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing. Most mutations identified are missense and de novo. Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS. PMID:24403048

  9. Potential Link between the Sphingosine-1-Phosphate (S1P) System and Defective Alveolar Macrophage Phagocytic Function in Chronic Obstructive Pulmonary Disease (COPD)

    PubMed Central

    Barnawi, Jameel; Tran, Hai; Jersmann, Hubertus; Pitson, Stuart; Roscioli, Eugene; Hodge, Greg; Meech, Robyn; Haberberger, Rainer; Hodge, Sandra

    2015-01-01

    patient-derived macrophages. Antagonising SIPR5 significantly improved phagocytosis. Conclusion Our results suggest a potential link between the S1P signalling system and defective macrophage phagocytic function in COPD and advise therapeutic targets. PMID:26485657

  10. The Effects of Computer Anxiety and Technostress, as Functions of Resistance to Change, on the Staff of the 18 Founding OhioLINK Libraries as the OhioLINK Automated System Is Initiated.

    ERIC Educational Resources Information Center

    Popovich, Donna

    This descriptive study surveys the staff of all 18 founding member libraries of OhioLINK to see whether or not they prefer the new system or the old one and why. The purpose of the study is to determine if resistance to change, computer anxiety and technostress can be found in libraries converting their automated systems over to the OhioLINK…

  11. Initial evidence for the link between activities and health: Associations between a balance of activities, functioning and serum levels of cytokines and C-reactive protein.

    PubMed

    Dür, Mona; Steiner, Günter; Stoffer, Michaela Alexandra; Fialka-Moser, Veronika; Kautzky-Willer, Alexandra; Dejaco, Clemens; Ekmekcioglu, Cem; Prodinger, Birgit; Binder, Alexa; Smolen, Josef; Stamm, Tanja Alexandra

    2016-03-01

    Growing evidence shows interrelations of psychological factors, neurological and immunological processes. Therefore, constructs like a balance of activities, the so called "occupational balance", could also have biological correlates. The aim of this study was to investigate potential associations between occupational balance, functioning, cytokines and C-reactive protein (CRP) in patients suffering from a chronic inflammatory disease like rheumatoid arthritis (RA) and healthy people. Moreover, we wanted to explore potential differences in gender and employment status. A descriptive study in patients with RA and healthy people was conducted using the Occupational Balance-Questionnaire (OB-Quest) and the Short-Form 36 Health Survey (SF-36). Serum levels of cytokines, such as interleukin 6 (IL-6) and 8 (IL-8), interferon alpha (INFα), tumour necrosis factor alpha (TNFα), rheumatoid factor (RF) and of CRP were measured. Descriptive statistics, as well as Mann-Whitney U tests and Spearmen's rank correlation coefficients (rs) were calculated. One-hundred-thirty-two patients with RA and 76 healthy people participated. Occupational balance was associated with functioning, cytokines and CRP. The strongest associations were identified in the unemployed healthy-people sample with cytokines and CRP being within the normal range. For example, the OB-Quest item challenging activities was associated with IL-8 (rs=-0.63, p=0.04) and the SF-36 sub-scale bodily pain was associated with IFNα (rs=-0.69, p=0.02). The items rest and sleep (rs=-0.71, p=0.01) and variety of different activities (rs=-0.74, p<0.01) correlated with the SF-36 sub-scale social functioning. Employed and unemployed people differed in their age and CRP levels. Additionally, gender differences were found in two OB-Quest items in that fewer women were able to adapt their activities to changing living conditions and fewer men were overstressed. In conclusion, we found preliminary biological evidence for the link

  12. Initial evidence for the link between activities and health: Associations between a balance of activities, functioning and serum levels of cytokines and C-reactive protein.

    PubMed

    Dür, Mona; Steiner, Günter; Stoffer, Michaela Alexandra; Fialka-Moser, Veronika; Kautzky-Willer, Alexandra; Dejaco, Clemens; Ekmekcioglu, Cem; Prodinger, Birgit; Binder, Alexa; Smolen, Josef; Stamm, Tanja Alexandra

    2016-03-01

    Growing evidence shows interrelations of psychological factors, neurological and immunological processes. Therefore, constructs like a balance of activities, the so called "occupational balance", could also have biological correlates. The aim of this study was to investigate potential associations between occupational balance, functioning, cytokines and C-reactive protein (CRP) in patients suffering from a chronic inflammatory disease like rheumatoid arthritis (RA) and healthy people. Moreover, we wanted to explore potential differences in gender and employment status. A descriptive study in patients with RA and healthy people was conducted using the Occupational Balance-Questionnaire (OB-Quest) and the Short-Form 36 Health Survey (SF-36). Serum levels of cytokines, such as interleukin 6 (IL-6) and 8 (IL-8), interferon alpha (INFα), tumour necrosis factor alpha (TNFα), rheumatoid factor (RF) and of CRP were measured. Descriptive statistics, as well as Mann-Whitney U tests and Spearmen's rank correlation coefficients (rs) were calculated. One-hundred-thirty-two patients with RA and 76 healthy people participated. Occupational balance was associated with functioning, cytokines and CRP. The strongest associations were identified in the unemployed healthy-people sample with cytokines and CRP being within the normal range. For example, the OB-Quest item challenging activities was associated with IL-8 (rs=-0.63, p=0.04) and the SF-36 sub-scale bodily pain was associated with IFNα (rs=-0.69, p=0.02). The items rest and sleep (rs=-0.71, p=0.01) and variety of different activities (rs=-0.74, p<0.01) correlated with the SF-36 sub-scale social functioning. Employed and unemployed people differed in their age and CRP levels. Additionally, gender differences were found in two OB-Quest items in that fewer women were able to adapt their activities to changing living conditions and fewer men were overstressed. In conclusion, we found preliminary biological evidence for the link

  13. Protein-tyrosine phosphatase-alpha and Src functionally link focal adhesions to the endoplasmic reticulum to mediate interleukin-1-induced Ca2+ signaling.

    PubMed

    Wang, Qin; Rajshankar, Dhaarmini; Branch, Donald R; Siminovitch, Katherine A; Herrera Abreu, Maria Teresa; Downey, Gregory P; McCulloch, Christopher A

    2009-07-31

    Calcium (Ca2+) signaling by the pro-inflammatory cytokine interleukin-1 (IL-1) is dependent on focal adhesions, which contain diverse structural and signaling proteins including protein phosphatases. We examined here the role of protein-tyrosine phosphatase (PTP) alpha in regulating IL-1-induced Ca2+ signaling in fibroblasts. IL-1 promoted recruitment of PTPalpha to focal adhesions and endoplasmic reticulum (ER) fractions, as well as tyrosine phosphorylation of the ER Ca2+ release channel IP3R. In response to IL-1, catalytically active PTPalpha was required for Ca2+ release from the ER, Src-dependent phosphorylation of IP3R1 and accumulation of IP3R1 in focal adhesions. In pulldown assays and immunoprecipitations PTPalpha was required for the association of PTPalpha with IP3R1 and c-Src, and this association was increased by IL-1. Collectively, these data indicate that PTPalpha acts as an adaptor to mediate functional links between focal adhesions and the ER that enable IL-1-induced Ca2+ signaling.

  14. Protein-tyrosine Phosphatase-α and Src Functionally Link Focal Adhesions to the Endoplasmic Reticulum to Mediate Interleukin-1-induced Ca2+ Signaling*

    PubMed Central

    Wang, Qin; Rajshankar, Dhaarmini; Branch, Donald R.; Siminovitch, Katherine A.; Abreu, Maria Teresa Herrera; Downey, Gregory P.; McCulloch, Christopher A.

    2009-01-01

    Calcium (Ca2+) signaling by the pro-inflammatory cytokine interleukin-1 (IL-1) is dependent on focal adhesions, which contain diverse structural and signaling proteins including protein phosphatases. We examined here the role of protein-tyrosine phosphatase (PTP) α in regulating IL-1-induced Ca2+ signaling in fibroblasts. IL-1 promoted recruitment of PTPα to focal adhesions and endoplasmic reticulum (ER) fractions, as well as tyrosine phosphorylation of the ER Ca2+ release channel IP3R. In response to IL-1, catalytically active PTPα was required for Ca2+ release from the ER, Src-dependent phosphorylation of IP3R1 and accumulation of IP3R1 in focal adhesions. In pulldown assays and immunoprecipitations PTPα was required for the association of PTPα with IP3R1 and c-Src, and this association was increased by IL-1. Collectively, these data indicate that PTPα acts as an adaptor to mediate functional links between focal adhesions and the ER that enable IL-1-induced Ca2+ signaling. PMID:19497848

  15. Chip-SIP: Stable Isotope Probing of RNA combining phylogenetic microarrays and Secondary Ion Mass Spectrometry (NanoSIMS) to link structure and function in microbial systems (Invited)

    NASA Astrophysics Data System (ADS)

    Mayali, X.; Weber, P. K.; Mabery, S.; Dekas, A.; Pett-Ridge, J.

    2013-12-01

    A primary goal of microbial ecology is to understand the biogeochemical role of individual microbial taxa in the environment. Our approach to tackle this challenge (Chip-SIP) involves the combination of high-density phylogenetic microarrays ('chips') and Stable Isotope Probing (SIP) to directly link identity and function. Microbial communities are incubated in the presence of substrate(s) enriched in 13C or 15N, RNA is extracted and hybridized onto a microarray synthesized on a conductive surface, and the array is analyzed with a NanoSIMS imaging mass spectrometer to quantify isotopic enrichment of individual probes. After testing the method with mixtures of stable isotope labeled laboratory isolates, we have investigated organic and inorganic carbon and nitrogen incorporation by microbial taxa in various ecosystems including San Francisco Bay, the coastal Pacific Ocean, California soils, and the hindguts of wood-eating beetles. We will summarize the methodology, describe the types of questions it has allowed us to investigate, and discuss some testable hypotheses about biogeochemical cycling in various environments that can benefit from this approach.

  16. Glycosylation-deficient mutations in tissue-nonspecific alkaline phosphatase impair its structure and function and are linked to infantile hypophosphatasia.

    PubMed

    Komaru, Keiichi; Satou, Yasuhito; Al-Shawafi, Hiba A; Numa-Kinjoh, Natsuko; Sohda, Miwa; Oda, Kimimitsu

    2016-03-01

    Tissue-nonspecific alkaline phosphatase (TNSALP) is a membrane glycoprotein with a proposed role in bone mineralization. Indeed, mutations in TNSALP have been identified in patients with hypophosphatasia (HPP), a genetic disease characterized by hypomineralization of bone and teeth and a deficiency in serum ALP activity. TNSALP has five potential N-glycosylation sites at N140, N230, N271, N303 and N430 by standard nomenclature. A mutation at one of these sites, N430, was recently detected in a patient with infantile HPP. Using site-directed mutagenesis, we demonstrated that TNSALP has five N-glycans in transfected COS-1 cells and that individual single N-glycan deletion mutants of TNSALP retain the dimeric structure required for ALP activity, excluding the possibility that any single N-glycan plays a vital role in the structure and function of TNSALP. However, we found that TNSALP (N430Q) and TNSALP (N430E) mutants, but not a TNSALP (N430D) mutant, failed to form dimers. The TNSALP (N430S) mutant linked to infantile HPP was glycosylation-defective and unable to dimerise, similar to TNSALP (N430Q) and TNSALP (N430E) mutants; therefore, TNSALP (N430S) was established as a severe allele without strong ALP activity. By contrast to individual single N-glycan deletion mutants, TNSALP devoid of all five N-glycans was present to a much lesser extent than wild-type TNSALP in transfected cells, possibly reflecting its instability. A comprehensive analysis of a series of multiple N-glycan depletion mutants in TNSALP revealed that three N-glycans on N230, N271 and N303 were the minimal requirement for the structure and function of TNSALP and a prerequisite for its stable expression in a cell.

  17. The ADHD-linked human dopamine D4 receptor variant D4.7 induces over-suppression of NMDA receptor function in prefrontal cortex.

    PubMed

    Qin, Luye; Liu, Wenhua; Ma, Kaijie; Wei, Jing; Zhong, Ping; Cho, Kei; Yan, Zhen

    2016-11-01

    The human dopamine D4 receptor (hD4R) variants with long tandem repeats in the third intracellular loop have been strongly associated with attention deficit hyperactivity disorder (ADHD) and risk taking behaviors. To understand the potential molecular mechanism underlying the connection, we have investigated the synaptic function of human D4R polymorphism by virally expressing the ADHD-linked 7-repeat allele, hD4.7, or its normal counterpart, hD4.4, in the prefrontal cortex (PFC) of D4R knockout mice. We found that hD4R bound to the SH3 domain of PSD-95 in a state-dependent manner. Activation of hD4.7 caused more reduction of NR1/PSD-95 binding and NR1 surface expression than hD4.4 in PFC slices. Moreover, the NMDAR-mediated excitatory postsynaptic currents (NMDAR-EPSC) in PFC pyramidal neurons were suppressed to a larger extent by hD4.7 than hD4.4 activation. Direct stimulation of NMDARs with the partial agonist d-cycloserine prevented the NMDAR hypofunction induced by hD4.7 activation. Moreover, hD4.7-expressing mice exhibited the increased exploratory and novelty seeking behaviors, mimicking the phenotypic hallmark of human ADHD. d-cycloserine administration ameliorated the ADHD-like behaviors in hD4.7-expressing mice. Our results suggest that over-suppression of NMDAR function may underlie the role of hD4.7 in ADHD, and enhancing NMDAR signaling may be a viable therapeutic strategy to ADHD humans carrying the D4.7 allele. PMID:27475724

  18. A case study of single hygroscopicity parameter and its link to the functional groups and phase transition for urban aerosols in Taipei City

    NASA Astrophysics Data System (ADS)

    Hung, Hui-Ming; Hsu, Chia-Hung; Lin, Wei-Ting; Chen, Yu-Quan

    2016-05-01

    The hygroscopicity, functional groups and phase transitions of urban aerosol particles in Taipei City were studied using a cloud condensation nuclei counter (CCNc) with a scanning mobility particle sizer (SMPS) and an attenuated total reflectance with infrared (ATR-IR) detection technique. With the assumption of larger particles being activated first, the derived single hygroscopicity parameter (κ) exhibited an increasing trend with particle size, i.e., from 0.022 ± 0.01 at 87 ± 10 nm to 0.13 ± 0.03 at 240 ± 20 nm. The collected size-selected particles were characterized using ATR-IR for the functional groups of alkyl, carbonyl, ammonium, sulfate and nitrate, which showed various size dependence patterns, linked to different formation mechanisms. The hygroscopic response based on the ratio (xW_solute) for sample film of absorption by the enhanced water-stretching peak to that by the selected solute showed a better consistency with pure ammonium sulfate for sub-micron size particles. Based on the derived ammonium sulfate volume fraction from IR analysis, the κ received from CCNc measurements was concluded mainly contributed by ammonium sulfate for sub-micrometer particles. The increasing trend of sodium nitrate absorbance at aerosol diameter ≥1 μm was due to a reaction of nitric acid with sea salt particles. The micrometer sized particles were apparent not only in a significantly higher xW_solute than pure sodium nitrate but also had a deliquescence RH of 69 ± 1%, similar to that of sodium nitrate-sodium chloride mixtures. Overall, the organic species in this study exhibited a low hygroscopicity with less than 0.036 of contribution for the overall κ, and the major hygroscopic material of urban aerosols consisted primarily of ammonium sulfate in the sub-micrometer particles and sodium nitrate with sea salt in the coarse particles.

  19. The ADHD-linked human dopamine D4 receptor variant D4.7 induces over-suppression of NMDA receptor function in prefrontal cortex.

    PubMed

    Qin, Luye; Liu, Wenhua; Ma, Kaijie; Wei, Jing; Zhong, Ping; Cho, Kei; Yan, Zhen

    2016-11-01

    The human dopamine D4 receptor (hD4R) variants with long tandem repeats in the third intracellular loop have been strongly associated with attention deficit hyperactivity disorder (ADHD) and risk taking behaviors. To understand the potential molecular mechanism underlying the connection, we have investigated the synaptic function of human D4R polymorphism by virally expressing the ADHD-linked 7-repeat allele, hD4.7, or its normal counterpart, hD4.4, in the prefrontal cortex (PFC) of D4R knockout mice. We found that hD4R bound to the SH3 domain of PSD-95 in a state-dependent manner. Activation of hD4.7 caused more reduction of NR1/PSD-95 binding and NR1 surface expression than hD4.4 in PFC slices. Moreover, the NMDAR-mediated excitatory postsynaptic currents (NMDAR-EPSC) in PFC pyramidal neurons were suppressed to a larger extent by hD4.7 than hD4.4 activation. Direct stimulation of NMDARs with the partial agonist d-cycloserine prevented the NMDAR hypofunction induced by hD4.7 activation. Moreover, hD4.7-expressing mice exhibited the increased exploratory and novelty seeking behaviors, mimicking the phenotypic hallmark of human ADHD. d-cycloserine administration ameliorated the ADHD-like behaviors in hD4.7-expressing mice. Our results suggest that over-suppression of NMDAR function may underlie the role of hD4.7 in ADHD, and enhancing NMDAR signaling may be a viable therapeutic strategy to ADHD humans carrying the D4.7 allele.

  20. Regulatory T Cell Deficiency and Immune dysregulation, Polyendocrinopathy, Enteropathy, X-Linked-Like Disorder Due to Loss of Function Mutations in LRBA

    PubMed Central

    Charbonnier, Louis-Marie; Janssen, Erin; Chou, Janet; Ohsumi, Toshiro K.; Keles, Sevgi; Hsu, Joyce T.; Massaad, Michel J.; Garcia-Lloret, Maria; Hanna-Wakim, Rima; Dbaibo, Ghassan; Alangari, Abdullah A.; Alsultan, Abdulrahman; Al-Zahrani, Daifulah; Geha, Raif S.; Chatila, Talal A.

    2014-01-01

    Background A number of heritable immune dysregulatory diseases result from defects affecting T regulatory (TR) cell development and/or function. They include Immune dysregulation, Polyendocrinopathy, Enteropathy, X-Linked (IPEX), due to mutations in FOXP3, and IPEX-like disorders caused by mutations in IL2RA, STAT5b and STAT1. However, the genetic defects underlying many cases of IPEX-like disorders remain unknown. Objective We sought to identify the genetic abnormalities in subjects with idiopathic IPEX-like disorders. Methods We performed whole exome and targeted gene sequencing, and phenotypic and functional analyses of TR cells. Results A child who presented with an IPEX-like syndrome and severe TR cell deficiency was found to harbor a nonsense mutation in the gene encoding LPS-responsive beige-like anchor (LRBA), previously implicated as cause of common variable immunodeficiency with autoimmunity. Analysis of subjects with LRBA deficiency revealed marked TR cell depletion, profoundly decreased expression of canonical TR cell markers, including FOXP3, CD25, Helios, and CTLA4 and impaired TR cell-mediated suppression. There was skewing in favor of memory T cells and intense autoantibody production with marked expansion of T follicular helper and contraction of T follicular regulatory cells. Whereas the frequency of recent thymic emigrants and the differentiation of induced TR cells were normal, LRBA-deficient T cells exhibited increased apoptosis and reduced activities of the metabolic sensors mammalian target of rapamycin 1 and 2 complexes. Conclusion LRBA deficiency is a novel cause of IPEX-like syndrome and TR cell deficiency associated with metabolic dysfunction and increased apoptosis of TR cells. PMID:25468195

  1. Metformin-induced mitochondrial function and ABCD2 up-regulation in X-linked adrenoleukodystrophy involves AMP-activated protein kinase.

    PubMed

    Singh, Jaspreet; Olle, Brittany; Suhail, Hamid; Felicella, Michelle M; Giri, Shailendra

    2016-07-01

    peroxisomal disorder X-linked adrenoleukodystrophy (X-ALD). We document the therapeutic potential of FDA approved drug, Metformin, for X-ALD by targeting AMPK. Metformin induced peroxisomal Abcd2 levels in vitro and in vivo. Metformin lowered VLCFA levels, improved mitochondrial function and ameliorated inflammatory gene expression in X-ALD patient-derived cells. Metformin-induced Abcd2 levels were dependent on AMPKα1, a metabolic and anti-inflammatory gene, recently documented by our laboratory to play a putative role in X-ALD pathology. Read the Editorial Highlight for this article on page 10.

  2. Metformin-induced mitochondrial function and ABCD2 up-regulation in X-linked adrenoleukodystrophy involves AMP-activated protein kinase.

    PubMed

    Singh, Jaspreet; Olle, Brittany; Suhail, Hamid; Felicella, Michelle M; Giri, Shailendra

    2016-07-01

    peroxisomal disorder X-linked adrenoleukodystrophy (X-ALD). We document the therapeutic potential of FDA approved drug, Metformin, for X-ALD by targeting AMPK. Metformin induced peroxisomal Abcd2 levels in vitro and in vivo. Metformin lowered VLCFA levels, improved mitochondrial function and ameliorated inflammatory gene expression in X-ALD patient-derived cells. Metformin-induced Abcd2 levels were dependent on AMPKα1, a metabolic and anti-inflammatory gene, recently documented by our laboratory to play a putative role in X-ALD pathology. Read the Editorial Highlight for this article on page 10. PMID:26849413

  3. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    PubMed Central

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-01-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  4. Quantifying the allosteric properties of Escherichia coli carbamyl phosphate synthetase: determination of thermodynamic linked-function parameters in an ordered kinetic mechanism.

    PubMed

    Braxton, B L; Mullins, L S; Raushel, F M; Reinhart, G D

    1992-03-01

    The effects of the allosteric ligands UMP, IMP, and ornithine on the partial reactions catalyzed by Escherichia coli carbamyl phosphate synthetase have been examined. Both of these reactions, a HCO3(-)-dependent ATP synthesis reaction and a carbamyl phosphate-dependent ATP synthesis reaction, follow bimolecular ordered sequential kinetic mechanisms. In the ATPase reaction, MgATP binds before HCO3- as established previously for the overall reaction catalyzed by carbamyl phosphate synthetase [Raushel, F. M., Anderson, P. M., & Villafranca, J. J. (1978) Biochemistry 17, 5587-5591]. The initial velocity kinetics for the ATP synthesis reaction indicate that MgADP binds before carbamyl phosphate in an equilibrium ordered mechanism except in the presence of ornithine. Determination of true thermodynamic linked-function parameters describing the impact of allosteric ligands on the binding interactions of the first substrate to bind in an ordered mechanism requires experiments to be performed in which both substrates are varied even if only one is apparently affected by the allosteric ligands. In so doing, we have found that IMP has little effect on the overall reaction of either of these two partial reactions. UMP and ornithine, which have a pronounced effect on the apparent Km for MgATP in the overall reaction, both substantially change the thermodynamic dissociation constant for MgADP from the binary E-MgADP complex, Kia, in the ATP synthesis reaction, with UMP increasing Kia 15-fold and ornithine decreasing Kia by 18-fold. By contrast, only UMP substantially affects the Kia for MgATP in the ATPase reaction, increasing it by 5-fold.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1531767

  5. Function of Integrin-Linked Kinase in Modulating the Stemness of IL-6-Abundant Breast Cancer Cells by Regulating γ-Secretase-Mediated Notch1 Activation in Caveolae.

    PubMed

    Hsu, En-Chi; Kulp, Samuel K; Huang, Han-Li; Tu, Huang-Ju; Salunke, Santosh B; Sullivan, Nicholas J; Sun, Duxin; Wicha, Max S; Shapiro, Charles L; Chen, Ching-Shih

    2015-06-01

    Interleukin-6 (IL-6) and Notch signaling are important regulators of breast cancer stem cells (CSCs), which drive the malignant phenotype through self-renewal, differentiation, and development of therapeutic resistance. We investigated the role of integrin-linked kinase (ILK) in regulating IL-6-driven Notch1 activation and the ability to target breast CSCs through ILK inhibition. Ectopic expression/short hairpin RNA-mediated knockdown of ILK, pharmacological inhibition of ILK with the small molecule T315, Western blot analysis, immunofluorescence, and luciferase reporter assays were used to evaluate the regulation of IL-6-driven Notch1 activation by ILK in IL-6-producing triple-negative breast cancer cell lines (MDA-MB-231, SUM-159) and in MCF-7 and MCF-7(IL-6) cells. The effects of ILK on γ-secretase complex assembly and cellular localization were determined by immunofluorescence, Western blots of membrane fractions, and immunoprecipitation. In vivo effects of T315-induced ILK inhibition on CSCs in SUM-159 xenograft models were assessed by mammosphere assays, flow cytometry, and tumorigenicity assays. Results show that the genetic knockdown or pharmacological inhibition of ILK suppressed Notch1 activation and the abundance of the γ-secretase components presenilin-1, nicastrin, and presenilin enhancer 2 at the posttranscriptional level via inhibition of caveolin-1-dependent membrane assembly of the γ-secretase complex. Accordingly, knockdown of ILK inhibited breast CSC-like properties in vitro and the breast CSC subpopulation in vivo in xenograft tumor models. Based on these findings, we propose a novel function of ILK in regulating γ-secretase-mediated Notch1 activation, which suggests the targeting of ILK as a therapeutic approach to suppress IL-6-induced breast CSCs.

  6. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community.

    PubMed

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-03-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  7. Renal Integrin-Linked Kinase Depletion Induces Kidney cGMP-Axis Upregulation: Consequences on Basal and Acutely Damaged Renal Function

    PubMed Central

    Cano-Peñalver, José Luis; Griera, Mercedes; García-Jerez, Andrea; Hatem-Vaquero, Marco; Ruiz-Torres, María Piedad; Rodríguez-Puyol, Diego; de Frutos, Sergio; Rodríguez-Puyol, Manuel

    2015-01-01

    Soluble guanylyl cyclase (sGC) is activated by nitric oxide (NO) and produces cGMP, which activates cGMP-dependent protein kinases (PKG) and is hydrolyzed by specific phosphodiesterases (PDE). The vasodilatory and cytoprotective capacity of cGMP-axis activation results in a therapeutic strategy for several pathologies. Integrin-linked kinase (ILK), a major scaffold protein between the extracellular matrix and intracellular signaling pathways, may modulate the expression and functionality of the cGMP-axis–related proteins. We introduce ILK as a novel modulator in renal homeostasis as well as a potential target for cisplatin (CIS)-induced acute kidney injury (AKI) improvement. We used an adult mice model of depletion of ILK (cKD-ILK), which showed basal increase of sGC and PKG expressions and activities in renal cortex when compared with wildtype (WT) littermates. Twenty-four h activation of sGC activation with NO enhanced the filtration rate in cKD-ILK. During AKI, cKD-ILK maintained the cGMP-axis upregulation with consequent filtration rates enhancement and ameliorated CIS-dependent tubular epithelial-to-mesenchymal transition and inflammation and markers. To emphasize the role of cGMP-axis upregulation due to ILK depletion, we modulated the cGMP axis under AKI in vivo and in renal cultured cells. A suboptimal dose of the PDE inhibitor ZAP enhanced the beneficial effects of the ILK depletion in AKI mice. On the other hand, CIS increased contractility-related events in cultured glomerular mesangial cells and necrosis rates in cultured tubular cells; ILK depletion protected the cells while sGC blockade with ODQ fully recovered the damage. PMID:26562149

  8. Multiple actions of φ-LITX-Lw1a on ryanodine receptors reveal a functional link between scorpion DDH and ICK toxins

    PubMed Central

    Smith, Jennifer J.; Vetter, Irina; Lewis, Richard J.; Peigneur, Steve; Tytgat, Jan; Lam, Alexander; Gallant, Esther M.; Beard, Nicole A.; Alewood, Paul F.; Dulhunty, Angela F.

    2013-01-01

    We recently reported the isolation of a scorpion toxin named U1-liotoxin-Lw1a (U1-LITX-Lw1a) that adopts an unusual 3D fold termed the disulfide-directed hairpin (DDH) motif, which is the proposed evolutionary structural precursor of the three-disulfide-containing inhibitor cystine knot (ICK) motif found widely in animals and plants. Here we reveal that U1-LITX-Lw1a targets and activates the mammalian ryanodine receptor intracellular calcium release channel (RyR) with high (fM) potency and provides a functional link between DDH and ICK scorpion toxins. Moreover, U1-LITX-Lw1a, now described as φ-liotoxin-Lw1a (φ-LITX-Lw1a), has a similar mode of action on RyRs as scorpion calcines, although with significantly greater potency, inducing full channel openings at lower (fM) toxin concentrations whereas at higher pM concentrations increasing the frequency and duration of channel openings to a submaximal state. In addition, we show that the C-terminal residue of φ-LITX-Lw1a is crucial for the increase in full receptor openings but not for the increase in receptor subconductance opening, thereby supporting the two-binding-site hypothesis of scorpion toxins on RyRs. φ-LITX-Lw1a has potential both as a pharmacological tool and as a lead molecule for the treatment of human diseases that involve RyRs, such as malignant hyperthermia and polymorphic ventricular tachycardia. PMID:23671114

  9. Na+/K+-ATPase Is Present in Scrapie-Associated Fibrils, Modulates PrP Misfolding In Vitro and Links PrP Function and Dysfunction

    PubMed Central

    Graham, James F.; Kurian, Dominic; Agarwal, Sonya; Toovey, Lorna; Hunt, Lawrence; Kirby, Louise; Pinheiro, Teresa J. T.; Banner, Steven J.; Gill, Andrew C.

    2011-01-01

    Transmissible spongiform encephalopathies are characterised by widespread deposition of fibrillar and/or plaque-like forms of the prion protein. These aggregated forms are produced by misfolding of the normal prion protein, PrPC, to the disease-associated form, PrPSc, through mechanisms that remain elusive but which require either direct or indirect interaction between PrPC and PrPSc isoforms. A wealth of evidence implicates other non-PrP molecules as active participants in the misfolding process, to catalyse and direct the conformational conversion of PrPC or to provide a scaffold ensuring correct alignment of PrPC and PrPSc during conversion. Such molecules may be specific to different scrapie strains to facilitate differential prion protein misfolding. Since molecular cofactors may become integrated into the growing protein fibril during prion conversion, we have investigated the proteins contained in prion disease-specific deposits by shotgun proteomics of scrapie-associated fibrils (SAF) from mice infected with 3 different strains of mouse-passaged scrapie. Concomitant use of negative control preparations allowed us to identify and discount proteins that are enriched non-specifically by the SAF isolation protocol. We found several proteins that co-purified specifically with SAF from infected brains but none of these were reproducibly and demonstrably specific for particular scrapie strains. The α-chain of Na+/K+-ATPase was common to SAF from all 3 strains and we tested the ability of this protein to modulate in vitro misfolding of recombinant PrP. Na+/K+-ATPase enhanced the efficiency of disease-specific conversion of recombinant PrP suggesting that it may act as a molecular cofactor. Consistent with previous results, the same protein inhibited fibrillisation kinetics of recombinant PrP. Since functional interactions between PrPC and Na+/K+-ATPase have previously been reported in astrocytes, our data highlight this molecule as a key link between PrP function

  10. Characterization of a newly identified mycobacterial tautomerase with promiscuous dehalogenase and hydratase activities reveals a functional link to a recently diverged cis-3-chloroacrylic acid dehalogenase.

    PubMed

    Baas, Bert-Jan; Zandvoort, Ellen; Wasiel, Anna A; Quax, Wim J; Poelarends, Gerrit J

    2011-04-12

    The enzyme cis-3-chloroacrylic acid dehalogenase (cis-CaaD) is found in a bacterial pathway that degrades a synthetic nematocide, cis-1,3-dichloropropene, introduced in the 20th century. The previously determined crystal structure of cis-CaaD and its promiscuous phenylpyruvate tautomerase (PPT) activity link this dehalogenase to the tautomerase superfamily, a group of homologous proteins that are characterized by a catalytic amino-terminal proline and a β-α-β structural fold. The low-level PPT activity of cis-CaaD, which may be a vestige of the function of its progenitor, prompted us to search the databases for a homologue of cis-CaaD that was annotated as a putative tautomerase and test both its PPT and cis-CaaD activity. We identified a mycobacterial cis-CaaD homologue (designated MsCCH2) that shares key sequence and active site features with cis-CaaD. Kinetic and 1H NMR spectroscopic studies show that MsCCH2 functions as an efficient PPT and exhibits low-level promiscuous dehalogenase activity, processing both cis- and trans-3-chloroacrylic acid. To further probe the active site of MsCCH2, the enzyme was incubated with 2-oxo-3-pentynoate (2-OP). At pH 8.5, MsCCH2 is inactivated by 2-OP due to the covalent modification of Pro-1, suggesting that Pro-1 functions as a nucleophile at pH 8.5 and attacks 2-OP in a Michael-type reaction. At pH 6.5, however, MsCCH2 exhibits hydratase activity and converts 2-OP to acetopyruvate, which implies that Pro-1 is cationic at pH 6.5 and not functioning as a nucleophile. At pH 7.5, the hydratase and inactivation reactions occur simultaneously. From these results, it can be inferred that Pro-1 of MsCCH2 has a pKa value that lies in between that of a typical tautomerase (pKa of Pro-1∼6) and that of cis-CaaD (pKa of Pro-1∼9). The shared activities and structural features, coupled with the intermediate pKa of Pro-1, suggest that MsCCH2 could be characteristic of an evolutionary intermediate along the past route for the

  11. Intracellular routing in breast cancer cells of streptavidin-conjugated trastuzumab Fab fragments linked to biotinylated doxorubicin-functionalized metal chelating polymers.

    PubMed

    Liu, Peng; Cai, Zhongli; Kang, Jae W; Boyle, Amanda J; Adams, Jarret; Lu, Yijie; Ngo Ndjock Mbong, Ghislaine; Sidhu, Sachdev; Reilly, Raymond M; Winnik, Mitchell A

    2014-03-10

    We describe the synthesis of a heterotelechelic metal-chelating polymer (Bi-MCP-Dox), a polyacrylamide with a number average degree of polymerization DPn = 50 (PDI = 1.2), with biotin (Bi) and doxorubicin (Dox) as functional chain ends and diethylenetriaminepentaacetic acid (DTPA) pendant groups as the binding sites for metal ions. We compared its behavior in cell-uptake experiments with a similar polymer (Bi-MCP) without Dox. These MCPs were complexed with trastuzumab Fab (tmFab) fragments covalently linked to streptavidin (SAv) to form tmFab-SAv-Bi-MCP-Dox and tmFab-SAv-Bi-MCP via the strong affinity between Bi and SAv. tmFab targets human epidermal growth factor receptor-2 (HER2), which is overexpressed on certain human breast cancer cells. Surface plasmon resonance (SPR) experiments with the extracellular domain (ECD) of HER2 showed that incorporation of the MCPs in these complexes had no significant effect on the association or dissociation rate with the HER2 ECD and the dissociation constants. The tmFab-complexed MCPs were subsequently labeled with (111)In (an Auger electron emitting radionuclide). Auger electrons can cause lethal DNA double strand breaks (DSBs) but only if they are emitted intracellularly and especially, in close proximity to the nucleus. To evaluate the cellular and nuclear uptake of tmFab-SAv-Bi-MCP-Dox, we incubated HER2+ SK-BR-3 human breast cancer cells with the complexes saturated with stable In(3+) and visualized their distribution by confocal fluorescence microscopy, monitoring the fluorescence of Dox. In parallel, we carried out cell fractionation studies on tmFab-SAv-Bi-MCP-Dox and on tmFab-SAv-Bi-MCP labeled with (111)In. Both radiolabeled complexes showed cell internalization and nuclear localization. We conclude that metal-chelating polymers with this composition appear to encourage internalization, nuclear uptake, and chromatin (DNA) binding of trastuzumab fragments modified with streptavidin in human breast cancer cells

  12. Functional Role of mTORC2 versus Integrin-Linked Kinase in Mediating Ser473-Akt Phosphorylation in PTEN-Negative Prostate and Breast Cancer Cell Lines.

    PubMed

    Lee, Su-Lin; Chou, Chih-Chien; Chuang, Hsiao-Ching; Hsu, En-Chi; Chiu, Po-Chen; Kulp, Samuel K; Byrd, John C; Chen, Ching-Shih

    2013-01-01

    Although the rictor-mTOR complex (mTORC2) has been shown to act as phosphoinositide-dependent kinase (PDK)2 in many cell types, other kinases have also been implicated in mediating Ser473-Akt phosphorylation. Here, we demonstrated the cell line specificity of integrin-linked kinase (ILK) versus mTORC2 as PDK2 in LNCaP and PC-3 prostate and MDA-MB-468 breast cancer cells, of which the PTEN-negative status allowed the study of Ser473-Akt phosphorylation independent of external stimulation. PC-3 and MDA-MB-468 cells showed upregulated ILK expression relative to LNCaP cells, which expressed a high abundance of mTOR. Exposure to Ku-0063794, a second-generation mTOR inhibitor, decreased Ser473-Akt phosphorylation in LNCaP cells, but not in PC-3 or MDA-MB-468 cells. In contrast, treatment with T315, a novel ILK inhibitor, reduced the phosphorylation of Ser473-Akt in PC-3 and MDA-MB-468 cells without affecting that in LNCaP cells. This cell line specificity was verified by comparing Ser473-Akt phosphorylation status after genetic knockdown of rictor, ILK, and other putative Ser-473-Akt kinases. Genetic knockdown of rictor, but not ILK or the other kinases examined, inhibited Ser473-Akt phosphorylation in LNCaP cells. Conversely, PC-3 and MDA-MB-468 cells were susceptible to the effect of ILK silencing on Ser473-Akt phosphorylation, while knockdown of rictor or any of the other target kinases had no appreciable effect. Co-immunoprecipitation analysis demonstrated the physical interaction between ILK and Akt in PC-3 cells, and T315 blocked ILK-mediated Ser473 phosphorylation of bacterially expressed Akt. ILK also formed complexes with rictor in PC-3 and MDA-MB-468 cells that were disrupted by T315, but such complexes were not observed in LNCaP cells. In the PTEN-functional MDA-MB-231 cell line, both T315 and Ku-0063794 suppressed EGF-induced Ser473-Akt phosphorylation. Inhibition of ILK by T315 or siRNA-mediated knockdown suppressed epithelial-mesenchymal transition in MDA

  13. Functional Role of mTORC2 versus Integrin-Linked Kinase in Mediating Ser473-Akt Phosphorylation in PTEN-Negative Prostate and Breast Cancer Cell Lines

    PubMed Central

    Chuang, Hsiao-Ching; Hsu, En-Chi; Chiu, Po-Chen; Kulp, Samuel K.; Byrd, John C.; Chen, Ching-Shih

    2013-01-01

    Although the rictor-mTOR complex (mTORC2) has been shown to act as phosphoinositide-dependent kinase (PDK)2 in many cell types, other kinases have also been implicated in mediating Ser473-Akt phosphorylation. Here, we demonstrated the cell line specificity of integrin-linked kinase (ILK) versus mTORC2 as PDK2 in LNCaP and PC-3 prostate and MDA-MB-468 breast cancer cells, of which the PTEN-negative status allowed the study of Ser473-Akt phosphorylation independent of external stimulation. PC-3 and MDA-MB-468 cells showed upregulated ILK expression relative to LNCaP cells, which expressed a high abundance of mTOR. Exposure to Ku-0063794, a second-generation mTOR inhibitor, decreased Ser473-Akt phosphorylation in LNCaP cells, but not in PC-3 or MDA-MB-468 cells. In contrast, treatment with T315, a novel ILK inhibitor, reduced the phosphorylation of Ser473-Akt in PC-3 and MDA-MB-468 cells without affecting that in LNCaP cells. This cell line specificity was verified by comparing Ser473-Akt phosphorylation status after genetic knockdown of rictor, ILK, and other putative Ser-473-Akt kinases. Genetic knockdown of rictor, but not ILK or the other kinases examined, inhibited Ser473-Akt phosphorylation in LNCaP cells. Conversely, PC-3 and MDA-MB-468 cells were susceptible to the effect of ILK silencing on Ser473-Akt phosphorylation, while knockdown of rictor or any of the other target kinases had no appreciable effect. Co-immunoprecipitation analysis demonstrated the physical interaction between ILK and Akt in PC-3 cells, and T315 blocked ILK-mediated Ser473 phosphorylation of bacterially expressed Akt. ILK also formed complexes with rictor in PC-3 and MDA-MB-468 cells that were disrupted by T315, but such complexes were not observed in LNCaP cells. In the PTEN-functional MDA-MB-231 cell line, both T315 and Ku-0063794 suppressed EGF-induced Ser473-Akt phosphorylation. Inhibition of ILK by T315 or siRNA-mediated knockdown suppressed epithelial-mesenchymal transition in MDA

  14. Kinetics of template-directed pyrophosphate-linked dideoxyguanylate synthesis as a function of 2-MeImpdG and poly(C) concentration: insights into the mechanism

    NASA Technical Reports Server (NTRS)

    Kanavarioti, A.; Gangopadhyay, S.

    1999-01-01

    Aqueous solutions of deoxyguanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpdG, yield primarily deoxyguanosine 5'-monophosphate, 5'dGMP, and pyrophosphate-linked dideoxyguanylate, dG5'ppdG, abbreviated G2p (see Chart 1). The initial rate of G2p formation, d[G2p]/dt in M h-1, determined at 23 degrees C, pH 7.8, 1.0 M NaCl and 0.2 M Mg2+ by timed high-performance liquid chromatography (HPLC) analysis, exhibits a second-order dependence on 2-MeImpdG concentration, [G]o, indicating a bimolecular mechanism of dimerization in the range 0.02 M < or = [G]o < or = 0.09 M. In the presence of polycytidylate, poly(C), G2p synthesis is accelerated and oligodeoxyguanylate products are formed by incorporation of 2-MeImpdG molecules. The kinetics of G2p formation as a function of both monomer and polymer concentration, expressed in C equivalents, were also determined under the above conditions and exhibited a complex behavior. Specifically, at a constant [poly(C)], values of d[G2p]/dt typically increased with [G]o with a parabolic upward curvature. At a constant [G]o, values of d[G2p]/dt increase with [poly(C)], but level off at the higher poly(C) concentrations. As [G]o increases this saturation occurs at a higher poly(C) concentration, a result opposite to expectation for a simple complexation of two reacting monomers with the catalyst prior to reaction. Nevertheless, these results are shown to be quantitatively consistent with a template-directed (TD) mechanism of dimerization where poly(C) acts as the template to bind 2-MeImpdG in a cooperative manner and lead, for the first time, to the formulation of principles that govern template-directed chemistry. Analysis of the kinetic data via a proposed TD cooperative model provides association constants for the affinity between polymer and monomer and the intrinsic reactivity of 2-MeImpdG toward pyrophosphate synthesis. To the best of our knowledge, poly(C)/2-MeImpdG is the first system that could serve as a textbook example of

  15. Functional Role of mTORC2 versus Integrin-Linked Kinase in Mediating Ser473-Akt Phosphorylation in PTEN-Negative Prostate and Breast Cancer Cell Lines.

    PubMed

    Lee, Su-Lin; Chou, Chih-Chien; Chuang, Hsiao-Ching; Hsu, En-Chi; Chiu, Po-Chen; Kulp, Samuel K; Byrd, John C; Chen, Ching-Shih

    2013-01-01

    Although the rictor-mTOR complex (mTORC2) has been shown to act as phosphoinositide-dependent kinase (PDK)2 in many cell types, other kinases have also been implicated in mediating Ser473-Akt phosphorylation. Here, we demonstrated the cell line specificity of integrin-linked kinase (ILK) versus mTORC2 as PDK2 in LNCaP and PC-3 prostate and MDA-MB-468 breast cancer cells, of which the PTEN-negative status allowed the study of Ser473-Akt phosphorylation independent of external stimulation. PC-3 and MDA-MB-468 cells showed upregulated ILK expression relative to LNCaP cells, which expressed a high abundance of mTOR. Exposure to Ku-0063794, a second-generation mTOR inhibitor, decreased Ser473-Akt phosphorylation in LNCaP cells, but not in PC-3 or MDA-MB-468 cells. In contrast, treatment with T315, a novel ILK inhibitor, reduced the phosphorylation of Ser473-Akt in PC-3 and MDA-MB-468 cells without affecting that in LNCaP cells. This cell line specificity was verified by comparing Ser473-Akt phosphorylation status after genetic knockdown of rictor, ILK, and other putative Ser-473-Akt kinases. Genetic knockdown of rictor, but not ILK or the other kinases examined, inhibited Ser473-Akt phosphorylation in LNCaP cells. Conversely, PC-3 and MDA-MB-468 cells were susceptible to the effect of ILK silencing on Ser473-Akt phosphorylation, while knockdown of rictor or any of the other target kinases had no appreciable effect. Co-immunoprecipitation analysis demonstrated the physical interaction between ILK and Akt in PC-3 cells, and T315 blocked ILK-mediated Ser473 phosphorylation of bacterially expressed Akt. ILK also formed complexes with rictor in PC-3 and MDA-MB-468 cells that were disrupted by T315, but such complexes were not observed in LNCaP cells. In the PTEN-functional MDA-MB-231 cell line, both T315 and Ku-0063794 suppressed EGF-induced Ser473-Akt phosphorylation. Inhibition of ILK by T315 or siRNA-mediated knockdown suppressed epithelial-mesenchymal transition in MDA

  16. White matter injury and microglia/macrophage polarization are strongly linked with age-related long-term deficits in neurological function after stroke.

    PubMed

    Suenaga, Jun; Hu, Xiaoming; Pu, Hongjian; Shi, Yejie; Hassan, Sulaiman Habib; Xu, Mingyue; Leak, Rehana K; Stetler, R Anne; Gao, Yanqin; Chen, Jun

    2015-10-01

    , aged mice exhibited significantly reduced M2 polarization compared to young adults. Remarkably, we discovered a strong positive correlation between favorable neurological outcomes after dMCAO and MBP levels or the number of M2 microglia/macrophages. In conclusion, our studies suggest that the distal MCAO stroke model consistently results in ischemic brain injury with long-term behavioral deficits, and is therefore suitable for the evaluation of long-term stroke outcomes. Furthermore, aged mice exhibit deterioration of functional outcomes after stroke and this deterioration is linked to white matter damage and reductions in M2 microglia/macrophage polarization.

  17. White matter injury and microglia/macrophage polarization are strongly linked with age-related long-term deficits in neurological function after stroke

    PubMed Central

    Suenaga, Jun; Hu, Xiaoming; Pu, Hongjian; Shi, Yejie; Hassan, Sulaiman Habib; Xu, Mingyue; Leak, Rehana K.; Stetler, R. Anne; Gao, Yanqin; Chen, Jun

    2015-01-01

    , aged mice exhibited significantly reduced M2 polarization compared to young adults. Remarkably, we discovered a strong positive correlation between favorable neurological outcomes after dMCAO and MBP levels or the number of M2 microglia/macrophages. In conclusion, our studies suggest that the distal MCAO stroke model consistently results in ischemic brain injury with long-term behavioral deficits, and is therefore suitable for the evaluation of long-term stroke outcomes. Furthermore, aged mice exhibit deterioration of functional outcomes after stroke and this deterioration is linked to white matter damage and reductions in M2 microglia/macrophage polarization. PMID:25836044

  18. Structure-Property Relationships in Porous 3-D Nanostructures as a Function of Preparation Conditions: Isocyanate Cross-Linked Silica Aerogels

    NASA Technical Reports Server (NTRS)

    Meador, Mary Ann B.; Capadona, Lynn A.; McCorkle, Linda; Padadopoulos, Demetrios S.; Leventis, Nicholas

    2007-01-01

    Sol-gel derived silica aerogels are attractive candidates for many unique thermal, optical, catalytic, and chemical applications because of their low density and high mesoporosity. However, their inherent fragility has restricted use of aerogel monoliths to applications where they are not subject to any load. We have previously reported cross-linking the mesoporous silica structure of aerogels with di-isocyanates, styrenes or epoxies reacting with amine decorated silica surfaces. These approaches have been shown to significantly increase the strength of aerogels with only a small effect on density or porosity. Though density is a prime predictor of properties such as strength and thermal conductivity for aerogels, it is becoming clear from previous studies that varying the silica backbone and size of the polymer cross-link independently can give rise to combinations of properties which cannot be predicted from density alone. Herein, we examine the effects of four processing parameters for producing this type of polymer cross-linked aerogel on properties of the resulting monoliths. We focus on the results of C-13 CP-MAS NMR which gives insight to the size and structure of polymer cross-link present in the monoliths, and relates the size of the cross-links to microstructure, mechanical properties and other characteristics of the materials obtained.

  19. Structure-Property Relationships in Porous 3-D Nanostructures as a Function of Preparation Conditions: Isocyanate Cross-Linked Silica Aerogels

    NASA Technical Reports Server (NTRS)

    Meador, Mary Ann B.; Capadona, Lynn A.; McCorkle, Linda; Papadopoulos, Demetrios S.; Leventis, Nicholas

    2007-01-01

    Sol-gel derived silica aerogels are attractive candidates for many unique thermal, optical, catalytic, and chemical applications because of their low density and high mesoporosity. However, their inherent fragility has restricted use of aerogel monoliths to applications where they are not subject to any load. We have previously reported cross-linking the mesoporous silica structure of aerogels with di-isocyanates, styrenes or epoxies reacting with amine decorated silica surfaces. These approaches have been shown to significantly increase the strength of aerogels with only a small effect on density or porosity. Though density is a prime predictor of properties such as strength and thermal conductivity for aerogels, it is becoming clear from previous studies that varying the silica backbone and size of the polymer cross-link independently can give rise to combinations of properties which cannot be predicted from density alone. Herein, we examine the effects of four processing parameters for producing this type of polymer cross-linked aerogel on properties of the resulting monoliths. We focus on the results of 13C CP-MAS NMR which gives insight to the size and structure of polymer cross-link present in the monoliths, and relates the size of the cross-links to microstructure, mechanical properties and other characteristics of the materials obtained.

  20. Sympathetic- and Parasympathetic-Linked Cardiac Function and Prediction of Externalizing Behavior, Emotion Regulation, and Prosocial Behavior among Preschoolers Treated for ADHD

    ERIC Educational Resources Information Center

    Beauchaine, Theodore P.; Gatzke-Kopp, Lisa; Neuhaus, Emily; Chipman, Jane; Reid, M. Jamila; Webster-Stratton, Carolyn

    2013-01-01

    Objective: To evaluate measures of cardiac activity and reactivity as prospective biomarkers of treatment response to an empirically supported behavioral intervention for attention-deficit/hyperactivity disorder (ADHD). Method: Cardiac preejection period (PEP), an index of sympathetic-linked cardiac activity, and respiratory sinus arrhythmia…

  1. Sex-linked dominant

    MedlinePlus

    Inheritance - sex-linked dominant; Genetics - sex-linked dominant; X-linked dominant; Y-linked dominant ... can be either an autosomal chromosome or a sex chromosome. It also depends on whether the trait ...

  2. Association between Community Ambulation Walking Patterns and Cognitive Function in Patients with Parkinson's Disease: Further Insights into Motor-Cognitive Links

    PubMed Central

    Weiss, Aner; Herman, Talia; Giladi, Nir; Hausdorff, Jeffrey M.

    2015-01-01

    Background. Cognitive function is generally evaluated based on testing in the clinic, but this may not always reflect real-life function. We tested whether parameters derived from long-term, continuous monitoring of gait are associated with cognitive function in patients with Parkinson's disease (PD). Methods. 107 patients with PD (age: 64.9 ± 9.3 yrs; UPDRS motor sum “off”: 40.4 ± 13.2; 25.23% women) wore a 3D accelerometer on their lower back for 3 days. Computerized measures of global cognitive function, executive function, attention, and nonverbal memory were assessed. Three-day acceleration derived measures included cadence, variability, bilateral coordination, and dynamic postural control. Associations between the acceleration derived measures and cognitive function were determined. Results. Linear regression showed associations between vertical gait variability and cadence and between global cognitive score, attention, and executive function (p ≤ 0.048). Dynamic postural control was associated with global cognitive score and attention (p ≤ 0.027). Nonverbal memory was not associated with the acceleration-derived measures. Conclusions. These findings suggest that metrics derived from a 3-day worn body-fixed sensor reflect cognitive function, further supporting the idea that the gait pattern may be altered as cognition declines and that gait provides a window into cognitive function in patients with PD. PMID:26605103

  3. Linking network topology to function. Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O.C. Martin, A. Krzywicki and M. Zagorski

    NASA Astrophysics Data System (ADS)

    di Bernardo, Diego

    2016-07-01

    that confers phenotypic robustness to the cell? All of these questions can be tackled only by understanding the guiding principles linking network topology to network function.

  4. Sympathetic- and Parasympathetic-linked Cardiac Function and Prediction of Externalizing Behavior, Emotion Regulation, and Prosocial Behavior among Preschoolers Treated for ADHD

    PubMed Central

    Beauchaine, Theodore P.; Gatzke-Kopp, Lisa; Neuhaus, Emily; Chipman, Jane; Reid, M. Jamila; Webster-Stratton, Carolyn

    2014-01-01

    Objective To evaluate measures of cardiac activity and reactivity as prospective biomarkers of treatment response to an empirically-supported behavioral intervention for attention-deficit/hyperactivity disorder (ADHD). Method Cardiac pre-ejection period (PEP), an index of sympathetic-linked cardiac activity, and respiratory sinus arrhythmia (RSA), and index of parasympathetic-linked cardiac activity, were assessed among 99 preschool children (ages 4–6 years) with ADHD both at rest and in response to behavioral challenge, before participants and their parents completed one of two versions of the Incredible Years parent and child interventions. Results Main effects of PEP activity and reactivity, and of RSA activity and reactivity were found. Although sample-wide improvements in behavior were observed at post treatment, those who exhibited lengthened cardiac PEP at rest and reduced PEP reactivity to incentives scored higher on measures of conduct problems and aggression both before and after treatment. In contrast, children who exhibited lower baseline RSA and greater RSA withdrawal scored lower on prosocial behavior before and after treatment. Finally, children who exhibited greater RSA withdrawal scored lower on emotion regulation before and after treatment. Conclusions We discuss these findings in terms of (a) individual differences in underlying neurobiological systems subserving appetitive (i.e., approach) motivation, emotion regulation, and social affiliation, and (b) the need to develop more intensive interventions targeting neurobiologically vulnerable children. PMID:23544677

  5. Synthesis of a novel β-ketoenamine-linked conjugated microporous polymer with Nsbnd H functionalized pore surface for carbon dioxide capture

    NASA Astrophysics Data System (ADS)

    Shuangzhi, Chai; Liu, Haohan; Zhang, Xue; Han, Yang; Hu, Nantao; Wei, Liangming; Cong, Fengsong; Wei, Hao; Wang, Lin

    2016-10-01

    A novel β-ketoenamine-linked conjugated microporous polymer (KECMP-1) was synthesized via Schiff base condensation between 1,3,5-triformylphloroglucinol and m-phenylenediamine by conventional solvothermal synthesis without a template or a metal catalyst. KECMP-1 exhibits a considerable Brunauer-Emmett-Teller specific surface area (691 m2 g-1) and high physicochemical stability. By utilizing the bottom-up strategy, the surfaces of the pore walls were covered with the Nsbnd H sites, together with their microporous structures, lead to the high carbon dioxide (CO2) adsorption capability (10.5 wt% at 273 K and 1.0 bar) and heat of adsorption (34.6 kJ mol-1).

  6. Arthrobacter aurescens TC1 Atrazine Catabolism Genes trzN, atzB, and atzC Are Linked on a 160-Kilobase Region and Are Functional in Escherichia coli

    PubMed Central

    Sajjaphan, Kannika; Shapir, Nir; Wackett, Lawrence P.; Palmer, Michael; Blackmon, Barbara; Tomkins, Jeff; Sadowsky, Michael J.

    2004-01-01

    Arthrobacter aurescens strain TC1 metabolizes atrazine to cyanuric acid via TrzN, AtzB, and AtzC. The complete sequence of a 160-kb bacterial artificial chromosome clone indicated that trzN, atzB, and atzC are linked on the A. aurescens genome. TrzN, AtzB, and AtzC were shown to be functional in Escherichia coli. Hybridization studies localized trzN, atzB, and atzC to a 380-kb plasmid in A. aurescens strain TC1. PMID:15240330

  7. Investigating the Links between the Subcomponents of Executive Function and Academic Achievement: A Cross-Cultural Analysis of Chinese and American Preschoolers

    ERIC Educational Resources Information Center

    Lan, Xuezhao; Legare, Cristine H.; Ponitz, Claire Cameron; Li, Su; Morrison, Frederick J.

    2011-01-01

    Little is known about how components of executive function (EF) jointly and uniquely predict different aspects of academic achievement and how this may vary across cultural contexts. In the current study, 119 Chinese and 139 American preschoolers were tested on a battery of EF tasks (i.e., inhibition, working memory, and attentional control) as…

  8. The severity of mammary gland developmental defects is linked to the overall functional status of Cx43 as revealed by genetically modified mice

    PubMed Central

    Stewart, Michael K. G.; Gong, Xiang-Qun; Barr, Kevin J.; Bai, Donglin; Fishman, Glenn I.; Laird, Dale W.

    2012-01-01

    Genetically modified mice mimicking ODDD (oculodentodigital dysplasia), a disease characterized by reduced Cx43 (connexin 43)-mediated gap junctional intercellular communication, represent an in vivo model to assess the role of Cx43 in mammary gland development and function. We previously reported that severely compromised Cx43 function delayed mammary gland development and impaired milk ejection in mice that harboured a G60S Cx43 mutant, yet there are no reports of lactation defects in ODDD patients. To address this further, we obtained a second mouse model of ODDD expressing an I130T Cx43 mutant to assess whether a mutant with partial gap junction channel activity would be sufficient to retain mammary gland development and function. The results of the present study show that virgin Cx43I130T/+ mice exhibited a temporary delay in ductal elongation at 4 weeks. In addition, Cx43I130T/+ mice develop smaller mammary glands at parturition due to reduced cell proliferation despite similar overall gland architecture. Distinct from Cx43G60S/+ mice, Cx43I130T/+ mice adequately produce and deliver milk to pups, suggesting that milk ejection is unaffected. Thus the present study suggests that a loss-of-function mutant of Cx43 with partial gap junction channel coupling conductance results in a less severe mammary gland phenotype, which may partially explain the lack of reported lactation defects associated with ODDD patients. PMID:23075222

  9. Genotypic variation in traits linked to climate and aboveground productivity in a widespread C4 grass: Evidence for a functional trait syndrome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Growth and leaf functional trait variation among genotypes of a geographically widespread dominant species could provide insight into mechanisms of local adaptation and may be important for predicting species and ecosystem responses to environmental change. Under common garden conditions, we grew n...

  10. Post-synthetic modification of an amino-functionalized metal-organic framework for highly efficient enrichment of N-linked glycopeptides

    NASA Astrophysics Data System (ADS)

    Ma, Wen; Xu, Linnan; Li, Ze; Sun, Yunlong; Bai, Yu; Liu, Huwei

    2016-05-01

    A maltose-functionalized metal-organic framework (MOF), MIL-101(Cr)-maltose, was developed via a simple two step post-synthetic modification of MIL-101(Cr)-NH2. With the use of this nanomaterial, 33 glycopeptides were detected from the digest of human immunoglobulin G, demonstrating its high efficiency in glycoproteomic analysis. More importantly, the generic functionalization route from amino-derived MOFs opens a new perspective in material design in sample preparation.A maltose-functionalized metal-organic framework (MOF), MIL-101(Cr)-maltose, was developed via a simple two step post-synthetic modification of MIL-101(Cr)-NH2. With the use of this nanomaterial, 33 glycopeptides were detected from the digest of human immunoglobulin G, demonstrating its high efficiency in glycoproteomic analysis. More importantly, the generic functionalization route from amino-derived MOFs opens a new perspective in material design in sample preparation. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02490d

  11. A Pil1–Sle1–Syj1–Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation

    PubMed Central

    Kabeche, Ruth; Roguev, Assen; Krogan, Nevan J.; Moseley, James B.

    2014-01-01

    ABSTRACT Stable compartments of the plasma membrane promote a wide range of cellular functions. In yeast cells, cytosolic structures called eisosomes generate prominent cortical invaginations of unknown function. Through a series of genetic screens in fission yeast, we found that the eisosome proteins Pil1 and Sle1 function with the synaptojanin-like lipid phosphatase Syj1 and its ligand Tax4. This genetic pathway connects eisosome function with the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] in cells. Defects in PI(4,5)P2 regulation led to eisosome defects, and we found that the core eisosome protein Pil1 can bind to and tubulate liposomes containing PI(4,5)P2. Mutations in components of the Pil1–Sle1–Syj1–Tax4 pathway suppress the growth and morphology defects of TORC2 mutants, indicating that eisosome-dependent regulation of PI(4,5)P2 feeds into signal transduction pathways. We propose that the geometry of membrane invaginations generates spatial and temporal signals for lipid-mediated signaling events in cells. PMID:24434583

  12. Defects of T-cell effector function and post-thymic maturation in X-linked hyper-IgM syndrome

    PubMed Central

    Jain, Ashish; Atkinson, T. Prescott; Lipsky, Peter E.; Slater, Jay E.; Nelson, David L.; Strober, Warren

    1999-01-01

    X-linked hyper-IgM syndrome (XHIM) results from mutations in the gene encoding for CD40 ligand (CD154). Patients with the syndrome suffer from infections with opportunistic pathogens such as Cryptosporidium and Pneumocystis carinii. In this study, we demonstrate that activated T cells from patients with XHIM produce markedly reduced levels of IFN-γ, fail to induce antigen-presenting cells to synthesize IL-12, and induce greatly reduced levels of TNF-α. In addition, we show that the patients’ circulating T lymphocytes of both the CD4+ and CD8+ subsets contain a markedly reduced antigen-primed population, as determined by CD45RO expression. Finally, we demonstrate that the defects in antigen priming are likely due to the lack of CD154 expression and insufficient costimulation of T cells by CD80/CD86 interactions. Taken together, this study offers a basis for the increased susceptibility of patients with XHIM to certain opportunistic infections. PMID:10207167

  13. Oxidase-deficient neutrophils from X-linked chronic granulomatous disease iPS cells: functional correction by zinc finger nuclease–mediated safe harbor targeting

    PubMed Central

    Zou, Jizhong; Sweeney, Colin L.; Chou, Bin-Kuan; Choi, Uimook; Pan, Jason; Wang, Hongmei; Dowey, Sarah N.

    2011-01-01

    We have developed induced pluripotent stem cells (iPSCs) from a patient with X-linked chronic granulomatous disease (X-CGD), a defect of neutrophil microbicidal reactive oxygen species (ROS) generation resulting from gp91phox deficiency. We demonstrated that mature neutrophils differentiated from X-CGD iPSCs lack ROS production, reproducing the pathognomonic CGD cellular phenotype. Targeted gene transfer into iPSCs, with subsequent selection and full characterization to ensure no off-target changes, holds promise for correction of monogenic diseases without the insertional mutagenesis caused by multisite integration of viral or plasmid vectors. Zinc finger nuclease–mediated gene targeting of a single-copy gp91phox therapeutic minigene into one allele of the “safe harbor” AAVS1 locus in X-CGD iPSCs without off-target inserts resulted in sustained expression of gp91phox and substantially restored neutrophil ROS production. Our findings demonstrate how precise gene targeting may be applied to correction of X-CGD using zinc finger nuclease and patient iPSCs. PMID:21411759

  14. Linking the solution viscosity of an IgG2 monoclonal antibody to its structure as a function of pH and temperature.

    PubMed

    Cheng, Weiqiang; Joshi, Sangeeta B; Jain, Nishant Kumar; He, Feng; Kerwin, Bruce A; Volkin, David B; Middaugh, C Russell

    2013-12-01

    Although the viscosity of concentrated antibody solutions has been the focus of many recent studies, less attention has been concentrated on how changes in protein structure impact viscosity. This study examines viscosity profiles of an immunoglobulin G (IgG) 2 monoclonal antibody at 150 mg/mL as a function of temperature and pH. Although the structure of the antibody at pH 4.0-7.0 was comparable at lower temperatures as measured by second derivative UV absorbance and Fourier transform infrared spectroscopy, differences in 8-anilino-1-naphthalene sulfonate (ANS) fluorescence intensity indicated small structural alterations as a function of pH. Below the structural transition onset temperature, the viscosity profiles were pH dependent and linearly correlated with fluorescence intensity, and followed semilogarithmic behavior as a function of temperature. The transitions of the viscosity profiles correlated well with the major structure transitions at a protein concentration of 150 mg/mL. The viscosity correlated particularly well with ANS fluorescence intensity at 0.2 mg/mL below and above the structural transition temperatures. These results suggest: (1) ANS can be an important measure of the overall structure and (2) hydrophobic interactions and charge-charge interactions are the two major physical factors that contribute collectively to the high viscosity of concentrated IgG solutions.

  15. Pseudogenization of sopA and sopE2 is functionally linked and contributes to virulence of Salmonella enterica serovar Typhi.

    PubMed

    Valenzuela, L M; Hidalgo, A A; Rodríguez, L; Urrutia, I M; Ortega, A P; Villagra, N A; Paredes-Sabja, D; Calderón, I L; Gil, F; Saavedra, C P; Mora, G C; Fuentes, J A

    2015-07-01

    The difference in host range between Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. enterica serovar Typhi (S. Typhi) can be partially attributed to pseudogenes. Pseudogenes are genomic segments homologous to functional genes that do not encode functional products due to the presence of genetic defects. S. Typhi lacks several protein effectors implicated in invasion or other important processes necessary for full virulence of S. Typhimurium. SopA and SopE2, effectors that have been lost by pseudogenization in S. Typhi, correspond to an ubiquitin ligase involved in cytokine production by infected cells, and to a guanine exchange factor necessary for invasion of epithelial cells, respectively. We hypothesized that sopA and/or sopE pseudogenization contributed to the virulence of S. Typhi. In this work, we found that S. Typhi expressing S. Typhimurium sopE2 exhibited a decreased invasion in different epithelial cell lines compared with S. Typhi WT. S. Typhimurium sopA completely abolished the hypo-invasive phenotype observed in S. Typhi expressing S. Typhimurium sopE2, suggesting that functional SopA and SopE2 participate concertedly in the invasion process. Finally, the expression of S. Typhimurium sopA and/or sopE2 in S. Typhi, determined changes in the secretion of IL-8 and IL-18 in infected epithelial cells.

  16. Repairing the Brain by SCF+G-CSF Treatment at 6 Months Postexperimental Stroke: Mechanistic Determination of the Causal Link Between Neurovascular Regeneration and Motor Functional Recovery.

    PubMed

    Cui, Lili; Wang, Dandan; McGillis, Sandra; Kyle, Michele; Zhao, Li-Ru

    2016-06-01

    Stroke, a leading cause of adult disability in the world, is a severe medical condition with limited treatment. Physical therapy, the only treatment available for stroke rehabilitation, appears to be effective within 6 months post-stroke. Here, we have mechanistically determined the efficacy of combined two hematopoietic growth factors, stem cell factor (SCF) and granulocyte-colony stimulating factor (G-CSF; SCF + G-CSF), in brain repair 6 months after cortical infarct induction in the transgenic mice carrying yellow fluorescent protein in Layer V pyramidal neurons (Thy1-YFP-H). Using a combination of live brain imaging, whole brain imaging, molecular manipulation, synaptic and vascular assessments, and motor function examination, we found that SCF + G-CSF promoted mushroom spine formation, enlarged postsynaptic membrane size, and increased postsynaptic density-95 accumulation and blood vessel density in the peri-infarct cavity cortex; and that SCF + G-CSF treatment improved motor functional recovery. The SCF + G-CSF-enhanced motor functional recovery was dependent on the synaptic and vascular regeneration in the peri-infarct cavity cortex. These data suggest that a stroke-damaged brain is repairable by SCF + G-CSF even 6 months after the lesion occurs. This study provides novel insights into the development of new restorative strategies for stroke recovery. PMID:27511907

  17. Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases.

    PubMed

    Banerjee, Antara; Chakraborty, Subhadip; Chakraborty, Abhijit; Chakrabarti, Saikat; Ray, Kunal

    2016-01-01

    Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulations-based structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis, and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas. PMID:27243976

  18. Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases

    PubMed Central

    Chakrabarti, Saikat; Ray, Kunal

    2016-01-01

    Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulations-based structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis, and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas. PMID:27243976

  19. Surface-Based fMRI-Driven Diffusion Tractography in the Presence of Significant Brain Pathology: A Study Linking Structure and Function in Cerebral Palsy

    PubMed Central

    Cunnington, Ross; Boyd, Roslyn N.; Rose, Stephen E.

    2016-01-01

    Diffusion MRI (dMRI) tractography analyses are difficult to perform in the presence of brain pathology. Automated methods that rely on cortical parcellation for structural connectivity studies often fail, while manually defining regions is extremely time consuming and can introduce human error. Both methods also make assumptions about structure-function relationships that may not hold after cortical reorganisation. Seeding tractography with functional-MRI (fMRI) activation is an emerging method that reduces these confounds, but inherent smoothing of fMRI signal may result in the inclusion of irrelevant pathways. This paper describes a novel fMRI-seeded dMRI-analysis pipeline based on surface-meshes that reduces these issues and utilises machine-learning to generate task specific white matter pathways, minimising the requirement for manually-drawn ROIs. We directly compared this new strategy to a standard voxelwise fMRI-dMRI approach, by investigating correlations between clinical scores and dMRI metrics of thalamocortical and corticomotor tracts in 31 children with unilateral cerebral palsy. The surface-based approach successfully processed more participants (87%) than the voxel-based approach (65%), and provided significantly more-coherent tractography. Significant correlations between dMRI metrics and five clinical scores of function were found for the more superior regions of these tracts. These significant correlations were stronger and more frequently found with the surface-based method (15/20 investigated were significant; R2 = 0.43–0.73) than the voxelwise analysis (2 sig. correlations; 0.38 & 0.49). More restricted fMRI signal, better-constrained tractography, and the novel track-classification method all appeared to contribute toward these differences. PMID:27487011

  20. Surface-Based fMRI-Driven Diffusion Tractography in the Presence of Significant Brain Pathology: A Study Linking Structure and Function in Cerebral Palsy.

    PubMed

    Reid, Lee B; Cunnington, Ross; Boyd, Roslyn N; Rose, Stephen E

    2016-01-01

    Diffusion MRI (dMRI) tractography analyses are difficult to perform in the presence of brain pathology. Automated methods that rely on cortical parcellation for structural connectivity studies often fail, while manually defining regions is extremely time consuming and can introduce human error. Both methods also make assumptions about structure-function relationships that may not hold after cortical reorganisation. Seeding tractography with functional-MRI (fMRI) activation is an emerging method that reduces these confounds, but inherent smoothing of fMRI signal may result in the inclusion of irrelevant pathways. This paper describes a novel fMRI-seeded dMRI-analysis pipeline based on surface-meshes that reduces these issues and utilises machine-learning to generate task specific white matter pathways, minimising the requirement for manually-drawn ROIs. We directly compared this new strategy to a standard voxelwise fMRI-dMRI approach, by investigating correlations between clinical scores and dMRI metrics of thalamocortical and corticomotor tracts in 31 children with unilateral cerebral palsy. The surface-based approach successfully processed more participants (87%) than the voxel-based approach (65%), and provided significantly more-coherent tractography. Significant correlations between dMRI metrics and five clinical scores of function were found for the more superior regions of these tracts. These significant correlations were stronger and more frequently found with the surface-based method (15/20 investigated were significant; R2 = 0.43-0.73) than the voxelwise analysis (2 sig. correlations; 0.38 & 0.49). More restricted fMRI signal, better-constrained tractography, and the novel track-classification method all appeared to contribute toward these differences. PMID:27487011

  1. Radical SAM, A Novel Protein Superfamily Linking Unresolved Steps in Familiar Biosynthetic Pathways with Radical Mechanisms: Functional Characterization Using New Analysis and Information Visualization Methods

    SciTech Connect

    Sofia, Heidi J.; Chen, Guang; Hetzler, Elizabeth G.; Reyes Spindola, Jorge F.; Miller, Nancy E.

    2001-03-01

    A large protein superfamily with over 500 members has been discovered and analyzed using powerful new bioinformatics and information visualization methods. Evidence exists that these proteins generate a 5?-deoxyadenosyl radical by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. Radical SAM superfamily proteins function in DNA precursor, vitamin, cofactor, antibiotic, and herbicide biosynthesis in a collection of basic and familiar pathways. One of the members is interferon-inducible and is considered a candidate drug target for osteoporosis. The identification of this superfamily suggests that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways.

  2. Linking Geomorphic Processes and Ecologic Functions Over Long Channel Segments And Retaining Fine Details- Let’s Have Our Cake And Eat It Too (Invited)

    NASA Astrophysics Data System (ADS)

    Pasternack, G. B.; Bratovich, P.; Reedy, G.; Johnson, T.; Massa, D.; Bergman, J.; Purdy, C.; Campos, C.

    2009-12-01

    River scientists have long struggled with the conundrum of scaling observations made at a small number of locations to explain phenomena over long river segments. Some chose to sparsely distribute samples through a segment and interpolate, while others chose to densely sample a few locations and extrapolate. Thankfully, we are rapidly achieving the science and technology to directly observe a whole system at the finely detailed level necessary to capture actual processes of interest. For example, LIDAR and boat-based topographic surveying methods can now yield affordable, comprehensive mapping and re-mapping of channels with a resolution of 1 m2. Blimp-based aerial photos can image riverbeds with 1-10 mm resolution. 2D hydraulic models can now efficiently simulate physical habitat conditions over tens of km of channel at 1 m2 resolution. Diverse fish surveying methods can also pinpoint locations of fish occurrence and habitat utilization with 1 m2 accuracy. Dense, expansive, inexpensive datasets are the new paradigm for river science in the 21st century. The question now is how do we assimilate all of these layers of data to produce a systematic assessment of the status of a riverine ecosystem that identifies the key linkages that should be central to river management and rehabilitation? To gain insight into this topic, a multidisciplinary team of scientists representing 17 stakeholder groups has developed a biophysical monitoring and evaluation plan that makes use of new technologies to investigate the 39-km long, regulated, gravel-bed lower Yuba River in Northern California. So far data from weekly redd surveys and acoustic tagging of adult Pacific salmonids have been linked to geomorphic and hydraulic processes. One key finding is that multiple scales of channel nonuniformity have been found to play an important role in controlling the spatial pattern of channel change, which in turn affects persistence and maintenance of mesohabitats, which in turn delivers an

  3. The PIKfyve–ArPIKfyve–Sac3 triad in human breast cancer: Functional link between elevated Sac3 phosphatase and enhanced proliferation of triple negative cell lines

    SciTech Connect

    Ikonomov, Ognian C. Filios, Catherine Sbrissa, Diego Chen, Xuequn Shisheva, Assia

    2013-10-18

    Highlights: •We assess PAS complex proteins and phosphoinositide levels in breast cancer cells. •Sac3 and ArPIKfyve are markedly elevated in triple-negative breast cancer cells. •Sac3 silencing inhibits proliferation in triple-negative breast cancer cell lines. •Phosphoinositide profiles are altered in breast cancer cells. •This is the first evidence linking high Sac3 with breast cancer cell proliferation. -- Abstract: The phosphoinositide 5-kinase PIKfyve and 5-phosphatase Sac3 are scaffolded by ArPIKfyve in the PIKfyve–ArPIKfyve–Sac3 (PAS) regulatory complex to trigger a unique loop of PtdIns3P–PtdIns(3,5)P{sub 2} synthesis and turnover. Whereas the metabolizing enzymes of the other 3-phosphoinositides have already been implicated in breast cancer, the role of the PAS proteins and the PtdIns3P–PtdIns(3,5)P{sub 2} conversion is unknown. To begin elucidating their roles, in this study we monitored the endogenous levels of the PAS complex proteins in cell lines derived from hormone-receptor positive (MCF7 and T47D) or triple-negative breast cancers (TNBC) (BT20, BT549 and MDA-MB-231) as well as in MCF10A cells derived from non-tumorigenic mastectomy. We report profound upregulation of Sac3 and ArPIKfyve in the triple negative vs. hormone-sensitive breast cancer or non-tumorigenic cells, with BT cell lines showing the highest levels. siRNA-mediated knockdown of Sac3, but not that of PIKfyve, significantly inhibited proliferation of BT20 and BT549 cells. In these cells, knockdown of ArPIKfyve had only a minor effect, consistent with a primary role for Sac3 in TNBC cell proliferation. Intriguingly, steady-state levels of PtdIns(3,5)P{sub 2} in BT20 and T47D cells were similar despite the 6-fold difference in Sac3 levels between these cell lines. However, steady-state levels of PtdIns3P and PtdIns5P, both regulated by the PAS complex, were significantly reduced in BT20 vs. T47D or MCF10A cell lines, consistent with elevated Sac3 affecting directly or

  4. A new link between stress response and nucleolar function during pollen development in Arabidopsis mediated by AtREN1 protein.

    PubMed

    Reňák, David; Gibalová, Antónia; Solcová, Katarzyna; Honys, David

    2014-03-01

    Heat shock transcription factors (Hsfs) are involved in multiple aspects of stress response and plant growth. However, their role during male gametophyte development is largely unknown, although the generative phase is the most sensitive and critical period in the plant life cycle. Based on a wide screen of T-DNA mutant lines, we identified the atren1 mutation (restricted to nucleolus1) in early male gametophytic gene At1g77570, which has the closest homology to HSFA5 gene, the member of a heat shock transcription factor (HSF) gene family. The mutation causes multiple defects in male gametophyte development in both structure and function. Because the mutation disrupts an early acting (AtREN1) gene, these pollen phenotype abnormalities appear from bicellular pollen stage to pollen maturation. Moreover, the consequent progamic phase is compromised as well as documented by pollen germination defects and limited transmission via male gametophyte. In addition, atren1/- plants are defective in heat stress (HS) response and produce notably higher proportion of aberrant pollen grains. AtREN1 protein is targeted specifically to the nucleolus that, together with the increased size of the nucleolus in atren1 pollen, suggests that it is likely to be involved in ribosomal RNA biogenesis or other nucleolar functions.

  5. Genotypic variation in traits linked to climate and aboveground productivity in a widespread C₄ grass: evidence for a functional trait syndrome.

    PubMed

    Aspinwall, Michael J; Lowry, David B; Taylor, Samuel H; Juenger, Thomas E; Hawkes, Christine V; Johnson, Mari-Vaughn V; Kiniry, James R; Fay, Philip A

    2013-09-01

    Examining intraspecific variation in growth and function in relation to climate may provide insight into physiological evolution and adaptation, and is important for predicting species responses to climate change. Under common garden conditions, we grew nine genotypes of the C₄ species Panicum virgatum originating from different temperature and precipitation environments. We hypothesized that genotype productivity, morphology and physiological traits would be correlated with climate of origin, and a suite of adaptive traits would show high broad-sense heritability (H(2)). Genotype productivity and flowering time increased and decreased, respectively, with home-climate temperature, and home-climate temperature was correlated with genotypic differences in a syndrome of morphological and physiological traits. Genotype leaf and tiller size, leaf lamina thickness, leaf mass per area (LMA) and C : N ratios increased with home-climate temperature, whereas leaf nitrogen per unit mass (Nm ) and chlorophyll (Chl) decreased with home-climate temperature. Trait variation was largely explained by genotypic differences (H(2) = 0.33-0.85). Our results provide new