Science.gov

Sample records for pa-08-098 functional links

  1. New wrapped distribution via Richard link function

    NASA Astrophysics Data System (ADS)

    Demirelli, Arzu Ekinci; Gürcan, Mehmet

    2017-07-01

    In this paper, we investigate a new wrapped distribution obtained from Richard link function. In the literature, many probability distributions are used wrapped form via normal, Cauchy, etc.. In this point, the most important characteristic of the Richard link function is that the flexible. Because of this feature Richard link function is useful. But, the Richard link function does not have a distribution form and analytical solution of parameter estimation. In this study we examined properties of wrapped Richard distribution and we have sampled for ant data.

  2. Transfer functions for a single flexible link

    SciTech Connect

    Wang, D. ); Vidyasagar, M. )

    1991-10-01

    This article examines some issues in the transfer function modeling of a single flexible link. Using the assumed-modes approach to represent the elastic deformation, one can find the transfer function between the torque input and the net tip deflection. It is shown here that when the number of modes is increased for more accurate modeling, the relative degree of the transfer function becomes ill defined. This can greatly affect the performance of a controller designed using this model. It is then shown that this problem occurs regardless of the method used to represent the elastic deformation. An alternate modeling approach is proposed that used the rigid body deformations minus the elastic deformations as the output. This solves this problem and results in a transfer function with a well-defined relative degree of two. Simulation results are presented that illustrate the advantages of using the proposed alternate transfer function.

  3. 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

  4. Using ecological production functions to link ecological ...

    EPA Pesticide Factsheets

    Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively little attention. Ecological production functions may be defined as usable expressions (i.e., models) of the processes by which ecosystems produce ES, often including external influences on those processes. We identify key attributes of EPFs and discuss both actual and idealized examples of their use to inform decision making. Whenever possible, EPFs should estimate final, rather than intermediate, ES. Although various types of EPFs have been developed, we suggest that EPFs are more useful for decision making if they quantify ES outcomes, respond to ecosystem condition, respond to stressor levels or management scenarios, reflect ecological complexity, rely on data with broad coverage, have performed well previously, are practical to use, and are open and transparent. In an example using pesticides, we illustrate how EPFs with these attributes could enable the inclusion of ES in ecological risk assessment. The biggest challenges to ES inclusion are limited data sets that are easily adapted for use in modeling EPFs and generally poor understanding of linkages among ecological components and the processes that ultimately deliver the ES. We conclude by advocating for the incorporation into E

  5. Using ecological production functions to link ecological ...

    EPA Pesticide Factsheets

    Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively little attention. Ecological production functions may be defined as usable expressions (i.e., models) of the processes by which ecosystems produce ES, often including external influences on those processes. We identify key attributes of EPFs and discuss both actual and idealized examples of their use to inform decision making. Whenever possible, EPFs should estimate final, rather than intermediate, ES. Although various types of EPFs have been developed, we suggest that EPFs are more useful for decision making if they quantify ES outcomes, respond to ecosystem condition, respond to stressor levels or management scenarios, reflect ecological complexity, rely on data with broad coverage, have performed well previously, are practical to use, and are open and transparent. In an example using pesticides, we illustrate how EPFs with these attributes could enable the inclusion of ES in ecological risk assessment. The biggest challenges to ES inclusion are limited data sets that are easily adapted for use in modeling EPFs and generally poor understanding of linkages among ecological components and the processes that ultimately deliver the ES. We conclude by advocating for the incorporation into E

  6. APP Function and Lipids: A Bidirectional Link.

    PubMed

    Grimm, Marcus O W; Mett, Janine; Grimm, Heike S; Hartmann, Tobias

    2017-01-01

    Extracellular neuritic plaques, composed of aggregated amyloid-β (Aβ) peptides, are one of the major histopathological hallmarks of Alzheimer's disease (AD), a progressive, irreversible neurodegenerative disorder and the most common cause of dementia in the elderly. One of the most prominent risk factor for sporadic AD, carrying one or two aberrant copies of the apolipoprotein E (ApoE) ε4 alleles, closely links AD to lipids. Further, several lipid classes and fatty acids have been reported to be changed in the brain of AD-affected individuals. Interestingly, the observed lipid changes in the brain seem not only to be a consequence of the disease but also modulate Aβ generation. In line with these observations, protective lipids being able to decrease Aβ generation and also potential negative lipids in respect to AD were identified. Mechanistically, Aβ peptides are generated by sequential proteolytic processing of the amyloid precursor protein (APP) by β- and γ-secretase. The α-secretase appears to compete with β-secretase for the initial cleavage of APP, preventing Aβ production. All APP-cleaving secretases as well as APP are transmembrane proteins, further illustrating the impact of lipids on Aβ generation. Beside the pathological impact of Aβ, accumulating evidence suggests that Aβ and the APP intracellular domain (AICD) play an important role in regulating lipid homeostasis, either by direct effects or by affecting gene expression or protein stability of enzymes involved in the de novo synthesis of different lipid classes. This review summarizes the current literature addressing the complex bidirectional link between lipids and AD and APP processing including lipid alterations found in AD post mortem brains, lipids that alter APP processing and the physiological functions of Aβ and AICD in the regulation of several lipid metabolism pathways.

  7. APP Function and Lipids: A Bidirectional Link

    PubMed Central

    Grimm, Marcus O. W.; Mett, Janine; Grimm, Heike S.; Hartmann, Tobias

    2017-01-01

    Extracellular neuritic plaques, composed of aggregated amyloid-β (Aβ) peptides, are one of the major histopathological hallmarks of Alzheimer’s disease (AD), a progressive, irreversible neurodegenerative disorder and the most common cause of dementia in the elderly. One of the most prominent risk factor for sporadic AD, carrying one or two aberrant copies of the apolipoprotein E (ApoE) ε4 alleles, closely links AD to lipids. Further, several lipid classes and fatty acids have been reported to be changed in the brain of AD-affected individuals. Interestingly, the observed lipid changes in the brain seem not only to be a consequence of the disease but also modulate Aβ generation. In line with these observations, protective lipids being able to decrease Aβ generation and also potential negative lipids in respect to AD were identified. Mechanistically, Aβ peptides are generated by sequential proteolytic processing of the amyloid precursor protein (APP) by β- and γ-secretase. The α-secretase appears to compete with β-secretase for the initial cleavage of APP, preventing Aβ production. All APP-cleaving secretases as well as APP are transmembrane proteins, further illustrating the impact of lipids on Aβ generation. Beside the pathological impact of Aβ, accumulating evidence suggests that Aβ and the APP intracellular domain (AICD) play an important role in regulating lipid homeostasis, either by direct effects or by affecting gene expression or protein stability of enzymes involved in the de novo synthesis of different lipid classes. This review summarizes the current literature addressing the complex bidirectional link between lipids and AD and APP processing including lipid alterations found in AD post mortem brains, lipids that alter APP processing and the physiological functions of Aβ and AICD in the regulation of several lipid metabolism pathways. PMID:28344547

  8. Small-Sample Equating Using a Synthetic Linking Function

    ERIC Educational Resources Information Center

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

    2008-01-01

    This study addressed the sampling error and linking bias that occur with small samples in a nonequivalent groups anchor test design. We proposed a linking method called the synthetic function, which is a weighted average of the identity function and a traditional equating function (in this case, the chained linear equating function). Specifically,…

  9. 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…

  10. 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…

  11. Functional synergy of actin filament cross-linking proteins.

    PubMed

    Tseng, Yiider; Schafer, Benjamin W; Almo, Steven C; Wirtz, Denis

    2002-07-12

    The organization of filamentous actin (F-actin) in resilient networks is coordinated by various F-actin cross-linking proteins. The relative tolerance of cells to null mutations of genes that code for a single actin cross-linking protein suggests that the functions of those proteins are highly redundant. This apparent functional redundancy may, however, reflect the limited resolution of available assays in assessing the mechanical role of F-actin cross-linking/bundling proteins. Using reconstituted F-actin networks and rheological methods, we demonstrate how alpha-actinin and fascin, two F-actin cross-linking/bundling proteins that co-localize along stress fibers and in lamellipodia, could synergistically enhance the resilience of F-actin networks in vitro. These two proteins can generate microfilament arrays that "yield" at a strain amplitude that is much larger than each one of the proteins separately. F-actin/alpha-actinin/fascin networks display strain-induced hardening, whereby the network "stiffens" under shear deformations, a phenomenon that is non-existent in F-actin/fascin networks and much weaker in F-actin/alpha-actinin networks. Strain-hardening is further enhanced at high rates of deformation and high concentrations of actin cross-linking proteins. A simplified model suggests that the optimum results of the competition between the increased stiffness of bundles and their decreased density of cross-links. Our studies support a re-evaluation of the notion of functional redundancy among cytoskeletal regulatory proteins.

  12. OPTIMIZING LINKED PERCEPTUAL CLASS FORMATION AND TRANSFER OF FUNCTION

    PubMed Central

    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 woman's voice would occasion the selection of any picture of the woman and vice versa. In addition, after learning to name the woman in the presence of one picture, that name would be uttered when presented with all of the images of the woman's face and all of the sounds of her voice. This study involved 15 participants and sought to (a) maximize the percentage of participants who formed linked perceptual classes, and (b) determine whether those classes acted as transfer networks, that is, whether the discriminative function of one class member would generalize to other members of the class and not to members of a different class. The rate of emergence of each linked perceptual class was maximized by establishing a single class-linking conditional relation between the clearest member of one class used as a sample stimulus and the most ambiguous member of the other class used as a comparison stimulus. Class formation was demonstrated using the serial and programmed presentation of A′–B′ probes that consisted of untrained pairs of stimuli drawn from the A′ and B′ classes. Most participants showed immediate emergence of the two linked perceptual classes. The remaining participants showed delayed emergence following a second exposure to each originally error-producing probes. Once the linked perceptual classes had emerged, a differential response to a specific member of one perceptual class generalized mostly or completely to the other members of that linked class and rarely, if ever, to members of the other linked class. Thus, generalization did not depend on the specific class members that had been used for

  13. Functional polymer laminates from hyperthermal hydrogen induced cross-linking.

    PubMed

    Thompson, David B; Trebicky, Tomas; Crewdson, Patrick; McEachran, Matthew J; Stojcevic, Goran; Arsenault, Gilles; Lau, Woon M; Gillies, Elizabeth R

    2011-12-20

    The use of a hyperthermal hydrogen induced cross-linking process to prepare laminates comprising polypropylene, poly(isobutylene-co-isoprene), and poly(vinyl acetate) is described. In this new, milder alternative to conventional plasma techniques, neutral molecular hydrogen projectiles were used to create carbon radicals on impacted surfaces by collision-induced dissociation of C-H bonds, and this process was used to cross-link polymers on a polypropylene surface. It was demonstrated that multiple layers of cross-linked materials could be added, creating polymer laminates with each layer introducing new functionalities and properties. In particular, the present work shows that the process is largely nondestructive toward ester functionalities. First, the esters were grafted to become nonleachable. Then, the esters were subsequently hydrolyzed to convert the surface from hydrophobic to hydrophilic. Afterward, the esters could be recovered by simple esterification demonstrating that further chemical transformations were possible.

  14. 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.

  15. 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

  16. Linking biodiversity to ecosystem function: implications for conservation ecology.

    PubMed

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

    2000-02-01

    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

  17. Fluxomics links cellular functional analyses to whole-plant phenotyping.

    PubMed

    Salon, Christophe; Avice, Jean-Christophe; Colombié, Sophie; Dieuaide-Noubhani, Martine; Gallardo, Karine; Jeudy, Christian; Ourry, Alain; Prudent, Marion; Voisin, Anne-Sophie; Rolin, Dominique

    2017-04-01

    Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

    PubMed

    Yvon-Durocher, Gabriel; Allen, Andrew P

    2012-11-05

    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.

  19. Improving nonlinear modeling capabilities of functional link adaptive filters.

    PubMed

    Comminiello, Danilo; Scarpiniti, Michele; Scardapane, Simone; Parisi, Raffaele; Uncini, Aurelio

    2015-09-01

    The functional link adaptive filter (FLAF) represents an effective solution for online nonlinear modeling problems. In this paper, we take into account a FLAF-based architecture, which separates the adaptation of linear and nonlinear elements, and we focus on the nonlinear branch to improve the modeling performance. In particular, we propose a new model that involves an adaptive combination of filters downstream of the nonlinear expansion. Such combination leads to a cooperative behavior of the whole architecture, thus yielding a performance improvement, particularly in the presence of strong nonlinearities. An advanced architecture is also proposed involving the adaptive combination of multiple filters on the nonlinear branch. The proposed models are assessed in different nonlinear modeling problems, in which their effectiveness and capabilities are shown.

  20. Spatial Colocalization and Functional Link of Purinosomes with Mitochondria

    PubMed Central

    French, Jarrod B.; Jones, Sara A.; Deng, Huayun; Pedley, Anthony M.; Kim, Doory; Chan, Chung Yu; Hu, Haibei; Pugh, Raymond J.; Zhao, Hong; Zhang, Youxin; Huang, Tony Jun; Fang, Ye; Zhuang, Xiaowei; Benkovic, Stephen J.

    2016-01-01

    Purine biosynthetic enzymes organize into dynamic cellular bodies called purinosomes. Little is known about the spatiotemporal control of these structures. Using super-resolution microscopy, we demonstrated that purinosomes colocalized with mitochondria, and these results were supported by isolation of purinosome enzymes with mitochondria. Moreover, the number of purinosome containing cells responded to dysregulation of mitochondrial function and metabolism. To explore the role of intracellular signaling, we performed a kinome screen using a label-free assay and identified that mTOR influenced purinosome assembly. mTOR inhibition disrupted purinosome-mitochondria colocalization and suppressed purinosome formation stimulated by mitochondria dysregulation. Collectively, our data suggests an mTOR-mediated link between purinosomes and mitochondria and suggests a general means by which mTOR regulates nucleotide metabolism by spatiotemporal control over protein association. PMID:26912862

  1. Link prediction boosted psychiatry disorder classification for functional connectivity network

    NASA Astrophysics Data System (ADS)

    Li, Weiwei; Mei, Xue; Wang, Hao; Zhou, Yu; Huang, Jiashuang

    2017-02-01

    Functional connectivity network (FCN) is an effective tool in psychiatry disorders classification, and represents cross-correlation of the regional blood oxygenation level dependent signal. However, FCN is often incomplete for suffering from missing and spurious edges. To accurate classify psychiatry disorders and health control with the incomplete FCN, we first `repair' the FCN with link prediction, and then exact the clustering coefficients as features to build a weak classifier for every FCN. Finally, we apply a boosting algorithm to combine these weak classifiers for improving classification accuracy. Our method tested by three datasets of psychiatry disorder, including Alzheimer's Disease, Schizophrenia and Attention Deficit Hyperactivity Disorder. The experimental results show our method not only significantly improves the classification accuracy, but also efficiently reconstructs the incomplete FCN.

  2. 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.

  3. 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.

  4. Nrf2 links epidermal barrier function with antioxidant defense

    PubMed Central

    Schäfer, Matthias; Farwanah, Hany; Willrodt, Ann-Helen; Huebner, Aaron J; Sandhoff, Konrad; Roop, Dennis; Hohl, Daniel; Bloch, Wilhelm; Werner, Sabine

    2012-01-01

    The skin provides an efficient permeability barrier and protects from microbial invasion and oxidative stress. Here, we show that these essential functions are linked through the Nrf2 transcription factor. To test the hypothesis that activation of Nrf2 provides skin protection under stress conditions, we determined the consequences of pharmacological or genetic activation of Nrf2 in keratinocytes. Surprisingly, mice with enhanced Nrf2 activity in keratinocytes developed epidermal thickening, hyperkeratosis and inflammation resembling lamellar ichthyosis. This resulted from upregulation of the cornified envelope proteins small proline-rich proteins (Sprr) 2d and 2h and of secretory leukocyte peptidase inhibitor (Slpi), which we identified as novel Nrf2 targets in keratinocytes. Since Sprrs are potent scavengers of reactive oxygen species and since Slpi has antimicrobial activities, their upregulation contributes to Nrf2's protective function. However, it also caused corneocyte fragility and impaired desquamation, followed by alterations in the epidermal lipid barrier, inflammation and overexpression of mitogens that induced keratinocyte hyperproliferation. These results identify an unexpected role of Nrf2 in epidermal barrier function, which needs to be considered for pharmacological use of Nrf2 activators. PMID:22383093

  5. Exploring the link between character, personality disorder, and neuropsychological function.

    PubMed

    Bergvall, A H; Nilsson, T; Hansen, S

    2003-11-01

    Personality deviations and deficits in cognitive executive function are common among forensic populations. The present study on incarcerated offenders explored whether there are links between the two domains. Personality was assessed using the Temperament and Character Inventory (TCI). Neuropsychological performance, including visual working memory, attentional set-shifting and planning, were tested with the Cambridge Neuropsychological Test Automated Battery (CANTAB). Subjects with personality disorders scored high on harm avoidance, and low on self-directedness and cooperativeness. Personality disordered offenders did not differ from the comparison groups (offenders without personality disorder, and non-criminal controls) with regard to CANTAB measures of visual working memory (delayed matching to sample, spatial working memory) and planning (Stockings of Cambridge), but they made a larger number of errors on the attentional set-shifting task. Dimensional analysis of the personality and neuropsychological variables revealed significant associations between self-directedness and cooperativeness on the one hand, and attentional set-shifting on the other. Intellectually disabled, non-criminal individuals (marginal mental retardation) who performed poorly on attentional set-shifting also scored low on self-directedness and cooperativeness. The results indicate that poor development of certain personality traits may be associated with deficits in neuropsychological functioning.

  6. Hypoxia and Brittlestars: Linking Physiology and Behaviour to Ecosystem Function.

    NASA Astrophysics Data System (ADS)

    Calder-Potts, R.; Spicer, J. I.; Calosi, P.; Findlay, H. S.; Widdicombe, S.

    2016-02-01

    Hypoxic events are increasing in frequency and duration, particularly in areas susceptible to eutrophication. Such events pose a growing threat to the health and function of marine ecosystems by altering large-scale biological and ecological processes. Linking how hypoxia impacts upon key benthic invertebrates, both in terms of their physiology and behaviour, to the disruption of ecosystem function and services is of primary importance. Station L4 forms part of the Western Channel Observatory, a long-standing oceanic time-series and marine biodiversity reference site. Recent observations indicate that L4 has experienced unusually large and long-lived spring blooms and seasonally driven periods of reduced O2 levels altering benthic community composition. Using a mesocosm experiment, we investigated the effects of short-term moderate hypoxia (14 d, 3.59 mg O2 L-1) and organism density (5, 9, 13, 17, and 21 ind. per aquarium) on the aerobic metabolism and reproductive biology of a key infaunal species, the brittlestar Amphiura filiformis. In addition, bioturbation parameters were recorded as a measure of organism activity, alongside nutrient flux measurements as a proxy for ecosystem function effects. Exposure to hypoxia resulted in reduced metabolism, and caused a delay in metabolic recovery rates once normoxic (8.09 mg O2 L-1) conditions were re-established. Additionally, hypoxia also caused a delay in females' reproductive cell development, smaller oocyte diameters, and a greater number of pre-vitellogenic oocytes present within the ovaries. Interestingly, while organism density had no significant effect on the physiological or histological traits examined, it did have a positive effect on bioturbation activity, an effect which was reduced by hypoxia. The observed disruptions to metabolic rates, reproductive biology and organisms' activity will be further discussed in terms of their ecological implications and possible long-term effects if repeated hypoxic events

  7. 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

  8. Visual Function in Carriers of X-Linked Retinitis Pigmentosa.

    PubMed

    Comander, Jason; Weigel-DiFranco, Carol; Sandberg, Michael A; Berson, Eliot L

    2015-09-01

    To determine the frequency and severity of visual function loss in female carriers of X-linked retinitis pigmentosa (XLRP). Case series. Two hundred seventy-six XLRP carriers with cross-sectional data (n = 242) and longitudinal data (n = 34; median follow-up, 16 years; follow-up range, 3-37 years). Half of the carriers were from RPGR- or RP2-genotyped families. Retrospective medical records review. Visual acuities, visual field areas, final dark adaptation thresholds, and full-field electroretinography (ERG) responses to 0.5-Hz and 30-Hz flashes. In genotyped families, 40% of carriers showed a baseline abnormality on at least 1 of 3 psychophysical tests. There was a wide range of function among carriers. For example, 3 of 121 (2%) genotyped carriers were legally blind because of poor visual acuity, some as young as 35 years. Visual fields were less affected than visual acuity. In all carriers, the average ERG amplitude to 30-Hz flashes was approximately 50% of normal, and the average exponential rate of amplitude loss over time was half that of XLRP males (3.7%/year vs. 7.4%/year, respectively). Among obligate carriers with affected fathers, sons, or both, 53 of 55 (96%) had abnormal baseline ERG results. Some carriers who initially had completely normal fundi in both eyes went on to experience moderately decreased vision, although not legal blindness. Among carriers with RPGR mutations, those with mutations in ORF15, compared with those in exons 1-14, had worse final dark adaptation thresholds and lower 0.5-Hz and 30-Hz ERG amplitudes. Most carriers of XLRP had mildly or moderately reduced visual function but rarely became legally blind. In most cases, obligate carriers could be identified by ERG testing. Carriers of RPGR ORF15 mutations tended to have worse visual function than carriers of RPGR exon 1 through 14 mutations. Because XLRP carrier ERG amplitudes and decay rates over time were on average half of those of affected men, these observations were

  9. 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

  10. 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…

  11. 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.

  12. Testing the Link between Functional Diversity and Ecosystem Functioning in a Minnesota Grassland Experiment

    PubMed Central

    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. PMID:23300787

  13. Mentalizing functions provide a conceptual link of brain function and social cognition in major mental disorders.

    PubMed

    Schnell, Knut

    2014-01-01

    The review presents a research perspective that defines mentalizing functions as a very promising topic to bridge psychopathology and neurobiological foundations of mental disorders. However, the high diversity of existing observations in mentalizing research calls for a structured assessment of functional mentalizing subdomains. A notable problem is the overlap of functional systems involved in mentalizing and emotion processing. A proposed solution is to conceptualize mentalizing functions due to their content (visuospatial vs. emotional) perspective and substrates (cognitive or explicit signals). This conceptual organization is mirrored in functional imaging experiments dissociating anteromedial and posterolateral brain regions, especially the involvement of the medial prefrontal cortex in mentalizing emotions and the temporoparietal cortex in visuospatial perspective taking. The present state and perspectives of mentalizing research are demonstrated in two major fields of mental disorders, depression and schizophrenia. In depression the existent contradictory findings demand a control of cognitive impairments, which are frequently associated with depressive disorders. In schizophrenia there is already consistent evidence that defines mentalizing functions as promising endophenotype, which can possibly link psychopathology to its neurobiological foundations.

  14. 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…

  15. 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…

  16. Linking structural features of protein complexes and biological function

    PubMed Central

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-01-01

    Protein–protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure–function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. PMID:26131659

  17. Linking structural dynamics and functional diversity in asymmetric catalysis.

    PubMed

    Nojiri, Akihiro; Kumagai, Naoya; Shibasaki, Masakatsu

    2009-03-18

    Proteins, the functional molecules in biological systems, are sophisticated chemical devices that have evolved over billions of years. Their function is intimately related to their three-dimensional structure and elegantly regulated by conformational changes through allosteric regulators and a number of reversible or unidirectional post-translational modifications. This functional diversification in response to external stimuli allows for an orderly and timely progression of intra- and extracellular events. In contrast, enantioselective catalysts generally exhibit limited conformational flexibility and thereby exert a single specific function. Exploiting the features of conformationally flexible asymmetric ligands and the variable coordination patterns of rare earth metals, we demonstrate dynamic structural and functional changes of a catalyst in asymmetric catalysis, leading to two distinct reaction outcomes in a single flask.

  18. 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

  19. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. 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. © 2010 Blackwell Publishing Ltd/CNRS.

  1. 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

  2. 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.

  3. Synthesis of chiral alpha-amino aldehydes linked by their amine function to solid support.

    PubMed

    Cantel, Sonia; Heitz, Annie; Martinez, Jean; Fehrentz, Jean-Alain

    2004-09-01

    The anchoring of an alpha-amino-acid derivative by its amine function on to a solid support allows some chemical reactions starting from the carboxylic acid function. This paper describes the preparation of alpha-amino aldehydes linked to the support by their amine function. This was performed by reduction with LiAlH4 of the corresponding Weinreb amide linked to the resin. The aldehydes obtained were then involved in Wittig or reductive amination reactions. In addition, the linked Weinreb amide was reacted with methylmagnesium bromide to yield the corresponding ketone. After cleavage from the support, the compounds were obtained in good to excellent yields and characterized.

  4. New link between conceptual density functional theory and electron delocalization.

    PubMed

    Matito, Eduard; Putz, Mihai V

    2011-11-17

    In this paper we give a new definition of the softness kernel based on the exchange-correlation density. This new kernel is shown to correspond to the change of electron fluctuation upon external perturbation, thus helping to bridge the gap between conceptual density functional theory and some tools describing electron localization in molecules. With the aid of a few computational calculations on diatomics we illustrate the performance of this new computational tool.

  5. 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…

  6. 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…

  7. Desmin Cytoskeleton Linked to Muscle Mitochondrial Distribution and Respiratory Function

    PubMed Central

    Milner, Derek J.; Mavroidis, Manolis; Weisleder, Noah; Capetanaki, Yassemi

    2000-01-01

    Ultrastructural studies have previously suggested potential association of intermediate filaments (IFs) with mitochondria. Thus, we have investigated mitochondrial distribution and function in muscle lacking the IF protein desmin. Immunostaining of skeletal muscle tissue sections, as well as histochemical staining for the mitochondrial marker enzymes cytochrome C oxidase and succinate dehydrogenase, demonstrate abnormal accumulation of subsarcolemmal clumps of mitochondria in predominantly slow twitch skeletal muscle of desmin-null mice. Ultrastructural observation of desmin-null cardiac muscle demonstrates in addition to clumping, extensive mitochondrial proliferation in a significant fraction of the myocytes, particularly after work overload. These alterations are frequently associated with swelling and degeneration of the mitochondrial matrix. Mitochondrial abnormalities can be detected very early, before other structural defects become obvious. To investigate related changes in mitochondrial function, we have analyzed ADP-stimulated respiration of isolated muscle mitochondria, and ADP-stimulated mitochondrial respiration in situ using saponin skinned muscle fibers. The in vitro maximal rates of respiration in isolated cardiac mitochondria from desmin-null and wild-type mice were similar. However, mitochondrial respiration in situ is significantly altered in desmin-null muscle. Both the maximal rate of ADP-stimulated oxygen consumption and the dissociation constant (Km) for ADP are significantly reduced in desmin-null cardiac and soleus muscle compared with controls. Respiratory parameters for desmin-null fast twitch gastrocnemius muscle were unaffected. Additionally, respiratory measurements in the presence of creatine indicate that coupling of creatine kinase and the adenine translocator is lost in desmin-null soleus muscle. This coupling is unaffected in cardiac muscle from desmin-null animals. All of these studies indicate that desmin IFs play a significant

  8. Lung morphometry: the link between structure and function.

    PubMed

    Weibel, Ewald R

    2017-03-01

    The study of the structural basis of gas exchange function in the lung depends on the availability of quantitative information that concerns the structures establishing contact between the air in the alveoli and the blood in the alveolar capillaries, which can be entered into physiological equations for predicting oxygen uptake. This information is provided by morphometric studies involving stereological methods and allows estimates of the pulmonary diffusing capacity of the human lung that agree, in experimental studies, with the maximal oxygen consumption. The basis for this "machine lung" structure lies in the complex design of the cells building an extensive air-blood barrier with minimal cell mass.

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

    PubMed Central

    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.

    2015-01-01

    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. PMID:24646613

  10. 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. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Functional analysis of RYR1 variants linked to malignant hyperthermia

    PubMed Central

    Stephens, Jeremy; Schiemann, Anja H.; Roesl, Cornelia; Miller, Dorota; Massey, Sean; Pollock, Neil; Bulger, Terasa; Stowell, Kathryn

    2016-01-01

    ABSTRACT Malignant hyperthermia manifests as a rapid and sustained rise in temperature in response to pharmacological triggering agents, e.g. inhalational anesthetics and the muscle relaxant suxamethonium. Other clinical signs include an increase in end-tidal CO2, increased O2 consumption, as well as tachycardia, and if untreated a malignant hyperthermia episode can result in death. The metabolic changes are caused by dysregulation of skeletal muscle Ca2+ homeostasis, resulting from a defective ryanodine receptor Ca2+ channel, which resides in the sarcoplasmic reticulum and controls the flux of Ca2+ ions from intracellular stores to the cytoplasm. Most genetic variants associated with susceptibility to malignant hyperthermia occur in the RYR1 gene encoding the ryanodine receptor type 1. While malignant hyperthermia susceptibility can be diagnosed by in vitro contracture testing of skeletal muscle biopsy tissue, it is advantageous to use DNA testing. Currently only 35 of over 400 potential variants in RYR1 have been classed as functionally causative of malignant hyperthermia and thus can be used for DNA diagnostic tests. Here we describe functional analysis of 2 RYR1 variants (c. 7042_7044delCAG, p.ΔGlu2348 and c.641C>T, p.Thr214Met) that occur in the same malignant hyperthermia susceptible family. The p.Glu2348 deletion, causes hypersensitivity to ryanodine receptor agonists using in vitro analysis of cloned human RYR1 cDNA expressed in HEK293T cells, while the Thr214Met substitution, does not appear to significantly alter sensitivity to agonist in the same system. We suggest that the c. 7042_7044delCAG, p.ΔGlu2348 RYR1 variant could be added to the list of diagnostic mutations for susceptibility to malignant hyperthermia. PMID:27857962

  12. Functional analysis of RYR1 variants linked to malignant hyperthermia.

    PubMed

    Stephens, Jeremy; Schiemann, Anja H; Roesl, Cornelia; Miller, Dorota; Massey, Sean; Pollock, Neil; Bulger, Terasa; Stowell, Kathryn

    2016-01-01

    Malignant hyperthermia manifests as a rapid and sustained rise in temperature in response to pharmacological triggering agents, e.g. inhalational anesthetics and the muscle relaxant suxamethonium. Other clinical signs include an increase in end-tidal CO2, increased O2 consumption, as well as tachycardia, and if untreated a malignant hyperthermia episode can result in death. The metabolic changes are caused by dysregulation of skeletal muscle Ca(2+) homeostasis, resulting from a defective ryanodine receptor Ca(2+) channel, which resides in the sarcoplasmic reticulum and controls the flux of Ca(2+) ions from intracellular stores to the cytoplasm. Most genetic variants associated with susceptibility to malignant hyperthermia occur in the RYR1 gene encoding the ryanodine receptor type 1. While malignant hyperthermia susceptibility can be diagnosed by in vitro contracture testing of skeletal muscle biopsy tissue, it is advantageous to use DNA testing. Currently only 35 of over 400 potential variants in RYR1 have been classed as functionally causative of malignant hyperthermia and thus can be used for DNA diagnostic tests. Here we describe functional analysis of 2 RYR1 variants (c. 7042_7044delCAG, p.ΔGlu2348 and c.641C>T, p.Thr214Met) that occur in the same malignant hyperthermia susceptible family. The p.Glu2348 deletion, causes hypersensitivity to ryanodine receptor agonists using in vitro analysis of cloned human RYR1 cDNA expressed in HEK293T cells, while the Thr214Met substitution, does not appear to significantly alter sensitivity to agonist in the same system. We suggest that the c. 7042_7044delCAG, p.ΔGlu2348 RYR1 variant could be added to the list of diagnostic mutations for susceptibility to malignant hyperthermia.

  13. 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.

  14. 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.

  15. Using ecological production functions to link ecological processes to ecosystem services.

    EPA Science Inventory

    Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively ...

  16. Using ecological production functions to link ecological processes to ecosystem services.

    EPA Science Inventory

    Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively ...

  17. 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…

  18. 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…

  19. Transceptors as a functional link of transporters and receptors

    PubMed Central

    Diallinas, George

    2017-01-01

    Cells need to communicate with their environment in order to obtain nutrients, grow, divide and respond to signals related to adaptation in changing physiological conditions or stress. A very basic question in biology is how cells, especially of those organisms living in rapidly changing habitats, sense their environment. Apparently, this question is of particular importance to all free-living microorganisms. The critical role of receptors, transporters and channels, transmembrane proteins located in the plasma membrane of all types of cells, in signaling environmental changes is well established. A relative newcomer in environment sensing are the so called transceptors, membrane proteins that possess both solute transport and receptor-like signaling activities. Now, the transceptor concept is further enlarged to include micronutrient sensing via the iron and zinc high-affinity transporters of Saccharomyces cerevisiae. Interestingly, what seems to underline the transport and/or sensing function of receptors, transporters and transceptors is ligand-induced conformational alterations recognized by downstream intracellular effectors. PMID:28357392

  20. Assessment of protein function following cross-linking by alpha-dicarbonyls.

    PubMed

    Miller, Antonia G; Gerrard, Juliet A

    2005-06-01

    Protein cross-linking via the Maillard reaction with alpha-dicarbonyl compounds has been the subject of intense scrutiny in the literature. We report here a study of the impact of this cross-linking on enzyme function. Protein function following glycation was examined by treating ribonuclease A with methylglyoxal, glyoxal, and diacetyl, which cross-linked the enzyme and impaired its activity. The effects of two reported Maillard reaction inhibitors, aminoguanidine and 3,5-dimethylpyrazole-1-carboxamidine, on the cross-linking reaction were assessed, with a parallel measurement of the effect on enzyme activity. The results demonstrate that preventing protein cross-linking does not necessarily preserve enzyme activity. These results cast doubt on the likely efficacy of some purported antiaging compounds in vivo.

  1. 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

  2. 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. © 2015, The International Biometric Society.

  3. 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

  4. Tyrosine-Selective Functionalization for Bio-Orthogonal Cross-Linking of Engineered Protein Hydrogels.

    PubMed

    Madl, Christopher M; Heilshorn, Sarah C

    2017-03-15

    Engineered protein hydrogels have shown promise as artificial extracellular matrix materials for the 3D culture of stem cells due to the ability to decouple hydrogel biochemistry and mechanics. The modular design of these proteins allows for incorporation of various bioactive sequences to regulate cellular behavior. However, the chemistry used to cross-link the proteins into hydrogels can limit what bioactive sequences can be incorporated, in order to prevent nonspecific cross-linking within the bioactive region. Bio-orthogonal cross-linking chemistries may allow for the incorporation of any arbitrary bioactive sequence, but site-selective and scalable incorporation of bio-orthogonal reactive groups such as azides that do not rely on commonly used amine-reactive chemistry is often challenging. In response, we have optimized the reaction of an azide-bearing 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) with engineered elastin-like proteins (ELPs) to selectively azide-functionalize tyrosine residues within the proteins. The PTAD-azide functionalized ELPs cross-link with bicyclononyne (BCN) functionalized ELPs via the strain-promoted azide-alkyne cycloaddition (SPAAC) reaction to form hydrogels. Human mesenchymal stem cells and murine neural progenitor cells encapsulated within these hydrogels remain highly viable and maintain their phenotypes in culture. Tyrosine-specific modification may expand the number of bioactive sequences that can be designed into protein-engineered materials by permitting incorporation of lysine-containing sequences without concern for nonspecific cross-linking.

  5. Ecosystem functions across trophic levels are linked to functional and phylogenetic diversity.

    PubMed

    Thompson, Patrick L; Davies, T Jonathan; Gonzalez, Andrew

    2015-01-01

    In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures.

  6. Ecosystem Functions across Trophic Levels Are Linked to Functional and Phylogenetic Diversity

    PubMed Central

    Thompson, Patrick L.; Davies, T. Jonathan; Gonzalez, Andrew

    2015-01-01

    In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures. PMID:25693188

  7. Protein functional links in Trypanosoma brucei, identified by gene fusion analysis

    PubMed Central

    2011-01-01

    Background Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit protein complex, or in a metabolic pathway. Gene fusion analysis has been used to identify protein functional links in prokaryotes as well as in eukaryotic model organisms, such as yeast and Drosophila. Results In this study we have extended this approach to include a number of recently sequenced protists, four of which are pathogenic, to identify fusion linked proteins in Trypanosoma brucei, the causative agent of African sleeping sickness. We have also examined the evolution of the gene fusion events identified, to determine whether they can be attributed to fusion or fission, by looking at the conservation of the fused genes and of the individual component genes across the major eukaryotic and prokaryotic lineages. We find relatively limited occurrence of gene fusions/fissions within the protist lineages examined. Our results point to two trypanosome-specific gene fissions, which have recently been experimentally confirmed, one fusion involving proteins involved in the same metabolic pathway, as well as two novel putative functional links between fusion-linked protein pairs. Conclusions This is the first study of protein functional links in T. brucei identified by gene fusion analysis. We have used strict thresholds and only discuss results which are highly likely to be genuine and which either have already been or can be experimentally verified. We discuss the possible impact of the identification of these novel putative protein-protein interactions, to the development of new trypanosome therapeutic drugs. PMID:21729286

  8. 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…

  9. 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…

  10. The Link between Emotion Regulation, Social Functioning, and Depression in Boys with ASD

    ERIC Educational Resources Information Center

    Pouw, Lucinda B. C.; Rieffe, Carolien; Stockmann, Lex; Gadow, Kenneth D.

    2013-01-01

    Purpose: Symptoms of depression are common in children and adolescents with an autism spectrum disorder (ASD), but information about underlying developmental factors is limited. Depression is often linked to aspects of emotional functioning such as coping strategies, but in children with ASD difficulties with social interactions are also a likely…

  11. The Link between Emotion Regulation, Social Functioning, and Depression in Boys with ASD

    ERIC Educational Resources Information Center

    Pouw, Lucinda B. C.; Rieffe, Carolien; Stockmann, Lex; Gadow, Kenneth D.

    2013-01-01

    Purpose: Symptoms of depression are common in children and adolescents with an autism spectrum disorder (ASD), but information about underlying developmental factors is limited. Depression is often linked to aspects of emotional functioning such as coping strategies, but in children with ASD difficulties with social interactions are also a likely…

  12. Imbalanced Functional Link between Valuation Networks in Abstinent Heroin-Dependent Subjects

    PubMed Central

    Xie, Chunming; Shao, Yongcong; Ma, Lin; Zhai, Tianye; Ye, Enmao; Fu, Liping; Bi, Guohua; Chen, Gang; Cohen, Alex; Li, Wenjun; Chen, Guangyu; Yang, Zheng; Li, Shi-Jiang

    2015-01-01

    Using neuroeconomic approaches, our findings demonstrate that the underlying duality of the β-δ discounting networks that jointly influence valuation is impaired to a pathogenic state in abstinent heroin dependents. The imbalanced functional link between the β-δ networks for valuation may orchestrate the irrational choice in drug addiction. PMID:23207652

  13. 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.

  14. Survey of Quantification and Distance Functions Used for Internet-based Weak-link Sociological Phenomena

    DTIC Science & Technology

    2016-03-01

    Distribution Unlimited Final Report on "Survey of Quantification and Distance Functions Used for Internet -based Weak-link Sociological Phenomena...journals: Number of Papers published in non peer-reviewed journals: Final Report on "Survey of Quantification and Distance Functions Used for Internet ...improve the efficiency of the computation in hoping to speed up the search. Due to the explosive increase of the webpages and the Internet surfers

  15. 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

  16. 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) .

  17. Linking morphological and functional variability in hand movement and silent reading.

    PubMed

    Sun, Z Y; Pinel, P; Rivière, D; Moreno, A; Dehaene, S; Mangin, J-F

    2016-09-01

    It is generally accepted in neuroscience that anatomy and function go hand in hand. Accordingly, a local morphological variability could lead to a corresponding functional variability. In this study, we tested this hypothesis by linking the variability of the cortical folding pattern of 252 right-handed subjects to the localization or the pattern of functional activations induced by hand motion or silent reading. Three regions are selected: the central sulcus, the precentral sulcus and the superior temporal sulcus (STS). "Essential morphological variability traits" are identified using a method building upon multidimensional scaling. The link between variability in anatomy and function is confirmed by the perfect match between the central sulcus morphological "hand knob" and the corresponding motor activation: as the location of the hand knob moves more or less dorsally along the central sulcus, the motor hand activation moves accordingly. Furthermore, the size of the left hand activation in the right hemisphere is correlated with the knob location in the central sulcus. A new link between functional and morphological variability is discovered relative to the location of a premotor activation induced by silent reading. While this reading activation is located next to the wall of the central sulcus when the hand knob has a ventral positioning, it is pushed into a deep gyrus interrupting the precentral sulcus when the knob is more dorsal. Finally, it is shown that the size of the reading activation along the STS is larger when the posterior branches are less developed.

  18. Linking functional group richness and ecosystem functions of dung beetles: an experimental quantification.

    PubMed

    Milotić, Tanja; Quidé, Stijn; Van Loo, Thomas; Hoffmann, Maurice

    2017-01-01

    Dung beetles form an insect group that fulfils important functions in terrestrial ecosystems throughout the world. These include nutrient cycling through dung removal, soil bioturbation, plant growth, secondary seed dispersal and parasite control. We conducted field experiments at two sites in the northern hemisphere temperate region in which dung removal and secondary seed dispersal were assessed. Dung beetles were classified in three functional groups, depending on their size and dung manipulation method: dwellers, large and small tunnelers. Other soil inhabiting fauna were included as a fourth functional group. Dung removal and seed dispersal by each individual functional group and combinations thereof were estimated in exclusion experiments using different dung types. Dwellers were the most diverse and abundant group, but tunnelers were dominant in terms of biomass. All dung beetle functional groups had a clear preference for fresh dung. The ecosystem services in dung removal and secondary seed dispersal provided by dung beetles were significant and differed between functional groups. Although in absolute numbers more dwellers were found, large tunnelers were disproportionally important for dung burial and seed removal. In the absence of dung beetles, other soil inhabiting fauna, such as earthworms, partly took over the dung decomposing role of dung beetles while most dung was processed when all native functional groups were present. Our results, therefore, emphasize the need to conserve functionally complete dung ecosystems to maintain full ecosystem functioning.

  19. Giving meaning to measure: linking self-reported fatigue and function to performance of everyday activities.

    PubMed

    Mallinson, Trudy; Cella, David; Cashy, John; Holzner, Bernhard

    2006-03-01

    Fatigue, a common symptom of cancer patients, particularly those on active treatment, is generally evaluated using self-report methods, yet it remains unclear how self-reported fatigue scores relate to performance of daily activities. This study examines the relationships among self-reported and performance-based measures of function in patients receiving chemotherapy (CT) to link self-reported fatigue measures to self-report and performance-based measures of function. Self-reported fatigue using the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) and self-reported physical function using the physical function 10 subscale of the Short Form 36 (SF-36) (PF-10) were measured in 64 patients within 2 weeks of beginning CT (n=64) and after three cycles of CT (n=48). Motor and cognitive functions were captured using five self-reported and seven observed-performance measures at each time point. Significant correlations between self-reported and observed measures ranged from 0.30 to 0.71. Self-reported fatigue correlated (0.30-0.45) with performance-based function. FACIT-F scores in the range of 30 and below and PF-10 scores in the range of 50 and below were related to an increased difficulty performing everyday activities. Observed measures of physical performance correlate moderately with self-reported fatigue and self-reported physical function. These relationships enable one to begin linking fatigue scores directly to a person's ability to perform everyday activities.

  20. Developing the group mind through functional subgrouping: linking systems-centered training (SCT) and interpersonal neurobiology.

    PubMed

    Gantt, Susan P; Agazarian, Yvonne M

    2010-10-01

    This article introduces the systems-centered concept of the "group mind" by linking systems-centered thinking and interpersonal neurobiology, building on Siegel's definition of mind as the process of regulating the flow of energy and information. Functional subgrouping, the systems-centered group method for resolving conflicts, discriminates and integrates the flow of energy and information within and between group members, subgroups, and the group-as-a-whole, thus potentiating survival, development, and transformation. This article uses the interpersonal neurobiological framework to discuss functional subgrouping as a tool for developing the group mind: considering how functional subgrouping facilitates emotional regulation, creates a secure relational context, and potentiates neural integration.

  1. 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

  2. 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

  3. Docosahexaenoic acid and cognitive function: Is the link mediated by the autonomic nervous system?

    PubMed Central

    Gustafson, Kathleen M.; Colombo, John; Carlson, Susan E.

    2013-01-01

    Docosahexaenoic acid is a long-chain polyunsaturated fatty acid that is found in large quantity in the brain and which has repeatedly been observed to be related in positive ways to both cognitive function and cardiovascular health. The mechanisms through which docosahexaenoic acid affects cognition are not well understood, but in this article, we propose a hypothesis that integrates the positive effects of docosahexaenoic acid in the cognitive and cardiovascular realms through the autonomic nervous system. The autonomic nervous system is known to regulate vital functions such as heart rate and respiration, and has also been linked to basic cognitive components related to arousal and attention. We review the literature from this perspective, and delineate the predictions generated by the hypothesis. In addition, we provide new data showing a link between docosahexaenoic acid and fetal heart rate that is consistent with the hypothesis. PMID:18930644

  4. 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

  5. Pulmonary function and adverse cardiovascular outcomes: Can cardiac function explain the link?

    PubMed

    Burroughs Peña, Melissa S; Dunning, Allison; Schulte, Phillip J; Durheim, Michael T; Kussin, Peter; Checkley, William; Velazquez, Eric J

    2016-12-01

    The complex interaction between pulmonary function, cardiac function and adverse cardiovascular events has only been partially described. We sought to describe the association between pulmonary function with left heart structure and function, all-cause mortality and incident cardiovascular hospitalization. This study is a retrospective analysis of patients evaluated in a single tertiary care medical center. We used multivariable linear regression analyses to examine the relationship between FVC and FEV1 with left ventricular ejection fraction (LVEF), left ventricular internal dimension in systole and diastole (LVIDS, LVIDD) and left atrial diameter, adjusting for baseline characteristics, right ventricular function and lung hyperinflation. We also used Cox proportional hazards models to examine the relationship between FVC and FEV1 with all-cause mortality and cardiac hospitalization. A total of 1807 patients were included in this analysis with a median age of 61 years and 50% were female. Decreased FVC and FEV1 were both associated with decreased LVEF. In individuals with FVC less than 2.75 L, decreased FVC was associated with increased all-cause mortality after adjusting for left and right heart echocardiographic variables (hazard ratio [HR] 0.49, 95% CI 0.29, 0.82, respectively). Decreased FVC was associated with increased cardiac hospitalization after adjusting for left heart size (HR 0.80, 95% CI 0.67, 0.96), even in patients with normal LVEF (HR 0.75, 95% CI 0.57, 0.97). In a tertiary care center reduced pulmonary function was associated with adverse cardiovascular events, a relationship that is not fully explained by left heart remodeling or right heart dysfunction. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Link functions in multi-locus genetic models: implications for testing, prediction, and interpretation.

    PubMed

    Clayton, David

    2012-05-01

    "Complex" diseases are, by definition, influenced by multiple causes, both genetic and environmental, and statistical work on the joint action of multiple risk factors has, for more than 40 years, been dominated by the generalized linear model (GLM). In genetics, models for dichotomous traits have traditionally been approached via the model of an underlying, normally distributed, liability. This corresponds to the GLM with binomial errors and a probit link function. Elsewhere in epidemiology, however, the logistic regression model, a GLM with logit link function, has been the tool of choice, largely because of its convenient properties in case-control studies. The choice of link function has usually been dictated by mathematical convenience, but it has some important implications in (a) the choice of association test statistic in the presence of existing strong risk factors, (b) the ability to predict disease from genotype given its heritability, and (c) the definition, and interpretation of epistasis (or epistacy). These issues are reviewed, and a new association test proposed.

  7. 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.

  8. Oxidative stress modulates mitochondrial failure and cyclophilin D function in X-linked adrenoleukodystrophy.

    PubMed

    López-Erauskin, Jone; Galino, Jorge; Bianchi, Patrizia; Fourcade, Stéphane; Andreu, Antoni L; Ferrer, Isidre; Muñoz-Pinedo, Cristina; Pujol, Aurora

    2012-12-01

    A common process associated with oxidative stress and severe mitochondrial impairment is the opening of the mitochondrial permeability transition pore, as described in many neurodegenerative diseases. Thus, inhibition of mitochondrial permeability transition pore opening represents a potential target for inhibiting mitochondrial-driven cell death. Among the mitochondrial permeability transition pore components, cyclophilin D is the most studied and has been found increased under pathological conditions. Here, we have used in vitro and in vivo models of X-linked adrenoleukodystrophy to investigate the relationship between the mitochondrial permeability transition pore opening and redox homeostasis. X-linked adrenoleukodystrophy is a neurodegenerative condition caused by loss of function of the peroxisomal ABCD1 transporter, in which oxidative stress plays a pivotal role. In this study, we provide evidence of impaired mitochondrial metabolism in a peroxisomal disease, as fibroblasts in patients with X-linked adrenoleukodystrophy cannot survive when forced to rely on mitochondrial energy production, i.e. on incubation in galactose. Oxidative stress induced under galactose conditions leads to mitochondrial damage in the form of mitochondrial inner membrane potential dissipation, ATP drop and necrotic cell death, together with increased levels of oxidative modifications in cyclophilin D protein. Moreover, we show increased expression levels of cyclophilin D in the affected zones of brains in patients with adrenomyeloneuropathy, in spinal cord of a mouse model of X-linked adrenoleukodystrophy (Abcd1-null mice) and in fibroblasts from patients with X-linked adrenoleukodystrophy. Notably, treatment with antioxidants rescues mitochondrial damage markers in fibroblasts from patients with X-linked adrenoleukodystrophy, including cyclophilin D oxidative modifications, and reverses cyclophilin D induction in vitro and in vivo. These findings provide mechanistic insight into the

  9. Oxidative stress modulates mitochondrial failure and cyclophilin D function in X-linked adrenoleukodystrophy

    PubMed Central

    López-Erauskin, Jone; Galino, Jorge; Bianchi, Patrizia; Fourcade, Stéphane; Andreu, Antoni L.; Ferrer, Isidre; Muñoz-Pinedo, Cristina

    2012-01-01

    A common process associated with oxidative stress and severe mitochondrial impairment is the opening of the mitochondrial permeability transition pore, as described in many neurodegenerative diseases. Thus, inhibition of mitochondrial permeability transition pore opening represents a potential target for inhibiting mitochondrial-driven cell death. Among the mitochondrial permeability transition pore components, cyclophilin D is the most studied and has been found increased under pathological conditions. Here, we have used in vitro and in vivo models of X-linked adrenoleukodystrophy to investigate the relationship between the mitochondrial permeability transition pore opening and redox homeostasis. X-linked adrenoleukodystrophy is a neurodegenerative condition caused by loss of function of the peroxisomal ABCD1 transporter, in which oxidative stress plays a pivotal role. In this study, we provide evidence of impaired mitochondrial metabolism in a peroxisomal disease, as fibroblasts in patients with X-linked adrenoleukodystrophy cannot survive when forced to rely on mitochondrial energy production, i.e. on incubation in galactose. Oxidative stress induced under galactose conditions leads to mitochondrial damage in the form of mitochondrial inner membrane potential dissipation, ATP drop and necrotic cell death, together with increased levels of oxidative modifications in cyclophilin D protein. Moreover, we show increased expression levels of cyclophilin D in the affected zones of brains in patients with adrenomyeloneuropathy, in spinal cord of a mouse model of X-linked adrenoleukodystrophy (Abcd1-null mice) and in fibroblasts from patients with X-linked adrenoleukodystrophy. Notably, treatment with antioxidants rescues mitochondrial damage markers in fibroblasts from patients with X-linked adrenoleukodystrophy, including cyclophilin D oxidative modifications, and reverses cyclophilin D induction in vitro and in vivo. These findings provide mechanistic insight into the

  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. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Linking social anxiety and adolescent romantic relationship functioning: indirect effects and the importance of peers.

    PubMed

    Hebert, Karen R; Fales, Jessica; Nangle, Douglas W; Papadakis, Alison A; Grover, Rachel L

    2013-11-01

    Peer relationships undergo dramatic shifts in form and function during adolescence, at the same time the incidence of socially evaluative fears sharply rises. Despite well-established links between social anxiety and broader interpersonal functioning, there is a dearth of research evaluating the impact of social anxiety on functioning in close relationships during this developmental stage. The present study examines the impact of social anxiety on functioning in close friendships and romantic relationships during adolescence. From a developmental psychopathology perspective, it was expected that social anxiety would influence functioning (quality, length, satisfaction) in romantic relationships through its influence on functioning in same- and other-sex friendships. Participants included 314 adolescents (60.5% female, 14-19 years of age) with a prior or current history of romantic relationship involvement. Structural equation modeling was used to test a mediation model positing an indirect pathway from social anxiety to romantic relationship functioning through functioning in close same- and other-sex friendships. Given known gender differences in social anxiety and relationship functioning, gender also was explored as a potential moderator. Results supported the hypothesized indirect pathway whereby social anxiety was associated with impairment in same-sex friendships; functioning in same-sex friendships was associated with functioning in other-sex friendships, which was associated, in turn, with functioning in romantic relationships. While the hypothesized indirect pathway was significant among both boys and girls, there was greater continuity of functioning between same- and other-sex friendships for girls. These findings highlight the importance of examining the multiple downstream effects of social anxiety on perceived social functioning in adolescence, and suggest that continuity may exist for maladaptive patterns of socialization, particularly across

  12. Linking Frailty Instruments to the International Classification of Functioning, Disability, and Health: A Systematic Review.

    PubMed

    Azzopardi, Roberta Vella; Vermeiren, Sofie; Gorus, Ellen; Habbig, Ann-Katrin; Petrovic, Mirko; Van Den Noortgate, Nele; De Vriendt, Patricia; Bautmans, Ivan; Beyer, Ingo

    2016-11-01

    To date, the major dilemma concerning frailty is the lack of a standardized language regarding its operationalization. Considering the demographic challenge that the world is facing, standardization of frailty identification is indeed the first step in tackling the burdensome consequences of frailty. To demonstrate this diversity in frailty assessment, the available frailty instruments have been linked to the International Classification of Functioning, Disability, and Health (ICF): a standardized and hierarchically coded language developed by World Health Organization regarding health conditions and their positive (functioning) and negative (disability) consequences. A systematic review on frailty instruments was carried out in PubMed, Web of Knowledge, and PsycINFO. The items of the identified frailty instruments were then linked to the ICF codes. 79 original or adapted frailty instruments were identified and categorized into single (n = 25) and multidomain (n = 54) groups. Only 5 frailty instruments (indexes) were linked to all 5 ICF components. Whereas the ICF components Body Functions and Activities and Participation were frequently linked to the frailty instruments, Body Structures, Environmental and Personal factors were sparingly represented mainly in the multidomain frailty instruments. This review highlights the heterogeneity in frailty operationalization. Environmental and personal factors should be given more thought in future frailty assessments. Being unambiguous, structured, and neutral, the ICF language allows comparing observations made with different frailty instruments. In conclusion, this systematic overview and ICF translation can be a cornerstone for future standardization of frailty assessment. Copyright © 2016 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

  13. 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.

  14. 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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

    2016-10-01

    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.

  17. Linking Functional Connectivity and Structural Connectivity Quantitatively: A Comparison of Methods.

    PubMed

    Huang, Haiqing; Ding, Mingzhou

    2016-03-01

    Structural connectivity in the brain is the basis of functional connectivity. Quantitatively linking the two, however, remains a challenge. For a pair of regions of interest (ROIs), anatomical connections derived from diffusion-weighted imaging are often quantified by fractional anisotropy (FA) or edge weight, whereas functional connections, derived from resting-state functional magnetic resonance imaging, can be characterized by non-time-series measures such as zero-lag cross correlation and partial correlation, as well as by time-series measures such as coherence and Granger causality. In this study, we addressed the question of linking structural connectivity and functional connectivity quantitatively by considering two pairs of ROIs, one from the default mode network (DMN) and the other from the central executive network (CEN), using two different data sets. Selecting (1) posterior cingulate cortex and medial prefrontal cortex of the DMN as the first pair of ROIs and (2) left dorsal lateral prefrontal cortex and left inferior parietal lobule of the CEN as the second pair of ROIs, we show that (1) zero-lag cross correlation, partial correlation, and pairwise Granger causality were not significantly correlated with either mean FA or edge weight and (2) conditional Granger causality (CGC) was significantly correlated with edge weight but not with mean FA. These results suggest that (1) edge weight may be a more appropriate measure to quantify the strength of the anatomical connection between ROIs and (2) CGC, which statistically removes common input and the indirect influences between a given ROI pair, may be a more appropriate measure to quantify the strength of the functional interaction enabled by the fibers linking the two ROIs.

  18. Assessment of safety effects for widening urban roadways in developing crash modification functions using nonlinearizing link functions.

    PubMed

    Park, Juneyoung; Abdel-Aty, Mohamed; Wang, Jung-Han; Lee, Chris

    2015-06-01

    Since a crash modification factor (CMF) represents the overall safety performance of specific treatments in a single fixed value, there is a need to explore the variation of CMFs with different roadway characteristics among treated sites over time. Therefore, in this study, we (1) evaluate the safety performance of a sample of urban four-lane roadway segments that have been widened with one through lane in each direction and (2) determine the relationship between the safety effects and different roadway characteristics over time. Observational before-after analysis with the empirical Bayes (EB) method was assessed in this study to evaluate the safety effects of widening urban four-lane roadways to six-lanes. Moreover, the nonlinearizing link functions were utilized to achieve better performance of crash modification functions (CMFunctions). The CMFunctions were developed using a Bayesian regression method including the estimated nonlinearizing link function to incorporate the changes in safety effects of the treatment over time. Data was collected for urban arterials in Florida, and the Florida-specific full SPFs were developed and used for EB estimation. The results indicated that the conversion of four-lane roadways to six-lane roadways resulted in a crash reduction of 15 percent for total crashes, and 24 percent for injury crashes on urban roadways. The results show that the safety effects vary across the sites with different roadway characteristics. In particular, LOS changes, time changes, and shoulder widths are significant parameters that affect the variation of CMFs. Moreover, it was found that narrowing shoulder and median widths to make space for an extra through lane shows a negative safety impact. It was also found that including the nonlinearizing link functions in developing CMFunctions shows more reliable estimates, if the variation of CMFs with specific parameters has a nonlinear relationship. The findings provide insights into the selection of

  19. 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.

  20. 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.

  1. Pipelined chebyshev functional link artificial recurrent neural network for nonlinear adaptive filter.

    PubMed

    Zhao, Haiquan; Zhang, Jiashu

    2010-02-01

    A novel nonlinear adaptive filter with pipelined Chebyshev functional link artificial recurrent neural network (PCFLARNN) is presented in this paper, which uses a modification real-time recurrent learning algorithm. The PCFLARNN consists of a number of simple small-scale Chebyshev functional link artificial recurrent neural network (CFLARNN) modules. Compared to the standard recurrent neural network (RNN), those modules of PCFLARNN can simultaneously be performed in a pipelined parallelism fashion, and this would lead to a significant improvement in its total computational efficiency. Furthermore, contrasted with the architecture of a pipelined RNN (PRNN), each module of PCFLARNN is a CFLARNN whose nonlinearity is introduced by enhancing the input pattern with Chebyshev functional expansion, whereas the RNN of each module in PRNN utilizing linear input and first-order recurrent term only fails to utilize the high-order terms of inputs. Therefore, the performance of PCFLARNN can further be improved at the cost of a slightly increased computational complexity. In addition, due to the introduced nonlinear functional expansion of each module in PRNN, the number of input signals can be reduced. Computer simulations have demonstrated that the proposed filter performs better than PRNN and RNN for nonlinear colored signal prediction, nonstationary speech signal prediction, and chaotic time series prediction.

  2. What are the links between maternal social status, hippocampal function, and HPA axis function in children?

    PubMed

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

    2013-09-01

    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.

  3. Functional link between ribosome formation and biogenesis of iron-sulfur proteins.

    PubMed

    Yarunin, Alexander; Panse, Vikram Govind; Petfalski, Elisabeth; Dez, Christophe; Tollervey, David; Hurt, Eduard C

    2005-02-09

    In genetic screens for ribosomal export mutants, we identified CFD1, NBP35 and NAR1 as factors involved in ribosome biogenesis. Notably, these components were recently reported to function in extramitochondrial iron-sulfur (Fe-S) cluster biosynthesis. In particular, Nar1 was implicated to generate the Fe-S clusters within Rli1, a potential substrate protein of unknown function. We tested whether the Fe-S protein Rli1 functions in ribosome formation. We report that rli1 mutants are impaired in pre-rRNA processing and defective in the export of both ribosomal subunits. In addition, Rli1p is associated with both pre-40S particles and mature 40S subunits, and with the eIF3 translation initiation factor complex. Our data reveal an unexpected link between ribosome biogenesis and the biosynthetic pathway of cytoplasmic Fe-S proteins.

  4. Functional link between ribosome formation and biogenesis of iron–sulfur proteins

    PubMed Central

    Yarunin, Alexander; Panse, Vikram Govind; Petfalski, Elisabeth; Dez, Christophe; Tollervey, David; Hurt, Ed

    2005-01-01

    In genetic screens for ribosomal export mutants, we identified CFD1, NBP35 and NAR1 as factors involved in ribosome biogenesis. Notably, these components were recently reported to function in extramitochondrial iron–sulfur (Fe–S) cluster biosynthesis. In particular, Nar1 was implicated to generate the Fe–S clusters within Rli1, a potential substrate protein of unknown function. We tested whether the Fe–S protein Rli1 functions in ribosome formation. We report that rli1 mutants are impaired in pre-rRNA processing and defective in the export of both ribosomal subunits. In addition, Rli1p is associated with both pre-40S particles and mature 40S subunits, and with the eIF3 translation initiation factor complex. Our data reveal an unexpected link between ribosome biogenesis and the biosynthetic pathway of cytoplasmic Fe–S proteins. PMID:15660135

  5. 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.

  6. Mining high-throughput experimental data to link gene and function

    PubMed Central

    Blaby-Haas, Crysten E.; de Crécy-Lagard, Valérie

    2011-01-01

    Nearly 2200 genomes encoding some 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function even when function is loosely and minimally defined as “belonging to a superfamily”. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these “unknowns” with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function. PMID:21310501

  7. Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss.

    PubMed

    Danovaro, Roberto; Gambi, Cristina; Dell'Anno, Antonio; Corinaldesi, Cinzia; Fraschetti, Simonetta; Vanreusel, Ann; Vincx, Magda; Gooday, Andrew J

    2008-01-08

    Recent investigations suggest that biodiversity loss might impair the functioning and sustainability of ecosystems. Although deep-sea ecosystems are the most extensive on Earth, represent the largest reservoir of biomass, and host a large proportion of undiscovered biodiversity, the data needed to evaluate the consequences of biodiversity loss on the ocean floor are completely lacking. Here, we present a global-scale study based on 116 deep-sea sites that relates benthic biodiversity to several independent indicators of ecosystem functioning and efficiency. We show that deep-sea ecosystem functioning is exponentially related to deep-sea biodiversity and that ecosystem efficiency is also exponentially linked to functional biodiversity. These results suggest that a higher biodiversity supports higher rates of ecosystem processes and an increased efficiency with which these processes are performed. The exponential relationships presented here, being consistent across a wide range of deep-sea ecosystems, suggest that mutually positive functional interactions (ecological facilitation) can be common in the largest biome of our biosphere. Our results suggest that a biodiversity loss in deep-sea ecosystems might be associated with exponential reductions of their functions. Because the deep sea plays a key role in ecological and biogeochemical processes at a global scale, this study provides scientific evidence that the conservation of deep-sea biodiversity is a priority for a sustainable functioning of the worlds' oceans.

  8. Cell wall-related proteins of unknown function: missing links in plant cell wall development.

    PubMed

    Mewalal, Ritesh; Mizrachi, Eshchar; Mansfield, Shawn D; Myburg, Alexander A

    2014-06-01

    Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. 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

  10. Sex differences in resting state brain function of cigarette smokers and links to nicotine dependence.

    PubMed

    Beltz, Adriene M; Berenbaum, Sheri A; Wilson, Stephen J

    2015-08-01

    Sex--a marker of biological and social individual differences--matters for drug use, particularly for cigarette smoking, which is the leading cause of preventable death in the United States. More men than women smoke, but women are less likely than men to quit. Resting state brain function, or intrinsic brain activity that occurs in the absence of a goal-directed task, is important for understanding cigarette smoking, as it has been shown to differentiate between smokers and nonsmokers. But, it is unclear whether and how sex influences the link between resting state brain function and smoking behavior. In this study, the authors demonstrate that sex is indeed associated with resting state connectivity in cigarette smokers, and that sex moderates the link between resting state connectivity and self-reported nicotine dependence. Using functional MRI and behavioral data from 50 adult daily smokers (23 women), the authors found that women had greater connectivity than men within the default mode network, and that increased connectivity within the reward network was related to increased nicotine tolerance in women but to decreased nicotine tolerance in men. Findings highlight the importance of sex-related individual differences reflected in resting state connectivity for understanding the etiology and treatment of substance use problems.

  11. Temperature-responsive cross-linked poly(epsilon-caprolactone) membrane that functions near body temperature.

    PubMed

    Uto, Koichiro; Yamamoto, Kazuya; Hirase, Shohei; Aoyagi, Takao

    2006-01-10

    The objective of this study is to develop a sensitive temperature-responsive material that would function near body temperature. To achieve this purpose, we compounded 2-branched and 4-branched poly(epsilon-caprolactone) macromonomers to modulate the transition temperatures of the resulting cross-linked materials. The temperature-responsive properties were studied using differential scanning calorimetry and X-ray diffraction measurements. As a result, the mixing ratios of each macromonomer or the total macromonomer concentrations were very dominant in modulating the transition temperatures. The materials could successfully control the permeation of the model drug, prednisolone, near body temperature.

  12. Novel Covalently Linked Insulin Dimer Engineered to Investigate the Function of Insulin Dimerization

    PubMed Central

    Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.; Huus, Kasper; Schlein, Morten; Pedersen, Thomas Å.; Kjeldsen, Thomas; Jensen, Knud J.; Hubálek, František

    2012-01-01

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability. PMID:22363506

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Linking Executive Function and Peer Problems from Early Childhood through Middle Adolescence

    PubMed Central

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

    2015-01-01

    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 = 1,164, 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 after school 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

  18. 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.

  19. Both α2,3- and α2,6-Linked Sialic Acids on O-Linked Glycoproteins Act as Functional Receptors for Porcine Sapovirus

    PubMed Central

    Alfajaro, Mia Madel; Kim, Ji-Yun; Park, Jun-Gyu; Son, Kyu-Yeol; Ryu, Eun-Hye; Sorgeloos, Frederic; Kwon, Hyung-Jun; Park, Su-Jin; Lee, Woo Song; Cho, Duck; Kwon, Joseph; Choi, Jong-Soon; Kang, Mun-Il; Goodfellow, Ian; Cho, Kyoung-Oh

    2014-01-01

    Sapovirus, a member of the Caliciviridae family, is an important cause of acute gastroenteritis in humans and pigs. Currently, the porcine sapovirus (PSaV) Cowden strain remains the only cultivable member of the Sapovirus genus. While some caliciviruses are known to utilize carbohydrate receptors for entry and infection, a functional receptor for sapovirus is unknown. To characterize the functional receptor of the Cowden strain of PSaV, we undertook a comprehensive series of protein-ligand biochemical assays in mock and PSaV-infected cell culture and/or piglet intestinal tissue sections. PSaV revealed neither hemagglutination activity with red blood cells from any species nor binding activity to synthetic histo-blood group antigens, indicating that PSaV does not use histo-blood group antigens as receptors. Attachment and infection of PSaV were markedly blocked by sialic acid and Vibrio cholerae neuraminidase (NA), suggesting a role for α2,3-linked, α2,6-linked or α2,8-linked sialic acid in virus attachment. However, viral attachment and infection were only partially inhibited by treatment of cells with sialidase S (SS) or Maackia amurensis lectin (MAL), both specific for α2,3-linked sialic acid, or Sambucus nigra lectin (SNL), specific for α2,6-linked sialic acid. These results indicated that PSaV recognizes both α2,3- and α2,6-linked sialic acids for viral attachment and infection. Treatment of cells with proteases or with benzyl 4-O-β-D-galactopyranosyl-β-D-glucopyranoside (benzylGalNAc), which inhibits O-linked glycosylation, also reduced virus binding and infection, whereas inhibition of glycolipd synthesis or N-linked glycosylation had no such effect on virus binding or infection. These data suggest PSaV binds to cellular receptors that consist of α2,3- and α2,6-linked sialic acids on glycoproteins attached via O-linked glycosylation. PMID:24901849

  20. Examining the link between information processing speed and executive functioning in multiple sclerosis.

    PubMed

    Drew, Margaret A; Starkey, Nicola J; Isler, Robert B

    2009-02-01

    Slowed information processing speed (IPS) is frequently reported in those with multiple sclerosis (MS), and at least 20% are compromised on some aspect of executive functioning also. However, any relationship between these two processes has not been examined. The Sternberg Memory Scanning Test, Processing Speed Index (WAIS-III), Delis Kaplan Executive Function System (D.KEFS), and Working Memory Index (WMS-III) were administered to 90 participants with MS. Their performance on the PSI was significantly below the normative scores but no deficits in memory scanning speed were evident. The initial response speed of the Sternberg and the PSI were more closely related to D.KEFS performance, particularly in timed tasks with a high cognitive demand (switching tasks). In contrast, memory scanning speed was related to working memory. This study reinforces the link between IPS and working memory in MS, and supports the suggestion that IPS is not a unitary construct.

  1. A link between attentional function, effective eye movements, and driving ability.

    PubMed

    Mackenzie, Andrew K; Harris, Julie M

    2017-02-01

    The misallocation of driver visual attention has been suggested as a major contributing factor to vehicle accidents. One possible reason is that the relatively high cognitive demands of driving limit the ability to efficiently allocate gaze. We present an experiment that explores the relationship between attentional function and visual performance when driving. Drivers performed 2 variations of a multiple-object tracking task targeting aspects of cognition including sustained attention, dual-tasking, covert attention, and visuomotor skill. They also drove a number of courses in a driving simulator. Eye movements were recorded throughout. We found that individuals who performed better in the cognitive tasks exhibited more effective eye movement strategies when driving, such as scanning more of the road, and they also exhibited better driving performance. We discuss the potential link between an individual's attentional function, effective eye movements, and driving ability. We also discuss the use of a visuomotor task in assessing driving behavior. (PsycINFO Database Record

  2. A Link Between Attentional Function, Effective Eye Movements, and Driving Ability

    PubMed Central

    2016-01-01

    The misallocation of driver visual attention has been suggested as a major contributing factor to vehicle accidents. One possible reason is that the relatively high cognitive demands of driving limit the ability to efficiently allocate gaze. We present an experiment that explores the relationship between attentional function and visual performance when driving. Drivers performed 2 variations of a multiple-object tracking task targeting aspects of cognition including sustained attention, dual-tasking, covert attention, and visuomotor skill. They also drove a number of courses in a driving simulator. Eye movements were recorded throughout. We found that individuals who performed better in the cognitive tasks exhibited more effective eye movement strategies when driving, such as scanning more of the road, and they also exhibited better driving performance. We discuss the potential link between an individual’s attentional function, effective eye movements, and driving ability. We also discuss the use of a visuomotor task in assessing driving behavior. PMID:27893270

  3. Rhodopsin: the Functional Significance of Asn-Linked Glycosylation and Other Post-translational Modifications

    PubMed Central

    Murray, Anne R.; Fliesler, Steven J.; Al-Ubaidi, Muayyad R.

    2010-01-01

    Rhodopsin, the G-protein coupled receptor in retinal rod photoreceptors, is a highly conserved protein that undergoes several types of post-translational modifications. These modifications are essential to maintain the protein’s structure as well as its proper function in the visual transduction cycle. Rhodopsin is N-glycosylated at Asn-2 and Asn-15 in its extracellular N-terminal domain. Mutations within the glycosylation consensus sequences of rhodopsin cause autosomal dominant retinitis pigmentosa, a disease that leads to blindness. Several groups have studied the role of rhodopsin’s N-linked glycan chains in protein structure and function using a variety of approaches. These include the generation of a transgenic mouse model, study of a naturally occurring mutant animal model, in vivo pharmacological inhibition of glycosylation, and in vitro analyses using transfected COS-1 cells. These studies have provided insights into the possible role of rhodopsin glycosylation, but have yielded conflicting results. PMID:19941415

  4. 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.

  5. Bayesian inference in an item response theory model with a generalized student t link function

    NASA Astrophysics Data System (ADS)

    Azevedo, Caio L. N.; Migon, Helio S.

    2012-10-01

    In this paper we introduce a new item response theory (IRT) model with a generalized Student t-link function with unknown degrees of freedom (df), named generalized t-link (GtL) IRT model. In this model we consider only the difficulty parameter in the item response function. GtL is an alternative to the two parameter logit and probit models, since the degrees of freedom (df) play a similar role to the discrimination parameter. However, the behavior of the curves of the GtL is different from those of the two parameter models and the usual Student t link, since in GtL the curve obtained from different df's can cross the probit curves in more than one latent trait level. The GtL model has similar proprieties to the generalized linear mixed models, such as the existence of sufficient statistics and easy parameter interpretation. Also, many techniques of parameter estimation, model fit assessment and residual analysis developed for that models can be used for the GtL model. We develop fully Bayesian estimation and model fit assessment tools through a Metropolis-Hastings step within Gibbs sampling algorithm. We consider a prior sensitivity choice concerning the degrees of freedom. The simulation study indicates that the algorithm recovers all parameters properly. In addition, some Bayesian model fit assessment tools are considered. Finally, a real data set is analyzed using our approach and other usual models. The results indicate that our model fits the data better than the two parameter models.

  6. Dynamics of the functional link between area MT LFPs and motion detection

    PubMed Central

    Smith, Jackson E. T.; Beliveau, Vincent; Schoen, Alan; Remz, Jordana; Zhan, Chang'an A.

    2015-01-01

    The evolution of a visually guided perceptual decision results from multiple neural processes, and recent work suggests that signals with different neural origins are reflected in separate frequency bands of the cortical local field potential (LFP). Spike activity and LFPs in the middle temporal area (MT) have a functional link with the perception of motion stimuli (referred to as neural-behavioral correlation). To cast light on the different neural origins that underlie this functional link, we compared the temporal dynamics of the neural-behavioral correlations of MT spikes and LFPs. Wide-band activity was simultaneously recorded from two locations of MT from monkeys performing a threshold, two-stimuli, motion pulse detection task. Shortly after the motion pulse occurred, we found that high-gamma (100–200 Hz) LFPs had a fast, positive correlation with detection performance that was similar to that of the spike response. Beta (10–30 Hz) LFPs were negatively correlated with detection performance, but their dynamics were much slower, peaked late, and did not depend on stimulus configuration or reaction time. A late change in the correlation of all LFPs across the two recording electrodes suggests that a common input arrived at both MT locations prior to the behavioral response. Our results support a framework in which early high-gamma LFPs likely reflected fast, bottom-up, sensory processing that was causally linked to perception of the motion pulse. In comparison, late-arriving beta and high-gamma LFPs likely reflected slower, top-down, sources of neural-behavioral correlation that originated after the perception of the motion pulse. PMID:25948867

  7. 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

  8. 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.

  9. Stable Isotope Probing: Linking Functional Activity to Specific Members of Microbial Communities

    SciTech Connect

    Kreuzer-Martin, Helen W.

    2007-03-12

    Abstract Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by detecting the appearance of the isotope in diagnostic molecules such as fatty acids and nucleic acids. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. SIP allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This mini-review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

  10. C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes.

    PubMed

    Sau, Sujay P; Hrdlicka, Patrick J

    2012-01-06

    Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.

  11. 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.

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  15. A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function.

    PubMed

    Kälin, Stefanie; Becker, Maike; Ott, Verena B; Serr, Isabelle; Hosp, Fabian; Mollah, Mohammad M H; Keipert, Susanne; Lamp, Daniel; Rohner-Jeanrenaud, Francoise; Flynn, Victoria K; Scherm, Martin G; Nascimento, Lucas F R; Gerlach, Katharina; Popp, Vanessa; Dietzen, Sarah; Bopp, Tobias; Krishnamurthy, Purna; Kaplan, Mark H; Serrano, Manuel; Woods, Stephen C; Tripal, Philipp; Palmisano, Ralf; Jastroch, Martin; Blüher, Matthias; Wolfrum, Christian; Weigmann, Benno; Ziegler, Anette-Gabriele; Mann, Matthias; Tschöp, Matthias H; Daniel, Carolin

    2017-09-05

    Obesity and type 2 diabetes are associated with metabolic defects and adipose tissue inflammation. Foxp3(+) regulatory T cells (Tregs) control tissue homeostasis by counteracting local inflammation. However, if and how T cells interlink environmental influences with adipocyte function remains unknown. Here, we report that enhancing sympathetic tone by cold exposure, beta3-adrenergic receptor (ADRB3) stimulation or a short-term high-calorie diet enhances Treg induction in vitro and in vivo. CD4(+) T cell proteomes revealed higher expression of Foxp3 regulatory networks in response to cold or ADRB3 stimulation in vivo reflecting Treg induction. Specifically, Ragulator-interacting protein C17orf59, which limits mTORC1 activity, was upregulated in CD4(+) T cells by either ADRB3 stimulation or cold exposure, suggesting contribution to Treg induction. By loss- and gain-of-function studies, including Treg depletion and transfers in vivo, we demonstrated that a T cell-specific Stat6/Pten axis links cold exposure or ADRB3 stimulation with Foxp3(+) Treg induction and adipose tissue function. Our findings offer a new mechanistic model in which tissue-specific Tregs maintain adipose tissue function. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed Central

    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.

    2009-01-01

    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 S. 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 prior 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 CRISPR (clustered regularly interspaced short palindromic repeat) sequences suggest that S. arenicola may possess a higher level of phage immunity, while a highly duplicated family of polymorphic membrane proteins provides evidence of a new mechanism of marine adaptation in Gram-positive bacteria. PMID:19474814

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. Partition function and astronomical observation of interstellar isomers: Is there a link?

    NASA Astrophysics Data System (ADS)

    Etim, Emmanuel E.; Arunan, Elangannan

    2017-02-01

    The unsuccessful astronomical searches for some important astrophysical and astrobiological molecules have been linked to the large partition function of these molecules. This letter reports an extensive investigation of the relationship between partition function and astronomical observation of interstellar isomers using high level quantum chemical calculations. 120 molecules from 30 different isomeric groups have been considered. Partition function and thermodynamic stabilities are determined for each set of isomeric species. From the results, there is no direct correlation between partition function and astronomical observation of the same isomeric species. Though interstellar formations processes are generally controlled by factors like kinetics, thermodynamics, formation and destruction pathways. However, the observation of the isomers seems to correlate well with thermodynamics. For instance, in all the groups considered, the astronomically detected isomers are the thermodynamically most stable molecules in their respective isomeric groups. The implications of these results in accounting for the limited number of known cyclic interstellar molecules, unsuccessful searches for amino acid and the possible molecules for astronomical observations are discussed.

  2. 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.

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

    PubMed Central

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

    2016-01-01

    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 martensii Karsch 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 luteus as 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 IC50 value 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 BmKDfsin4adopts 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. PMID:26817841

  4. 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

  5. An Annotated Bibliography of Resources on Educational Linking Agents: Roles, Functions, and Training Materials.

    ERIC Educational Resources Information Center

    Barth, Rodney J., Comp.

    The resources cited in this selected annotated bibliography are intended for linking agents, trainers of linking agents, managers of linking agents and their support systems, and educational policy makers. These resources, which date from 1975 to the present, variously refer to linking agents, change agents, extension agents, field agents, field…

  6. Effect of colicin K on a membrane-associated, energy-linked function.

    PubMed Central

    Sabet, S F

    1976-01-01

    The purpose of this work was in investigate the capability of cell extracts of Escherichia coli and E. coli treated with colicin K to catalyze the following energy-dependent reverse transhydrogenase reaction: NADP + NADH + ATP in equilibrium NADPH + NAD +ADP + Pi. Under anaerobic conditions this reaction requires the presence of a specific portion of the electron transport chain, a functional energy coupling system, including an adenosine triphosphatase, enzyme, and ATP as energy source. The ATP-linked reaction was partially inhibited in French press extracts of E. coli K-12 C600 cells that had been pretreated with colicin K but not in extracts from similarly treated cells of a colicin-tolerant mutant. Ultracentrifugation of extracts yielded particulate fractions competent in catalyzing the reaction; this reaction is substantially inhibited in fractions from colicin-treated cells. The extent of inhibition increased with increasing concentration of colicin. Supernatants also supported ATP-linked formation of NADPH, but this reaction was insensitive to the colicin effect. A comparison between the requirement of the reaction in supernatant and particulate fractions suggests that the reaction in the supernatant is different from the one inhibited by colicin. The ATP-hydrolyzing ability of particulate fractions from the control or treated bacteria was identical. Likewise, the electron transport chain was not affected by colicin treatment, as evidenced from lack of effect on NADH oxidase, succinic dehydrogenase, and NADPH-NAD transhydrogenase. It is concluded that colicin K interferes with the coupling of ATP the utilization of the intermediate for the ATP-linked transdehydrogenase reaction. PMID:4429

  7. 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

  8. Consumer trophic diversity as a fundamental mechanism linking predation and ecosystem functioning.

    PubMed

    Hines, Jes; Gessner, Mark O

    2012-11-01

    1. Primary production and decomposition, two fundamental processes determining the functioning of ecosystems, may be sensitive to changes in biodiversity and food web interactions. 2. The impacts of food web interactions on ecosystem functioning are generally quantified by experimentally decoupling these linked processes and examining either primary production-based (green) or decomposition-based (brown) food webs in isolation. This decoupling may strongly limit our ability to assess the importance of food web interactions on ecosystem processes. 3. To evaluate how consumer trophic diversity mediates predator effects on ecosystem functioning, we conducted a mesocosm experiment and a field study using an assemblage of invertebrates that naturally co-occur on North Atlantic coastal saltmarshes. We measured the indirect impact of predation on primary production and leaf decomposition as a result of prey communities composed of herbivores alone, detritivores alone or both prey in combination. 4. We find that primary consumers can influence ecosystem process rates not only within, but also across green and brown sub-webs. Moreover, by feeding on a functionally diverse consumer assemblage comprised of both herbivores and detritivores, generalist predators can diffuse consumer effects on decomposition, primary production and feedbacks between the two processes. 5. These results indicate that maintaining functional diversity among primary consumers can alter the consequences of traditional trophic cascades, and they emphasize the role of the detritus-based sub-web when seeking key biotic drivers of plant production. Clearly, traditional compartmentalization of empirical food webs can limit our ability to predict the influence of food web interactions on ecosystem functioning.

  9. Conserved properties of Drosophila Insomniac link sleep regulation and synaptic function.

    PubMed

    Li, Qiuling; Kellner, David A; Hatch, Hayden A M; Yumita, Tomohiro; Sanchez, Sandrine; Machold, Robert P; Frank, C Andrew; Stavropoulos, Nicholas

    2017-05-01

    Sleep is an ancient animal behavior that is regulated similarly in species ranging from flies to humans. Various genes that regulate sleep have been identified in invertebrates, but whether the functions of these genes are conserved in mammals remains poorly explored. Drosophila insomniac (inc) mutants exhibit severely shortened and fragmented sleep. Inc protein physically associates with the Cullin-3 (Cul3) ubiquitin ligase, and neuronal depletion of Inc or Cul3 strongly curtails sleep, suggesting that Inc is a Cul3 adaptor that directs the ubiquitination of neuronal substrates that impact sleep. Three proteins similar to Inc exist in vertebrates-KCTD2, KCTD5, and KCTD17-but are uncharacterized within the nervous system and their functional conservation with Inc has not been addressed. Here we show that Inc and its mouse orthologs exhibit striking biochemical and functional interchangeability within Cul3 complexes. Remarkably, KCTD2 and KCTD5 restore sleep to inc mutants, indicating that they can substitute for Inc in vivo and engage its neuronal targets relevant to sleep. Inc and its orthologs localize similarly within fly and mammalian neurons and can traffic to synapses, suggesting that their substrates may include synaptic proteins. Consistent with such a mechanism, inc mutants exhibit defects in synaptic structure and physiology, indicating that Inc is essential for both sleep and synaptic function. Our findings reveal that molecular functions of Inc are conserved through ~600 million years of evolution and support the hypothesis that Inc and its orthologs participate in an evolutionarily conserved ubiquitination pathway that links synaptic function and sleep regulation.

  10. Multimodal analyses identify linked functional and white matter abnormalities within the working memory network in schizophrenia.

    PubMed

    Sugranyes, Gisela; Kyriakopoulos, Marinos; Dima, Danai; O'Muircheartaigh, Jonathan; Corrigall, Richard; Pendelbury, Gabrielle; Hayes, Daniel; Calhoun, Vince D; Frangou, Sophia

    2012-07-01

    Dysconnectivity between brain regions is thought to underlie the cognitive abnormalities that characterise schizophrenia (SZ). Consistent with this notion functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) studies in SZ have reliably provided evidence of abnormalities in functional integration and in white matter connectivity. Yet little is known about how alterations at the functional level related to abnormalities in anatomical connectivity. We obtained fMRI data during the 2-back working memory task from 25 patients with SZ and 19 healthy controls matched for age, sex and IQ. DTI data were also acquired in the same session. In addition to conventional unimodal analyses we extracted "features" [contrast maps for fMRI and fractional anisotropy (FA) for DTI] that were subjected to joint independent component analysis (JICA) in order to examine interactions between fMRI and DTI data sources. Conventional unimodal analyses revealed both functional and structural deficits in patients with SZ. The JICA identified regions of joint, multimodal brain sources that differed in patients and controls. The fMRI source implicated regions within the anterior cingulate and ventrolateral prefrontal cortex and in the cuneus where patients showed relative hypoactivation and within the frontopolar cortex where patients showed relative hyperactivation. The DTI source localised reduced FA in patients in the splenium and posterior cingulum. This study promotes our understanding of structure-function relationships in SZ by characterising linked functional and white matter changes that contribute to working memory dysfunction in this disorder. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Multimodal analyses identify linked functional and white matter abnormalities within the working memory network in schizophrenia

    PubMed Central

    Sugranyes, Gisela; Kyriakopoulos, Marinos; Dima, Danai; O’Muircheartaigh, Jonathan; Corrigall, Richard; Pendelbury, Gabrielle; Hayes, Daniel; Calhoun, Vince D.; Frangou, Sophia

    2015-01-01

    Background Dysconnectivity between brain regions is thought to underlie the cognitive abnormalities that characterise schizophrenia (SZ). Consistent with this notion functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) studies in SZ have reliably provided evidence of abnormalities in functional integration and in white matter connectivity. Yet little is known about how alterations at the functional level related to abnormalities in anatomical connectivity. Methods We obtained fMRI data during the 2-back working memory task from 25 patients with SZ and 19 healthy controls matched for age, sex and IQ. DTI data were also acquired in the same session. In addition to conventional unimodal analyses we extracted “features” [contrast maps for fMRI and fractional anisotropy (FA) for DTI] that were subjected to joint independent component analysis (JICA) in order to examine interactions between fMRI and DTI data sources. Results Conventional unimodal analyses revealed both functional and structural deficits in patients with SZ. The JICA identified regions of joint, multimodal brain sources that differed in patients and controls. The fMRI source implicated regions within the anterior cingulate and ventrolateral prefrontal cortex and in the cuneus where patients showed relative hypoactivation and within the frontopolar cortex where patients showed relative hyperactivation. The DTI source localised reduced FA in patients in the splenium and posterior cingulum. Conclusions This study promotes our understanding of structure-function relationships in SZ by characterising linked functional and white matter changes that contribute to working memory dysfunction in this disorder. PMID:22475381

  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. 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.

  14. Nopp140 Functions as a Molecular Link Between the Nucleolus and the Coiled Bodies

    PubMed Central

    Isaac, Cynthia; Yang, Yunfeng; Thomas Meier, U.

    1998-01-01

    Coiled bodies are small nuclear organelles that are highly enriched in small nuclear RNAs, and that have long been thought to be associated with the nucleolus. Here we use mutational analysis, transient transfections, and the yeast two-hybrid system to show that the nucleolar phosphoprotein Nopp140 functions as a molecular link between the two prominent nuclear organelles. Exogenous Nopp140 accumulated in the nucleolus rapidly, but only after a lag phase in coiled bodies, suggesting a pathway between the two organelles. The expression of partial Nopp140 constructs exerted dominant negative effects on the endogenous Nopp140 by chasing it and other antigens that were common to both organelles out of the nucleolus. The alternating positively and negatively charged repeat domain of Nopp140 was required for targeting to both organelles. In addition, partial Nopp140 constructs caused formation of novel structures in the nucleoplasm and, in the case of the conserved carboxy terminus, led to the dispersal of coiled bodies. As a final link, we identified the coiled body–specific protein p80 coilin in a yeast two-hybrid screen with Nopp140. The interaction of the two proteins was confirmed by coimmunoprecipitation. Taken together, Nopp140 appeared to shuttle between the nucleolus and the coiled bodies, and to chaperone the transport of other molecules. PMID:9679133

  15. Modeling the link between soil microbial community structure and function in a bottom-up approach

    NASA Astrophysics Data System (ADS)

    Kaiser, C.; Richter, A.; Franklin, O.; Evans, S. E.; Dieckmann, U.

    2012-12-01

    Understanding mechanisms of soil carbon (C) turnover requires understanding the link between microbial community dynamics and soil decomposition processes. We present here an individual-based model that aims at elucidating this link by a bottom-up approach. Our approach differs from traditional soil C cycling models in that the overall dynamics of soil organic matter turnover emerges as the result of interactions between individual microbes at the soil microsite level, rather than being described by stock and flow rate equations at the bulk soil level. All soil microbes are modeled individually, each belonging to one of several functional groups defined by functional traits. Specifically, functional traits determine (1) growth and turnover rates, (2) production of extracellular enzymes and (3) microbial cell stoichiometry. Our model incorporates competition for space and nutrients (C and nitrogen, N) as well as synergistic interactions between individual microbes in a spatially structured environment represented by a two-dimensional grid. Due to different C and N limitations of different functional groups, community composition is sensitive to the availability of complex and labile C and N. Thus, altered resource availability changes microbial community composition, which in turn affects CO2 and N release from the soil. In our model, microbes constantly alter their own environment through the decomposition of different substrates, thereby exerting a feedback on community composition, which leads to a succession of microbial groups. We used the model's intrinsic link between resource availability, community dynamics and decomposition function to investigate the mechanism underlying the rhizosphere priming effect (i.e. increased decomposition of older soil C triggered by the input of labile C). In particular, we examined the spatial growth of a root releasing exudates of varying C:N ratios under the presence or absence of different functional groups. We find that a

  16. 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

  17. Remission of Depression in Parents: Links to Healthy Functioning in their Children

    PubMed Central

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

    2010-01-01

    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 7–17 years old (Mean=12.13, SD=2.31); 126 parents were in treatment for depression and 97 parents were nondepressed. Children were evaluated six times over two years. Changes in parents’ depressive symptoms predicted changes in children’s depressive symptoms over and above the effect of time; children’s symptoms significantly predicted parents’ symptoms. Trajectories of children’s depressive symptoms differed significantly for children of remitted versus nonremitted depressed parents, and these differences were significantly predicted by their parents’ level of depression. The relation between parents’ and children’s depressive symptoms was partially mediated by parental acceptance. PMID:21291439

  18. X-linked mental retardation: focus on synaptic function and plasticity.

    PubMed

    Humeau, Yann; Gambino, Frédéric; Chelly, Jamel; Vitale, Nicolas

    2009-04-01

    Among mental disorders, mental retardation has been shown to be caused by various factors including a large array of genetic mutations. On the basis of remarkable progress, the emerging view is that defects in the regulation of synaptic activity and morphogenesis of dendritic spines are apparently common features associated with mutations in several genes implicated in mental retardation. In this review, we will discuss X-linked MR-related gene products that are potentially involved in the normal structure and function of the synapses, with a particular focus on pre- and/or post-synaptic plasticity mechanisms. Progress in understanding the underlying conditions leading to mental retardation will undoubtedly be gained from a closer collaboration of geneticists, physiologists and cognitive neuroscientists, which should enable the establishment of standardized approaches.

  19. CanDiD: A Framework for Linking Executive Function and Education.

    PubMed

    Kamkar, Niki H; Morton, J B

    2017-01-01

    The close association between executive functions (EFs) and educational achievement has led to the idea that targeted EF training might facilitate learning and goal-directed behavior in the classroom. The evidence that training interventions have long-lasting and transferable effects is however decidedly mixed (Melby-Lervåg and Hulme, 2013; Simons et al., 2016). The goal of the current paper is to propose a new CanDiD framework for re-thinking EF and its links to education. Based on findings from basic EF research, the proposed CanDiD framework highlights dynamic and contextual influences on EF and emphasizes the importance of development and individual differences for understanding these effects. Implications for remedial interventions and curriculum design are discussed.

  20. 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.

  1. Structural flexibility allows the functional diversity of potyvirus genome-linked protein VPg.

    PubMed

    Rantalainen, Kimmo I; Eskelin, Katri; Tompa, Peter; Mäkinen, Kristiina

    2011-03-01

    Several viral genome-linked proteins (VPgs) of plant viruses are intrinsically disordered and undergo folding transitions in the presence of partners. This property has been postulated to be one of the factors that enable the functional diversity of the protein. We created a homology model of Potato virus A VPg and positioned the known functions and structural properties of potyviral VPgs on the novel structural model. The model suggests an elongated structure with a hydrophobic core composed of antiparallel β-sheets surrounded by helices and a positively charged contact surface where most of the known activities are localized. The model most probably represents the fold induced immediately after binding of VPg to a negatively charged lipid surface or to SDS. When the charge of the positive surface was lowered by lysine mutations, the efficiencies of in vitro NTP binding, uridylylation reaction, and unspecific RNA binding were reduced and in vivo the infectivity was debilitated. The most likely uridylylation site, Tyr63, locates to the positively charged surface. Surprisingly, a Tyr63Ala mutation did not prevent replication completely but blocked spreading of the virus. Based on the localization of Tyr119 in the model, it was hypothesized to serve as an alternative uridylylation site. Evidence to support the role of Tyr119 in replication was obtained which gives a positive example of the prediction power of the model. Taken together, our experimental data support the features presented in the model and the idea that the functional diversity is attributable to structural flexibility.

  2. Linking Neurons to Network Function and Behavior by Two-Photon Holographic Optogenetics and Volumetric Imaging.

    PubMed

    Dal Maschio, Marco; Donovan, Joseph C; Helmbrecht, Thomas O; Baier, Herwig

    2017-05-17

    We introduce a flexible method for high-resolution interrogation of circuit function, which combines simultaneous 3D two-photon stimulation of multiple targeted neurons, volumetric functional imaging, and quantitative behavioral tracking. This integrated approach was applied to dissect how an ensemble of premotor neurons in the larval zebrafish brain drives a basic motor program, the bending of the tail. We developed an iterative photostimulation strategy to identify minimal subsets of channelrhodopsin (ChR2)-expressing neurons that are sufficient to initiate tail movements. At the same time, the induced network activity was recorded by multiplane GCaMP6 imaging across the brain. From this dataset, we computationally identified activity patterns associated with distinct components of the elicited behavior and characterized the contributions of individual neurons. Using photoactivatable GFP (paGFP), we extended our protocol to visualize single functionally identified neurons and reconstruct their morphologies. Together, this toolkit enables linking behavior to circuit activity with unprecedented resolution. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Structural Flexibility Allows the Functional Diversity of Potyvirus Genome-Linked Protein VPg▿ §

    PubMed Central

    Rantalainen, Kimmo I.; Eskelin, Katri; Tompa, Peter; Mäkinen, Kristiina

    2011-01-01

    Several viral genome-linked proteins (VPgs) of plant viruses are intrinsically disordered and undergo folding transitions in the presence of partners. This property has been postulated to be one of the factors that enable the functional diversity of the protein. We created a homology model of Potato virus A VPg and positioned the known functions and structural properties of potyviral VPgs on the novel structural model. The model suggests an elongated structure with a hydrophobic core composed of antiparallel β-sheets surrounded by helices and a positively charged contact surface where most of the known activities are localized. The model most probably represents the fold induced immediately after binding of VPg to a negatively charged lipid surface or to SDS. When the charge of the positive surface was lowered by lysine mutations, the efficiencies of in vitro NTP binding, uridylylation reaction, and unspecific RNA binding were reduced and in vivo the infectivity was debilitated. The most likely uridylylation site, Tyr63, locates to the positively charged surface. Surprisingly, a Tyr63Ala mutation did not prevent replication completely but blocked spreading of the virus. Based on the localization of Tyr119 in the model, it was hypothesized to serve as an alternative uridylylation site. Evidence to support the role of Tyr119 in replication was obtained which gives a positive example of the prediction power of the model. Taken together, our experimental data support the features presented in the model and the idea that the functional diversity is attributable to structural flexibility. PMID:21177813

  4. 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. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Single-input/single-output transfer functions for a flexible slewing link

    NASA Technical Reports Server (NTRS)

    Barbieri, Enrique

    1993-01-01

    Truncated linear models based on constrained and unconstrained mode expansions for a flexible link with torque actuation at its hub led us to examine the behavior of the open-loop-zeros of five commonly used SISO transfer functions. We arrive at new conclusions with regard to minimum- and non-minimum-phase zeros, and passivity of the transfer functions. The flexible-to-rigid inertia (FRI) ratio plays an important role in the determination of these characteristics. This paper illustrates how the zero locations of some of the transfer functions are dramatically affected by the FRI ratio. We also investigate the performance of a hub angle, hub rate, and relative tip position static feedback controller based on a reduced-order constrained mode model when applied to both unconstrained and constrained mode models of the same dimension. Simulations indicate that the constrained model can be stable while the unconstrained model is not for high FRI ratios. Our findings can provide useful information to designers in cases where the controller is sensitive to the 1ocation of the plant's zeros.

  6. Direct link between RACK1 function and localization at the ribosome in vivo.

    PubMed

    Coyle, Scott M; Gilbert, Wendy V; Doudna, Jennifer A

    2009-03-01

    The receptor for activated C-kinase (RACK1), a conserved protein implicated in numerous signaling pathways, is a stoichiometric component of eukaryotic ribosomes located on the head of the 40S ribosomal subunit. To test the hypothesis that ribosome association is central to the function of RACK1 in vivo, we determined the 2.1-A crystal structure of RACK1 from Saccharomyces cerevisiae (Asc1p) and used it to design eight mutant versions of RACK1 to assess roles in ribosome binding and in vivo function. Conserved charged amino acids on one side of the beta-propeller structure were found to confer most of the 40S subunit binding affinity, whereas an adjacent conserved and structured loop had little effect on RACK1-ribosome association. Yeast mutations that confer moderate to strong defects in ribosome binding mimic some phenotypes of a RACK1 deletion strain, including increased sensitivity to drugs affecting cell wall biosynthesis and translation elongation. Furthermore, disruption of RACK1's position at the 40S ribosomal subunit results in the failure of the mRNA binding protein Scp160 to associate with actively translating ribosomes. These results provide the first direct evidence that RACK1 functions from the ribosome, implying a physical link between the eukaryotic ribosome and cell signaling pathways in vivo.

  7. Cilia in the nervous system: linking cilia function and neurodevelopmental disorders

    PubMed Central

    Lee, Ji E.; Gleeson, Joseph G.

    2014-01-01

    Purpose of review Ciliopathies are genetic disorders caused by defects of primary ciliary structure and/or function and are characterized by pleiotropic clinical features. The ciliopathies include several partially overlapping syndromes such as Joubert syndrome, Bardet–Biedl syndrome and Meckel–Gruber syndrome, all of which have pronounced neurodevelopmental features. Here we focus on potential roles of cilia in central nervous system function, to explore how impairments may cause brain malformation and neurodevelopmental disease. Recent findings Cilia have long been considered as ‘sensory cellular antennae’, responding as chemo-sensors, mechano-sensors and thermo-sensors, although their roles in development were not well understood until recently. The surprising finding that disparate syndromes are all due to defects of the primary cilia, along with the recent advances in genetics, has helped elucidate further roles of primary cilia beyond sensory functions. Several molecules that are associated with key signaling pathways have been discovered in primary cilia. These include sonic hedgehog, wingless, planar cell polarity and fibroblast growth factor, which are essential for many cellular processes. Additionally, mutations in ‘ciliome’ genes have largely shown developmental defects such as abnormal body axis and brain malformation, implying disrupted cilia-related signaling pathways. Accordingly, the emerging theme is that primary cilia may play roles as modulators of signal transduction to help shape cellular responses within the environmental context during both development and homeostasis. Summary The link between cilia and signal pathways has become a framework for understanding the pathogenesis of ciliopathies. Despite recent progress in ciliary biology, fundamental questions remain about how cilia regulate neuronal function in the central nervous system. Therefore, investigation of ciliary function in the nervous system may reveal cilia

  8. Cilia in the nervous system: linking cilia function and neurodevelopmental disorders.

    PubMed

    Lee, Ji E; Gleeson, Joseph G

    2011-04-01

    Ciliopathies are genetic disorders caused by defects of primary ciliary structure and/or function and are characterized by pleiotropic clinical features. The ciliopathies include several partially overlapping syndromes such as Joubert syndrome, Bardet-Biedl syndrome and Meckel-Gruber syndrome, all of which have pronounced neurodevelopmental features. Here we focus on potential roles of cilia in central nervous system function, to explore how impairments may cause brain malformation and neurodevelopmental disease. Cilia have long been considered as 'sensory cellular antennae', responding as chemo-sensors, mechano-sensors and thermo-sensors, although their roles in development were not well understood until recently. The surprising finding that disparate syndromes are all due to defects of the primary cilia, along with the recent advances in genetics, has helped elucidate further roles of primary cilia beyond sensory functions. Several molecules that are associated with key signaling pathways have been discovered in primary cilia. These include sonic hedgehog, wingless, planar cell polarity and fibroblast growth factor, which are essential for many cellular processes. Additionally, mutations in 'ciliome' genes have largely shown developmental defects such as abnormal body axis and brain malformation, implying disrupted cilia-related signaling pathways. Accordingly, the emerging theme is that primary cilia may play roles as modulators of signal transduction to help shape cellular responses within the environmental context during both development and homeostasis. The link between cilia and signal pathways has become a framework for understanding the pathogenesis of ciliopathies. Despite recent progress in ciliary biology, fundamental questions remain about how cilia regulate neuronal function in the central nervous system. Therefore, investigation of ciliary function in the nervous system may reveal cilia-modulating mechanisms in neurodevelopmental processes, as well

  9. Age-Related Long-Term Functional Results after Riboflavin UV A Corneal Cross-Linking.

    PubMed

    Caporossi, Aldo; Mazzotta, Cosimo; Baiocchi, Stefano; Caporossi, Tomaso; Denaro, Rosario

    2011-01-01

    Purpose. To report a comparative prospective long-term functional analysis after Riboflavin UV A corneal cross-linking (CXL) in three different age groups of patients affected by progressive keratoconus (KC). Methods. Functional analysis comprised paediatric patients (≤18 years) included 152 eyes (29.5%); intermediate group (19-26 years) 286 eyes (55.4%), and adults (≥27 years) 78 eyes (15.1%). CXL was performed according to the Siena protocol by using the Vega CBM (Caporossi-Baiocchi-Mazzotta) X linker (CSO, Florence, Italy) at Siena University by the same authors. Pre- and post-op examinations included UCVA, BSCVA, corneal topography, and surface aberrometry (CSO Eye Top, Florence, Italy), at 48 months followup. Results. At 48 months followup paediatrics, intermediate, and adult patients showed a mean gain in UCVA of +0.2, +0.14 and +0.12 Snellen lines. BSCVA gained by a mean of +0.21, +0.2, and +0.1 Snellen lines. K(max) was reduced by a mean value of -0.9 D, -0.6 D, and -0.5 D, respectively. Coma values improved by a mean of -0.45 μm, -0.91 μm, and -0.19 μm, respectively. Treatment ensured a long-term keratoconus stabilization in over 90% of treated patients. Conclusion. According to our long-term comparative results, epithelium-off Riboflavin UV A cross-linking should be the first choice therapy of progressive KC, particularly in paediatric age and patients under 26 years.

  10. Age-Related Long-Term Functional Results after Riboflavin UV A Corneal Cross-Linking

    PubMed Central

    Caporossi, Aldo; Mazzotta, Cosimo; Baiocchi, Stefano; Caporossi, Tomaso; Denaro, Rosario

    2011-01-01

    Purpose. To report a comparative prospective long-term functional analysis after Riboflavin UV A corneal cross-linking (CXL) in three different age groups of patients affected by progressive keratoconus (KC). Methods. Functional analysis comprised paediatric patients (≤18 years) included 152 eyes (29.5%); intermediate group (19–26 years) 286 eyes (55.4%), and adults (≥27 years) 78 eyes (15.1%). CXL was performed according to the Siena protocol by using the Vega CBM (Caporossi-Baiocchi-Mazzotta) X linker (CSO, Florence, Italy) at Siena University by the same authors. Pre- and post-op examinations included UCVA, BSCVA, corneal topography, and surface aberrometry (CSO Eye Top, Florence, Italy), at 48 months followup. Results. At 48 months followup paediatrics, intermediate, and adult patients showed a mean gain in UCVA of +0.2, +0.14 and +0.12 Snellen lines. BSCVA gained by a mean of +0.21, +0.2, and +0.1 Snellen lines. K max was reduced by a mean value of −0.9 D, −0.6 D, and −0.5 D, respectively. Coma values improved by a mean of −0.45 μm, −0.91 μm, and −0.19 μm, respectively. Treatment ensured a long-term keratoconus stabilization in over 90% of treated patients. Conclusion. According to our long-term comparative results, epithelium-off Riboflavin UV A cross-linking should be the first choice therapy of progressive KC, particularly in paediatric age and patients under 26 years. PMID:21837270

  11. 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

  12. Assessing intervention efficacy on high-risk drinkers using generalized linear mixed models with a new class of link functions.

    PubMed

    Prates, Marcos O; Aseltine, Robert H; Dey, Dipak K; Yan, Jun

    2013-11-01

    Unhealthy alcohol use is one of the leading causes of morbidity and mortality in the United States. Brief interventions with high-risk drinkers during an emergency department (ED) visit are of great interest due to their possible efficacy and low cost. In a collaborative study with patients recruited at 14 academic ED across the United States, we examined the self-reported number of drinks per week by each patient following the exposure to a brief intervention. Count data with overdispersion have been mostly analyzed with generalized linear mixed models (GLMMs), of which only a limited number of link functions are available. Different choices of link function provide different fit and predictive power for a particular dataset. We propose a class of link functions from an alternative way to incorporate random effects in a GLMM, which encompasses many existing link functions as special cases. The methodology is naturally implemented in a Bayesian framework, with competing links selected with Bayesian model selection criteria such as the conditional predictive ordinate (CPO). In application to the ED intervention study, all models suggest that the intervention was effective in reducing the number of drinks, but some new models are found to significantly outperform the traditional model as measured by CPO. The validity of CPO in link selection is confirmed in a simulation study that shared the same characteristics as the count data from high-risk drinkers. The dataset and the source code for the best fitting model are available in Supporting Information.

  13. Using joint ICA to link function and structure using MEG and DTI in schizophrenia.

    PubMed

    Stephen, J M; Coffman, B A; Jung, R E; Bustillo, J R; Aine, C J; Calhoun, V D

    2013-12-01

    In this study we employed joint independent component analysis (jICA) to perform a novel multivariate integration of magnetoencephalography (MEG) and diffusion tensor imaging (DTI) data to investigate the link between function and structure. This model-free approach allows one to identify covariation across modalities with different temporal and spatial scales [temporal variation in MEG and spatial variation in fractional anisotropy (FA) maps]. Healthy controls (HC) and patients with schizophrenia (SP) participated in an auditory/visual multisensory integration paradigm to probe cortical connectivity in schizophrenia. To allow direct comparisons across participants and groups, the MEG data were registered to an average head position and regional waveforms were obtained by calculating the local field power of the planar gradiometers. Diffusion tensor images obtained in the same individuals were preprocessed to provide FA maps for each participant. The MEG/FA data were then integrated using the jICA software (http://mialab.mrn.org/software/fit). We identified MEG/FA components that demonstrated significantly different (p<0.05) covariation in MEG/FA data between diagnostic groups (SP vs. HC) and three components that captured the predominant sensory responses in the MEG data. Lower FA values in bilateral posterior parietal regions, which include anterior/posterior association tracts, were associated with reduced MEG amplitude (120-170 ms) of the visual response in occipital sensors in SP relative to HC. Additionally, increased FA in a right medial frontal region was linked with larger amplitude late MEG activity (300-400 ms) in bilateral central channels for SP relative to HC. Step-wise linear regression provided evidence that right temporal, occipital and late central components were significant predictors of reaction time and cognitive performance based on the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) cognitive assessment

  14. Using joint ICA to link function and structure using MEG and DTI in schizophrenia

    PubMed Central

    Stephen, JM; Coffman, BA; Jung, RE; Bustillo, JR; Aine, CJ; Calhoun, VD

    2013-01-01

    In this study we employed joint independent component analysis (jICA) to perform a novel multivariate integration of magnetoencephalography (MEG) and diffusion tensor imaging (DTI) data to investigate the link between function and structure. This model-free approach allows one to identify covariation across modalities with different temporal and spatial scales [temporal variation in MEG and spatial variation in fractional anisotropy (FA) maps]. Healthy controls (HC) and patients with schizophrenia (SP) participated in an auditory/visual multisensory integration paradigm to probe cortical connectivity in schizophrenia. To allow direct comparisons across participants and groups, the MEG data were registered to an average head position and regional waveforms were obtained by calculating the local field power of the planar gradiometers. Diffusion tensor images obtained in the same individuals were preprocessed to provide FA maps for each participant. The MEG/FA data were then integrated using the jICA software (http://mialab.mrn.org/software/fit). We identified MEG/FA components that demonstrated significantly different (p < 0.05) covariation in MEG/FA data between diagnostic groups (SP vs. HC) and three components that captured the predominant sensory responses in the MEG data. Lower FA values in bilateral posterior parietal regions, which include anterior/posterior association tracts, were associated with reduced MEG amplitude (120-170 ms) of the visual response in occipital sensors in SP relative to HC. Additionally, increased FA in a right medial frontal region was linked with larger amplitude late MEG activity (300-400 ms) in bilateral central channels for SP relative to HC. Step-wise linear regression provided evidence that right temporal, occipital and late central components were significant predictors of reaction time and cognitive performance based on the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) cognitive assessment

  15. Protein O-linked ß-N-acetylglucosamine: A novel effector of cardiomyocyte metabolism and function

    PubMed Central

    Darley-Usmar, Victor M.; Ball, Lauren E.; Chatham, John C.

    2014-01-01

    The post-translational modification of serine and threonine residues of nuclear and cytoplasmic proteins by the O-linked attachment of the monosaccharide ß-N-acetyl-glucosamine (O-GlcNAc) is emerging as an important mechanism for the regulation of numerous biological processes critical for normal cell function. Active synthesis of O-GlcNAc is essential for cell viability and acute activation of pathways resulting in increased protein O-GlcNAc levels improves the tolerance of cells to a wide range of stress stimuli. Conversely sustained increases in O-GlcNAc levels have been implicated in numerous chronic disease states, especially as a pathogenic contributor to diabetic complications. There has been increasing interest in the role of O-GlcNAc in the heart and vascular system and acute activation of O-GlcNAc levels have been shown to reduce ischemia/reperfusion injury attenuate vascular injury responses as well mediate some of the detrimental effects of diabetes and hypertension on cardiac and vascular function. Here we provide an overview of our current understanding of pathways regulating protein O-GlcNAcylation, summarize the different methodologies for identifying and characterizing O-GlcNAcylated proteins and subsequently focus on two emerging areas: 1) the role of O-GlcNAc as a potential regulator of cardiac metabolism and 2) the cross talk between O-GlcNAc and reactive oxygen species. PMID:21878340

  16. Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

    SciTech Connect

    Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.; McCue, Lee Ann

    2013-10-01

    To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.

  17. A simple structure wavelet transform circuit employing function link neural networks and SI filters

    NASA Astrophysics Data System (ADS)

    Mu, Li; Yigang, He

    2016-12-01

    Signal processing by means of analog circuits offers advantages from a power consumption viewpoint. Implementing wavelet transform (WT) using analog circuits is of great interest when low-power consumption becomes an important issue. In this article, a novel simple structure WT circuit in analog domain is presented by employing functional link neural network (FLNN) and switched-current (SI) filters. First, the wavelet base is approximated using FLNN algorithms for giving a filter transfer function that is suitable for simple structure WT circuit implementation. Next, the WT circuit is constructed with the wavelet filter bank, whose impulse response is the approximated wavelet and its dilations. The filter design that follows is based on a follow-the-leader feedback (FLF) structure with multiple output bilinear SI integrators and current mirrors as the main building blocks. SI filter is well suited for this application since the dilation constant across different scales of the transform can be precisely implemented and controlled by the clock frequency of the circuit with the same system architecture. Finally, to illustrate the design procedure, a seventh-order FLNN-approximated Gaussian wavelet is implemented as an example. Simulations have successfully verified that the designed simple structure WT circuit has low sensitivity, low-power consumption and litter effect to the imperfections.

  18. Linking Functional Domains of the Human Insulin Receptor with the Bacterial Aspartate Receptor

    NASA Astrophysics Data System (ADS)

    Ellis, Leland; Morgan, David O.; Koshland, Daniel E.; Clauser, Eric; Moe, Gregory R.; Bollag, Gideon; Roth, Richard A.; Rutter, William J.

    1986-11-01

    A hybrid receptor has been constructed that is composed of the extracellular domain of the human insulin receptor fused to the transmembrane and cytoplasmic domains of the bacterial aspartate chemoreceptor. This hybrid protein can be expressed in rodent (CHO) cells and displays several functional features comparable to wild-type insulin receptor. It is localized to the cell surface, binds insulin with high affinity, forms oligomers, and is recognized by conformation-specific monoclonal antibodies. Although most of the expressed protein accumulates as a 180-kDa proreceptor, some processed 135-kDa receptor can be detected on the cell surface by covalent cross-linking. Expression of the hybrid receptor inhibits the insulin-activated uptake of 2-deoxyglucose by CHO cells. Thus, this hybrid is partially functional and can be processed; however, it is incapable of native transmembrane signaling. The results indicate that the intact domains of different types of receptors can retain some of the native features in a hybrid molecule but specific requirements will need to be satisfied for transmembrane signaling.

  19. 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.

  20. Using ecological production functions to link ecological processes to ecosystem services.

    PubMed

    Bruins, Randall Jf; Canfield, Timothy J; Duke, Clifford; Kapustka, Larry; Nahlik, Amanda M; Schäfer, Ralf B

    2017-01-01

    Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively little attention. Ecological production functions may be defined as usable expressions (i.e., models) of the processes by which ecosystems produce ES, often including external influences on those processes. We identify key attributes of EPFs and discuss both actual and idealized examples of their use to inform decision making. Whenever possible, EPFs should estimate final, rather than intermediate, ES. Although various types of EPFs have been developed, we suggest that EPFs are more useful for decision making if they quantify ES outcomes, respond to ecosystem condition, respond to stressor levels or management scenarios, reflect ecological complexity, rely on data with broad coverage, have performed well previously, are practical to use, and are open and transparent. In an example using pesticides, we illustrate how EPFs with these attributes could enable the inclusion of ES in ecological risk assessment. The biggest challenges to ES inclusion are limited data sets that are easily adapted for use in modeling EPFs and generally poor understanding of linkages among ecological components and the processes that ultimately deliver the ES. We conclude by advocating for the incorporation into EPFs of added ecological complexity and greater ability to represent the trade-offs among ES. Integr Environ Assess Manag 2017;13:52-61. © 2016 SETAC.

  1. 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.

  2. A generalized linear mixed model for longitudinal binary data with a marginal logit link function

    PubMed Central

    Parzen, Michael; Ghosh, Souparno; Lipsitz, Stuart; Sinha, Debajyoti; Fitzmaurice, Garrett M.; Mallick, Bani K.; Ibrahim, Joseph G.

    2010-01-01

    Summary Longitudinal studies of a binary outcome are common in the health, social, and behavioral sciences. In general, a feature of random effects logistic regression models for longitudinal binary data is that the marginal functional form, when integrated over the distribution of the random effects, is no longer of logistic form. Recently, Wang and Louis (2003) proposed a random intercept model in the clustered binary data setting where the marginal model has a logistic form. An acknowledged limitation of their model is that it allows only a single random effect that varies from cluster to cluster. In this paper, we propose a modification of their model to handle longitudinal data, allowing separate, but correlated, random intercepts at each measurement occasion. The proposed model allows for a flexible correlation structure among the random intercepts, where the correlations can be interpreted in terms of Kendall’s τ. For example, the marginal correlations among the repeated binary outcomes can decline with increasing time separation, while the model retains the property of having matching conditional and marginal logit link functions. Finally, the proposed method is used to analyze data from a longitudinal study designed to monitor cardiac abnormalities in children born to HIV-infected women. PMID:21532998

  3. Expression of integrin-linked kinase improves cardiac function in a swine model of myocardial infarction

    PubMed Central

    Lu, Wen; Xie, Jun; Gu, Rong; Xu, Biao

    2017-01-01

    Previous studies have described the beneficial effects of overexpressing integrin-linked kinase (ILK) after myocardial infarction (MI) in small animal models. However, the effects of ILK in pre-clinical large animals are not known. To move closer to clinical translation, we examined the effects of ILK gene transfer in a swine model of ischemic heart disease. Swine received percutaneous intracoronary injections of adenoviral vector expressing ILK (n=10) or empty ad-null (n=10) in the left anterior descending coronary artery (LAD) following LAD occlusion. Four weeks after transfection, we confirmed that transgene expression was restricted to the infarcted area in the cardiac tissue. Imaging studies demonstrated preserved cardiac function in the ILK group. ILK treatment was associated with reduced infarcted scar size and preserved left ventricular (LV) geometry (LV diameter and LV wall thickness). Enhanced angiogenesis was preserved in the ILK animals, along with reduction of apoptosis. ILK gene therapy improves cardiac remodeling and function in swine following MI associated with increased angiogenesis, reduced apoptosis, and increased cardiomyocyte proliferation with no signs of toxicity. These results may deliver a new approach to treat post-infarct remodeling and subsequent heart failure. PMID:28565779

  4. PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

    PubMed Central

    Gupte, Rebecca; Liu, Ziying; Kraus, W. Lee

    2017-01-01

    The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field. PMID:28202539

  5. PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes.

    PubMed

    Gupte, Rebecca; Liu, Ziying; Kraus, W Lee

    2017-01-15

    The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field. © 2017 Gupte et al.; Published by Cold Spring Harbor Laboratory Press.

  6. Link between mast cells and bacteria: Antimicrobial defense, function and regulation by cytokines.

    PubMed

    Conti, Pio; Carinci, Francesco; Caraffa, Alessandro; Ronconi, Gianpaolo; Lessiani, Gianfranco; Theoharides, Theoharis C

    2017-09-01

    Bacteria and their products, such as LPS, act on mast cells (MCs) to induce the secretion of multiple cytokines, including IL-1, TNF, IL-18 and IL-33, which can be dosed in the site of infected tissues. Antigen-binding IgE cross-links FcεRI on mast cells involves the generation and activation of PKCδ, ERK, tyrosine kinases (Syk and Lyn) and mitogen-activated protein kinases (MAPKs), inducing the release of chemical mediators which provoke inflammation and hypersensitive reaction. Other stimuli, including, cytokines, neuropeptides, chemical and physical activators, can also act on MCs to release a plethora of inflammatory compounds. Activated MCs produce a broad spectrum of inflammatory cytokines, chemokines, lipid compounds and vasoactive amines, all involved in immune response. By producing TNF, MCs have an antibacterial defense and a protective function; while pathogenic bacteria and their products, such as LPS, have an inflammatory response through MC activation. LPS binding TLR4 produce MC generation IL-1 family members, and chemokines, which may recruit inflammatory cells at the infection site; whereas in Kit(W/W-v) mice, where MCs are genetically absent, the inflammatory effect is not present. We report for the first time a link between MCs and bacteria emphasizing the mediation of inflammatory cytokines/chemokines. We can conclude that mast cells fight bacteria, and their immune response is perfectly integrated in the immune network. We hope that the understanding of microbial and mast cell interaction leads to more efficient therapeutic development in relation to microbial resistance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. A neural network that links brain function, white-matter structure and risky behavior.

    PubMed

    Kohno, Milky; Morales, Angelica M; Guttman, Zoe; London, Edythe D

    2017-04-01

    The ability to evaluate the balance between risk and reward and to adjust behavior accordingly is fundamental to adaptive decision-making. Although brain-imaging studies consistently have shown involvement of the dorsolateral prefrontal cortex, anterior insula and striatum during risky decision-making, activation in a neural network formed by these regions has not been linked to structural connectivity. Therefore, in this study, white-matter connectivity was measured with diffusion-weighted imaging in 40 healthy research participants who performed the Balloon Analogue Risk Task, a test of risky decision-making, during fMRI. Fractional anisotropy within a network that includes white-matter pathways connecting four regions (the prefrontal cortex, insula and midbrain to the striatum) was positively correlated with the number of risky choices and total amount earned on the task, and with the parametric modulation of activation in regions within the network to the level of risk during choice selection. Furthermore, analysis using a mixed model demonstrated how relationships of the parametric modulation of activation in each of the four aforementioned regions are related to risk probabilities, and how previous trial outcomes and task progression influence the choice to take risk. The present findings provide the first direct evidence that white-matter integrity is linked to function within previously identified components of a network that is activated during risky decision-making, and demonstrate that the integrity of white-matter tracts is critical in consolidating and processing signals between cortical and striatal circuits during the decision-making process.

  8. Linking human brain local activity fluctuations to structural and functional network architectures

    PubMed Central

    Baria, A.T.; Mansour, A.; Huang, L.; Baliki, M.N.; Cecchi, G.A.; Mesulam, M.M.; Apkarian, A.V.

    2013-01-01

    Activity of cortical local neuronal populations fluctuates continuously, and a large proportion of these fluctuations are shared across populations of neurons. Here we seek organizational rules that link these two phenomena. Using neuronal activity, as identified by functional MRI (fMRI) and for a given voxel or brain region, we derive a single measure of full bandwidth brain-oxygenation-level-dependent (BOLD) fluctuations by calculating the slope, α, for the log-linear power spectrum. For the same voxel or region, we also measure the temporal coherence of its fluctuations to other voxels or regions, based on exceeding a given threshold, Θ, for zero lag correlation, establishing functional connectivity between pairs of neuronal populations. From resting state fMRI, we calculated whole-brain group-averaged maps for α and for functional connectivity. Both maps showed similar spatial organization, with a correlation coefficient of 0.75 between the two parameters across all brain voxels, as well as variability with hodology. A computational model replicated the main results, suggesting that synaptic low-pass filtering can account for these interrelationships. We also investigated the relationship between α and structural connectivity, as determined by diffusion tensor imaging-based tractography. We observe that the correlation between α and connectivity depends on attentional state; specifically, α correlated more highly to structural connectivity during rest than while attending to a task. Overall, these results provide global rules for the dynamics between frequency characteristics of local brain activity and the architecture of underlying brain networks. PMID:23396160

  9. Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function.

    PubMed

    Nazarov, Petr V; Reinsbach, Susanne E; Muller, Arnaud; Nicot, Nathalie; Philippidou, Demetra; Vallar, Laurent; Kreis, Stephanie

    2013-03-01

    MicroRNAs (miRNAs) are ubiquitously expressed small non-coding RNAs that, in most cases, negatively regulate gene expression at the post-transcriptional level. miRNAs are involved in fine-tuning fundamental cellular processes such as proliferation, cell death and cell cycle control and are believed to confer robustness to biological responses. Here, we investigated simultaneously the transcriptional changes of miRNA and mRNA expression levels over time after activation of the Janus kinase/Signal transducer and activator of transcription (Jak/STAT) pathway by interferon-γ stimulation of melanoma cells. To examine global miRNA and mRNA expression patterns, time-series microarray data were analysed. We observed delayed responses of miRNAs (after 24-48 h) with respect to mRNAs (12-24 h) and identified biological functions involved at each step of the cellular response. Inference of the upstream regulators allowed for identification of transcriptional regulators involved in cellular reactions to interferon-γ stimulation. Linking expression profiles of transcriptional regulators and miRNAs with their annotated functions, we demonstrate the dynamic interplay of miRNAs and upstream regulators with biological functions. Finally, our data revealed network motifs in the form of feed-forward loops involving transcriptional regulators, mRNAs and miRNAs. Additional information obtained from integrating time-series mRNA and miRNA data may represent an important step towards understanding the regulatory principles of gene expression.

  10. Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function

    PubMed Central

    Nazarov, Petr V.; Reinsbach, Susanne E.; Muller, Arnaud; Nicot, Nathalie; Philippidou, Demetra; Vallar, Laurent; Kreis, Stephanie

    2013-01-01

    MicroRNAs (miRNAs) are ubiquitously expressed small non-coding RNAs that, in most cases, negatively regulate gene expression at the post-transcriptional level. miRNAs are involved in fine-tuning fundamental cellular processes such as proliferation, cell death and cell cycle control and are believed to confer robustness to biological responses. Here, we investigated simultaneously the transcriptional changes of miRNA and mRNA expression levels over time after activation of the Janus kinase/Signal transducer and activator of transcription (Jak/STAT) pathway by interferon-γ stimulation of melanoma cells. To examine global miRNA and mRNA expression patterns, time-series microarray data were analysed. We observed delayed responses of miRNAs (after 24–48 h) with respect to mRNAs (12–24 h) and identified biological functions involved at each step of the cellular response. Inference of the upstream regulators allowed for identification of transcriptional regulators involved in cellular reactions to interferon-γ stimulation. Linking expression profiles of transcriptional regulators and miRNAs with their annotated functions, we demonstrate the dynamic interplay of miRNAs and upstream regulators with biological functions. Finally, our data revealed network motifs in the form of feed-forward loops involving transcriptional regulators, mRNAs and miRNAs. Additional information obtained from integrating time-series mRNA and miRNA data may represent an important step towards understanding the regulatory principles of gene expression. PMID:23335783

  11. Sevoflurane Alters Spatiotemporal Functional Connectivity Motifs That Link Resting-State Networks during Wakefulness

    PubMed Central

    Kafashan, MohammadMehdi; Ching, ShiNung; Palanca, Ben J. A.

    2016-01-01

    Background: The spatiotemporal patterns of correlated neural activity during the transition from wakefulness to general anesthesia have not been fully characterized. Correlation analysis of blood-oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI) allows segmentation of the brain into resting-state networks (RSNs), with functional connectivity referring to the covarying activity that suggests shared functional specialization. We quantified the persistence of these correlations following the induction of general anesthesia in healthy volunteers and assessed for a dynamic nature over time. Methods: We analyzed human fMRI data acquired at 0 and 1.2% vol sevoflurane. The covariance in the correlated activity among different brain regions was calculated over time using bounded Kalman filtering. These time series were then clustered into eight orthogonal motifs using a K-means algorithm, where the structure of correlated activity throughout the brain at any time is the weighted sum of all motifs. Results: Across time scales and under anesthesia, the reorganization of interactions between RSNs is related to the strength of dynamic connections between member pairs. The covariance of correlated activity between RSNs persists compared to that linking individual member pairs of different RSNs. Conclusions: Accounting for the spatiotemporal structure of correlated BOLD signals, anesthetic-induced loss of consciousness is mainly associated with the disruption of motifs with intermediate strength within and between members of different RSNs. In contrast, motifs with higher strength of connections, predominantly with regions-pairs from within-RSN interactions, are conserved among states of wakefulness and sevoflurane general anesthesia. PMID:28082871

  12. Positive selection in octopus haemocyanin indicates functional links to temperature adaptation.

    PubMed

    Oellermann, Michael; Strugnell, Jan M; Lieb, Bernhard; Mark, Felix C

    2015-07-05

    Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the

  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. Morphological and functional correlations in riboflavin UV A corneal collagen cross-linking for keratoconus.

    PubMed

    Mazzotta, Cosimo; Caporossi, Tomaso; Denaro, Rosario; Bovone, Cristina; Sparano, Caterina; Paradiso, Anna; Baiocchi, Stefano; Caporossi, Aldo

    2012-05-01

    To investigate the correlations between corneal structural modifications assessed by in vivo corneal confocal microscopy with visual function [uncorrected visual acuity (UCVA), best spectacle-corrected visual acuity (BSCVA)] and morphological data (corneal topography, pachymetry, elevation analysis) after riboflavin UV A corneal collagen cross-linking (CXL) for the stabilization of progressive keratoconus. Forty-four eyes with progressive keratoconus were enrolled in the Siena Eye Cross Study (prospective nonrandomized phase II open trial). All eyes underwent Riboflavin UV A CXL. Preoperative and postoperative evaluation comprised: UCVA, BSCVA, optical pachymetry (Visante OCT, Zeiss, Germany), corneal topography (CSO, Florence, Italy) and tomography (Orbscan IIz; B&L, Rochester, NY, USA) and in vivo confocal microscopy (Heidelberg Retina Tomograph II; Rostock, Heidelberg Gmbh, Germany). Examinations were performed preoperatively 6 months and one day before treatment and at 1, 3, 6 and 12 months of follow-up. In vivo corneal confocal microscopy showed time-dependent postoperative epithelial and stromal modifications after cross-linking. Epithelial thinning associated with stromal oedema and keratocytes apoptosis explained initial tendency towards slightly reduced VA and more glare one month postoperatively in 70% of eyes. Furthermore, a statistically not significant early worsening of topographic mean K values was observed. Orbscan II analysis significantly underestimated pachymetric values after treatment. Pachymetric underestimation was rectified by high-resolution optical pachymetry provided by the Visante OCT system. After the third post-CXL month, epithelial thickening, disappearance of oedema and new collagen compaction recorded by in vivo corneal confocal microscopy explained the improvements in visual performance during the follow-up. Changes in stromal reflectivity and collagen compaction observed by in vivo confocal microscopy were associated with corneal

  15. Identification of new surfaces of cofilin that link mitochondrial function to the control of multi-drug resistance.

    PubMed

    Kotiadis, Vassilios N; Leadsham, Jane E; Bastow, Emma L; Gheeraert, Aline; Whybrew, Jennafer M; Bard, Martin; Lappalainen, Pekka; Gourlay, Campbell W

    2012-05-01

    ADF/cofilin family proteins are essential regulators of actin cytoskeletal dynamics. Recent evidence also implicates cofilin in the regulation of mitochondrial function. Here, we identify new functional surfaces of cofilin that are linked with mitochondrial function and stress responses in the budding yeast Saccharomyces cerevisiae. Our data link surfaces of cofilin that are involved in separable activities of actin filament disassembly or stabilisation, to the regulation of mitochondrial morphology and the activation status of Ras, respectively. Importantly, charge alterations to conserved surfaces of cofilin that do not interfere with its actin regulatory activity lead to a dramatic increase in respiratory function that triggers a retrograde signal to upregulate a battery of ABC transporters and concurrent metabolic changes that support multi-drug resistance. We hypothesise that cofilin functions within a bio-sensing system that connects the cytoskeleton and mitochondrial function to environmental challenge.

  16. Identification of new surfaces of cofilin that link mitochondrial function to the control of multi-drug resistance

    PubMed Central

    Kotiadis, Vassilios N.; Leadsham, Jane E.; Bastow, Emma L.; Gheeraert, Aline; Whybrew, Jennafer M.; Bard, Martin; Lappalainen, Pekka; Gourlay, Campbell W.

    2012-01-01

    ADF/cofilin family proteins are essential regulators of actin cytoskeletal dynamics. Recent evidence also implicates cofilin in the regulation of mitochondrial function. Here, we identify new functional surfaces of cofilin that are linked with mitochondrial function and stress responses in the budding yeast Saccharomyces cerevisiae. Our data link surfaces of cofilin that are involved in separable activities of actin filament disassembly or stabilisation, to the regulation of mitochondrial morphology and the activation status of Ras, respectively. Importantly, charge alterations to conserved surfaces of cofilin that do not interfere with its actin regulatory activity lead to a dramatic increase in respiratory function that triggers a retrograde signal to upregulate a battery of ABC transporters and concurrent metabolic changes that support multi-drug resistance. We hypothesise that cofilin functions within a bio-sensing system that connects the cytoskeleton and mitochondrial function to environmental challenge. PMID:22344251

  17. A high accuracy pedestrian detection system combining a cascade AdaBoost detector and random vector functional-link net.

    PubMed

    Wang, Zhihui; Yoon, Sook; Xie, Shan Juan; Lu, Yu; Park, Dong Sun

    2014-01-01

    In pedestrian detection methods, their high accuracy detection rates are always obtained at the cost of a large amount of false pedestrians. In order to overcome this problem, the authors propose an accurate pedestrian detection system based on two machine learning methods: cascade AdaBoost detector and random vector functional-link net. During the offline training phase, the parameters of a cascade AdaBoost detector and random vector functional-link net are trained by standard dataset. These candidates, extracted by the strategy of a multiscale sliding window, are normalized to be standard scale and verified by the cascade AdaBoost detector and random vector functional-link net on the online phase. Only those candidates with high confidence can pass the validation. The proposed system is more accurate than other single machine learning algorithms with fewer false pedestrians, which has been confirmed in simulation experiment on four datasets.

  18. A High Accuracy Pedestrian Detection System Combining a Cascade AdaBoost Detector and Random Vector Functional-Link Net

    PubMed Central

    Yoon, Sook; Xie, Shan Juan; Park, Dong Sun

    2014-01-01

    In pedestrian detection methods, their high accuracy detection rates are always obtained at the cost of a large amount of false pedestrians. In order to overcome this problem, the authors propose an accurate pedestrian detection system based on two machine learning methods: cascade AdaBoost detector and random vector functional-link net. During the offline training phase, the parameters of a cascade AdaBoost detector and random vector functional-link net are trained by standard dataset. These candidates, extracted by the strategy of a multiscale sliding window, are normalized to be standard scale and verified by the cascade AdaBoost detector and random vector functional-link net on the online phase. Only those candidates with high confidence can pass the validation. The proposed system is more accurate than other single machine learning algorithms with fewer false pedestrians, which has been confirmed in simulation experiment on four datasets. PMID:24959598

  19. Content analysis of 4 fear of falling rating scales by linking to the international classification of functioning, disability and health.

    PubMed

    Bladh, Stina; Nilsson, Maria H; Carlsson, Gunilla; Lexell, Jan

    2013-07-01

    To gain a deeper understanding of the content of 4 fear of falling (FOF) rating scales by linking them to the International Classification of Functioning, Disability and Health (ICF). Linking study according to the ICF linking rules. Not applicable. Not applicable. The rating scales were the Falls Efficacy Scale-International (FES-I), the Swedish version of the Falls Efficacy Scale (FES[S]), the Activities-specific Balance Confidence Scale (ABC), and the modified Survey of Activities and Fear of Falling in the Elderly (SAFFE). The process followed the established and updated linking rules. Three linkers independently identified all meaningful concepts in the rating scales and linked them to the most precise ICF categories. The linkers then discussed their results to reach consensus. If consensus was not attained, the linkers pursued the discussions with a fourth person to reach consensus. Not applicable. Most meaningful concepts from the overall questions were linked to the ICF component of body functions. Of the 62 items, all but one meaningful concept were linked to the component of activities and participation. All 4 rating scales covered the chapters of mobility and domestic life and had most linkages to the mobility chapter. The linking process revealed similarities and differences between the 4 FOF rating scales, as well as methodologic challenges in linking instruments to the ICF. By providing a content description that allows for a direct comparison of the rating scales, the results may be helpful when choosing an appropriate rating scale assessing FOF in clinical practice and research. A further head-to-head comparison through psychometric analyses is required to recommend appropriate FOF rating scales. Studies are also needed to investigate how the overall question and response categories of a rating scale affect respondents' answers. Copyright © 2013 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  20. 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.

  1. Linking magnetite in the abdomen of honey bees to a magnetoreceptive function

    PubMed Central

    Lambinet, Veronika; Hayden, Michael E.; Reigl, Katharina; Gomis, Surath

    2017-01-01

    Previous studies of magnetoreception in honey bees, Apis mellifera, focused on the identification of magnetic material, its formation, the location of the receptor and potential underlying sensory mechanisms, but never directly linked magnetic material to a magnetoreceptive function. In our study, we demonstrate that ferromagnetic material consistent with magnetite plays an integral role in the bees' magnetoreceptor. Subjecting lyophilized and pelletized bee tagmata to analyses by a superconducting quantum interference device generated a distinct hysteresis loop for the abdomen but not for the thorax or the head of bees, indicating the presence of ferromagnetic material in the bee abdomen. Magnetic remanence of abdomen pellets produced from bees that were, or were not, exposed to the 2.2-kOe field of a magnet while alive differed, indicating that magnet exposure altered the magnetization of this magnetite in live bees. In behavioural two-choice field experiments, bees briefly exposed to the same magnet, but not sham-treated control bees, failed to sense a custom-generated magnetic anomaly, indicating that magnet exposure had rendered the bees' magnetoreceptor dysfunctional. Our data support the conclusion that honey bees possess a magnetite-based magnetoreceptor located in the abdomen. PMID:28330921

  2. Chromium functionalized diglyme plasma polymer coating enhances enzyme-linked immunosorbent assay performance.

    PubMed

    Welch, Nicholas G; Madiona, Robert M T; Easton, Christopher D; Scoble, Judith A; Jones, Robert T; Muir, Benjamin W; Pigram, Paul J

    2016-11-10

    Ensuring the optimum orientation, conformation, and density of substrate-bound antibodies is critical for the success of sandwich enzyme-linked immunosorbent assays (ELISAs). In this work, the authors utilize a diethylene glycol dimethyl ether plasma polymer (DGpp) coating, functionalized with chromium within a 96 well plate for the enhanced immobilization of a capture antibody. For an equivalent amount of bound antibody, a tenfold improvement in the ELISA signal intensity is obtained on the DGpp after incubation with chromium, indicative of improved orientation on this surface. Time-of-flight secondary-ion-mass-spectrometry (ToF-SIMS) and principal component analysis were used to probe the molecular species at the surface and showed ion fragments related to lysine, methionine, histidine, and arginine coupled to chromium indicating candidate antibody binding sites. A combined x-ray photoelectron spectroscopy and ToF-SIMS analysis provided a surface molecular characterization that demonstrates antibody binding via the chromium complex. The DGpp+Cr surface treatment holds great promise for improving the efficacy of ELISAs.

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

    PubMed Central

    CHANDA, Anindya; ROZE, Ludmila; PASTOR, Alicia; FRAME, Melinda; LINZ, John E.

    2009-01-01

    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 36h 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. PMID:19358865

  4. Physicochemical and functional properties of ultrasonic-treated tragacanth hydrogels cross-linked to lysozyme.

    PubMed

    Koshani, Roya; Aminlari, Mahmoud

    2017-10-01

    The purpose of this study was to prepare, characterize and investigate physiochemical and functional attributes of hen egg white lysozyme (LZM) cross-linked with ultrasonic-treated tragacanth (US-treated TGC) under mild Maillard reactions conditions. FT-IR spectroscopy together with OPA assay revealed that covalent attachment of LZM with TCG's. Under optimum condition (pH=8.5, 60°C, RH=79%, 8 days), only one of the free amino group of LZM was blocked by TGC whereas under the same condition, US treated-TGC's blocked about three amino groups. The thermal stability of the LZM-TGC conjugates differed depending on the lengths of the main and branch chains. The microstructure of LZM-TGC conjugates was characterized by scanning electron microscopy. US-treated TGC-LZM exhibited improved solubility, emulsion properties, foam capacity and stability as compared with the native LZM. Since this gum is extensively used in food industry and application of LZM as a natural antimicrobial agents in different food systems is recommended and practiced in some countries, the results of this study indicates that a conjugated product of these two polymers combines different properties into one macromolecule and improves the property of each. These properties may make the conjugate an attractive food ingredient. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. 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

  6. 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

  7. Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).

    PubMed

    Engel, Annette Summers; Meisinger, Daniela B; Porter, Megan L; Payn, Robert A; Schmid, Michael; Stern, Libby A; Schleifer, K H; Lee, Natuschka M

    2010-01-01

    Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.

  8. Framework of Consciousness from Semblance of Activity at Functionally LINKed Postsynaptic Membranes

    PubMed Central

    Vadakkan, Kunjumon I.

    2010-01-01

    Consciousness is seen as a difficult “binding” problem. Binding, a process where different sensations evoked by an item are associated in the nervous system, can be viewed as a process similar to associative learning. Several reports that consciousness is associated with some form of memory imply that different forms of memories have a common feature contributing to consciousness. Based on a proposed synaptic mechanism capable of explaining different forms of memory, we developed a framework for consciousness. It is based on the formation of semblance of sensory stimulus from (1) synaptic semblances when excitatory postsynaptic potentials arrive at functionally LINKed postsynaptic membranes, and (2) network semblances when these potentials summate to elicit action potential initiating activity in a network of neurons. It is then possible to derive a framework for consciousness as a multi-dimensional semblance. According to this framework, a continuum of semblances formed from background sensory stimuli and oscillating neuronal activities serve to maintain consciousness. Feasibility of this framework to explain various physiological and pathological states of consciousness, its subjective nature and qualia is examined. PMID:21833231

  9. Integrin-linked kinase is an adaptor with essential functions during mouse development.

    PubMed

    Lange, Anika; Wickström, Sara A; Jakobson, Madis; Zent, Roy; Sainio, Kirsi; Fässler, Reinhard

    2009-10-15

    The development of multicellular organisms requires integrin-mediated interactions between cells and their extracellular environment. Integrin binding to extracellular matrix catalyses assembly of multiprotein complexes, which transduce mechanical and chemical signals that regulate many aspects of cell physiology. Integrin-linked kinase (Ilk) is a multifunctional protein that binds beta-integrin cytoplasmic domains and regulates actin dynamics by recruiting actin binding regulatory proteins such as alpha- and beta-parvin. Ilk has also been shown to possess serine/threonine kinase activity and to phosphorylate signalling proteins such as Akt1 and glycogen synthase kinase 3beta (Gsk3beta) in mammalian cells; however, these functions have been shown by genetic studies not to occur in flies and worms. Here we show that mice carrying point mutations in the proposed autophosphorylation site of the putative kinase domain and in the pleckstrin homology domain are normal. In contrast, mice with point mutations in the conserved lysine residue of the potential ATP-binding site of the kinase domain, which mediates Ilk binding to alpha-parvin, die owing to renal agenesis. Similar renal defects occur in alpha-parvin-null mice. Thus, we provide genetic evidence that the kinase activity of Ilk is dispensable for mammalian development; however, an interaction between Ilk and alpha-parvin is critical for kidney development.

  10. Linking lung function and inflammatory responses in ventilator-induced lung injury.

    PubMed

    Cannizzaro, Vincenzo; Hantos, Zoltan; Sly, Peter D; Zosky, Graeme R

    2011-01-01

    Despite decades of research, the mechanisms of ventilator-induced lung injury are poorly understood. We used strain-dependent responses to mechanical ventilation in mice to identify associations between mechanical and inflammatory responses in the lung. BALB/c, C57BL/6, and 129/Sv mice were ventilated using a protective [low tidal volume and moderate positive end-expiratory pressure (PEEP) and recruitment maneuvers] or injurious (high tidal volume and zero PEEP) ventilation strategy. Lung mechanics and lung volume were monitored using the forced oscillation technique and plethysmography, respectively. Inflammation was assessed by measuring numbers of inflammatory cells, cytokine (IL-6, IL-1β, and TNF-α) levels, and protein content of the BAL. Principal components factor analysis was used to identify independent associations between lung function and inflammation. Mechanical and inflammatory responses in the lung were dependent on ventilation strategy and mouse strain. Three factors were identified linking 1) pulmonary edema, protein leak, and macrophages, 2) atelectasis, IL-6, and TNF-α, and 3) IL-1β and neutrophils, which were independent of responses in lung mechanics. This approach has allowed us to identify specific inflammatory responses that are independently associated with overstretch of the lung parenchyma and loss of lung volume. These data provide critical insight into the mechanical responses in the lung that drive local inflammation in ventilator-induced lung injury and the basis for future mechanistic studies in this field.

  11. 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. © The Author(s) 2014.

  12. 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

  13. 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.

  14. Adaptively combined FIR and functional link artificial neural network equalizer for nonlinear communication channel.

    PubMed

    Zhao, Haiquan; Zhang, Jiashu

    2009-04-01

    This paper proposes a novel computational efficient adaptive nonlinear equalizer based on combination of finite impulse response (FIR) filter and functional link artificial neural network (CFFLANN) to compensate linear and nonlinear distortions in nonlinear communication channel. This convex nonlinear combination results in improving the speed while retaining the lower steady-state error. In addition, since the CFFLANN needs not the hidden layers, which exist in conventional neural-network-based equalizers, it exhibits a simpler structure than the traditional neural networks (NNs) and can require less computational burden during the training mode. Moreover, appropriate adaptation algorithm for the proposed equalizer is derived by the modified least mean square (MLMS). Results obtained from the simulations clearly show that the proposed equalizer using the MLMS algorithm can availably eliminate various intensity linear and nonlinear distortions, and be provided with better anti-jamming performance. Furthermore, comparisons of the mean squared error (MSE), the bit error rate (BER), and the effect of eigenvalue ratio (EVR) of input correlation matrix are presented.

  15. Acidocalcisomes are functionally linked to the contractile vacuole of Dictyostelium discoideum.

    PubMed

    Marchesini, Norma; Ruiz, Felix A; Vieira, Mauricio; Docampo, Roberto

    2002-03-08

    The mass-dense granules of Dictyostelium discoideum were shown to contain large amounts of phosphorus, magnesium, and calcium, as determined by x-ray microanalysis, either in situ or when purified using iodixanol gradient centrifugation. The high phosphorus content was due to the presence of pyrophosphate and polyphosphate, which were also present in the contractile vacuoles. Both organelles also possessed a vacuolar H(+)-ATPase, an H(+)-pyrophosphatase, and a Ca(2+)-ATPase, as determined by biochemical methods or by immunofluorescence microscopy. The H(+)-pyrophosphatase activity of isolated mass-dense granules was stimulated by potassium ions and inhibited by the pyrophosphate analogs aminomethylenediphosphonate and imidodiphosphate and by KF and N-ethylmaleimide in a dose-dependent manner. The mass-dense granules and the contractile vacuole appeared to contact each other when the cells were submitted to hyposmotic stress. Acetazolamide inhibited the carbonic anhydrase activity of the contractile vacuoles and prolonged their contraction cycle in a dose-dependent manner. Similar effects were observed with the anion exchanger inhibitor 4,4' -diisothiocyanatodihydrostilbene-2, 2' -disulfonic acid and the vacuolar H(+)-ATPase inhibitor bafilomycin A(1). Together, these results suggest that the mass-dense granules of D. discoideum are homologous to the acidocalcisomes described in protozoan parasites and are linked to the function of the contractile vacuole.

  16. Uncoupling of Energy-Linked Functions of Corn Mitochondria by Linoleic Acid and Monomethyldecenylsuccinic Acid 1

    PubMed Central

    Baddeley, M. Susan; Hanson, J. B.

    1967-01-01

    Linoleic acid and monomethyldecenylsuccinic acid were tested as uncoupling agents for energy linked functions of corn mitochondria. 2,4-dinitrophenol was used as a standard for comparison. Both compounds uncoupled oxidative phosphorylation, released oligomycin-blocked respiration, and accelerated adenosine triphosphatase. Linoleic acid uncoupled calcium-activated phosphate accumulation and the increase in light scattering that accompanies the accumulation. Unlike dinitrophenol, linoleic acid at 0.1 mm had a destructive effect on membrane semipermeability. Kinetic studies indicated that dinitrophenol and linoleic acid compete with phosphate for active sites in oxidative phosphorylation. Some linoleic acid is taken up by respiring mitochondria and a major share of the uptake is incorporated into phospholipids. Calcium ion and oligomycin promote the uptake, but coenzyme A does not. It is deduced that fatty acid probably attacks the non-phosphorylated intermediate, I∼X, producing X∼acyl. Uncoupling results from breakdown of X∼acyl, but sufficient X∼acyl is maintained to serve as a source of activated fatty acid. PMID:16656708

  17. Phosphorylation-dependent regulation of nuclear localization and functions of integrin-linked kinase

    PubMed Central

    Acconcia, Filippo; Barnes, Christopher J.; Singh, Rajesh R.; Talukder, Amjad H.; Kumar, Rakesh

    2007-01-01

    Integrin-linked kinase (ILK) is a phosphorylated protein that regulates physiological processes that overlap with those regulated by p21-activated kinase 1 (PAK1). Here we report the possible role of ILK phosphorylation by PAK1 in ILK-mediated signaling and intracellular translocation. We found that PAK1 phosphorylates ILK at threonine-173 and serine-246 in vitro and in vivo. Depletion of PAK1 decreased the levels of endogenous ILK phosphorylation in vivo. Mutation of PAK1 phosphorylation sites on ILK to alanine reduced cell motility and cell proliferation. Biochemical fractionation, confocal microscopy, and chromatin-interaction analyses of human cells revealed that ILK localizes predominantly in the cytoplasm but also resides in the nucleus. Transfection of MCF-7 cells with point mutants ILK-T173A, ILK-S246A, or ILK-T173A; S246A (ILK-DM) altered ILK localization. Selective depletion of PAK1 dramatically increased the nuclear and focal point accumulation of ILK, further demonstrating a role for PAK1 in ILK translocation. We also identified functional nuclear localization sequence and nuclear export sequence motifs in ILK, delineated an apparently integral role for ILK in maintaining normal nuclear integrity, and established that ILK interacts with the regulatory region of the CNKSR3 gene chromatin to negatively modulate its expression. Together, these results suggest that ILK is a PAK1 substrate, undergoes phosphorylation-dependent shuttling between the cell nucleus and cytoplasm, and interacts with gene-regulatory chromatin. PMID:17420447

  18. 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

  19. Linking magnetite in the abdomen of honey bees to a magnetoreceptive function.

    PubMed

    Lambinet, Veronika; Hayden, Michael E; Reigl, Katharina; Gomis, Surath; Gries, Gerhard

    2017-03-29

    Previous studies of magnetoreception in honey bees, Apis mellifera, focused on the identification of magnetic material, its formation, the location of the receptor and potential underlying sensory mechanisms, but never directly linked magnetic material to a magnetoreceptive function. In our study, we demonstrate that ferromagnetic material consistent with magnetite plays an integral role in the bees' magnetoreceptor. Subjecting lyophilized and pelletized bee tagmata to analyses by a superconducting quantum interference device generated a distinct hysteresis loop for the abdomen but not for the thorax or the head of bees, indicating the presence of ferromagnetic material in the bee abdomen. Magnetic remanence of abdomen pellets produced from bees that were, or were not, exposed to the 2.2-kOe field of a magnet while alive differed, indicating that magnet exposure altered the magnetization of this magnetite in live bees. In behavioural two-choice field experiments, bees briefly exposed to the same magnet, but not sham-treated control bees, failed to sense a custom-generated magnetic anomaly, indicating that magnet exposure had rendered the bees' magnetoreceptor dysfunctional. Our data support the conclusion that honey bees possess a magnetite-based magnetoreceptor located in the abdomen.

  20. Facile chemical functionalization of proteins through intein-linked yeast display.

    PubMed

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

    2013-09-18

    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.

  1. Sorption and degradation of phthalate esters by a novel functional hyper-cross-linked polymer.

    PubMed

    Shi, Jing; Li, Fei; Yin, Danyang; Xu, Zhengwen; Cheng, Ling

    2017-03-01

    A novel functional hyper-cross-linked polymer (NFHP) modified with trimethylamine was prepared. NFHP was characterized by FTIR, XPS, XRD, SEM and Micromeritics ASAP-2010 automatic surface area analysis instrument. Adsorption and hydrolysis degradation of phthalate acid esters (PAEs) by NFHP were also investigated as a function of temperature, equilibrium concentration and PAEs types. Results indicated that NFHP could adsorb and catalyze hydrolysis of PAEs simultaneously. There was a positive relationship between the removal capacity and temperature, equilibrium concentration, and PAEs hydrophobicity. However, the increase of PAEs equilibrium concentration and hydrophobicity resulted in the decreased level of their hydrolysis, while high temperature promoted the hydrolysis of PAEs. Film diffusion was the rate controlling step of the removal process. The apparent removal rate of PAEs increased as temperature increased due to the higher diffusion coefficient at higher temperature. The results of continuous fixed-bed runs demonstrated that NFHP was capable of synchronously removing PAEs and their hydrolysis products from tap water. In the effluent solution, the PAEs concentration was below the detection limit (0.01 mg/L) of HPLC within 1400 BVs. Moreover, the exhausted NFHP beads can be completely regenerated for repeated use. Physical adsorption, hydrolysis degradation and ion-exchange played significant roles in removing of PAEs and their hydrolysis products. The analysis of hydrolysis products, FTIR and XPS spectra proved that physical adsorption, hydrolysis and ion-exchange were the main removal mechanism. The results reported herein suggested that this novel material has a great potential in efficient removal of PAEs from wastewater.

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

    PubMed

    Sharma, Ankit; Ghatge, Madankumar; Mundkur, Lakshmi; Vangala, Rajani Kanth

    2016-05-01

    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 identified 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.

  3. Invariant Natural Killer T Cell Deficiency and Functional Impairment in Sleep Apnea: Links to Cancer Comorbidity.

    PubMed

    Gaoatswe, Gadintshware; Kent, Brian D; Corrigan, Michelle A; Nolan, Geraldine; Hogan, Andrew E; McNicholas, Walter T; O'Shea, Donal

    2015-10-01

    Emerging evidence links obstructive sleep apnea (OSA) with increased cancer incidence and mortality. Invariant natural killer T (iNKT) cells play an important role in cancer immunity. We hypothesized that patients with OSA have low number of circulating invariant natural killer T (iNKT) cells, which may also be functionally impaired. This study aims to evaluate the frequency of circulating iNKT cells in OSA. We evaluated the frequency of circulating iNKT cells by flow cytometry in 33 snorers being assessed for possible OSA. Using iNKT cell lines, we also evaluated the effect of exposure to hypoxia over 24 hours on apoptosis, cytotoxicity, and cytokine production. Teaching hospital based sleep unit and research laboratory. Thirty-three snorers were evaluated: 9 with no OSA (apnea-hypopnea frequency [AHI] < 5/h), 12 with mild-moderate OSA (AHI 5-30) and 12 with severe OSA (AHI > 30). Patients with severe OSA had considerably fewer iNKT cells (0.18%) compared to patients with mild-moderate (0.24%) or no OSA (0.35%), P = 0.0026. The frequency of iNKT cells correlated negatively with apnea-hypopnea index (r = -0.58, P = 0.001), oxygen desaturation index (r = -0.58, P = 0.0003), and SpO2% < 90% (r = -0.5407, P = 0.005). The frequency of iNKT cells increased following 12 months of nCPAP therapy (P = 0.015). Hypoxia resulted in increased apoptosis (P = 0.016) and impaired cytotoxicity (P = 0.035). Patients with obstructive sleep apnea (OSA) have significantly reduced levels of circulating invariant natural killer T (iNKT) cells and hypoxia leads to impaired iNKT cell function. These observations may partly explain the increased cancer risk reported in patients with OSA. © 2015 Associated Professional Sleep Societies, LLC.

  4. Using a trait-based approach to link microbial community composition and functioning to soil salinity

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Fierer, Noah; Rousk, Johannes

    2017-04-01

    Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared

  5. 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

  6. The Integral Membrane Protein Snl1p Is Genetically Linked to Yeast Nuclear Pore Complex Function

    PubMed Central

    Ho, Albert K.; Raczniak, Gregory A.; Ives, Eric B.; Wente, Susan R.

    1998-01-01

    Integral membrane proteins are predicted to play key roles in the biogenesis and function of nuclear pore complexes (NPCs). Revealing how the transport apparatus is assembled will be critical for understanding the mechanism of nucleocytoplasmic transport. We observed that expression of the carboxyl-terminal 200 amino acids of the nucleoporin Nup116p had no effect on wild-type yeast cells, but it rendered the nup116 null strain inviable at all temperatures and coincidentally resulted in the formation of nuclear membrane herniations at 23°C. To identify factors related to NPC function, a genetic screen for high-copy suppressors of this lethal nup116-C phenotype was conducted. One gene (designated SNL1 for suppressor of nup116-C lethal) was identified whose expression was necessary and sufficient for rescuing growth. Snl1p has a predicted molecular mass of 18.3 kDa, a putative transmembrane domain, and limited sequence similarity to Pom152p, the only previously identified yeast NPC-associated integral membrane protein. By both indirect immunofluorescence microscopy and subcellular fractionation studies, Snl1p was localized to both the nuclear envelope and the endoplasmic reticulum. Membrane extraction and topology assays suggested that Snl1p was an integral membrane protein, with its carboxyl-terminal region exposed to the cytosol. With regard to genetic specificity, the nup116-C lethality was also suppressed by high-copy GLE2 and NIC96. Moreover, high-copy SNL1 suppressed the temperature sensitivity of gle2–1 and nic96-G3 mutant cells. The nic96-G3 allele was identified in a synthetic lethal genetic screen with a null allele of the closely related nucleoporin nup100. Gle2p physically associated with Nup116p in vitro, and the interaction required the N-terminal region of Nup116p. Therefore, genetic links between the role of Snl1p and at least three NPC-associated proteins were established. We suggest that Snl1p plays a stabilizing role in NPC structure and function

  7. Non-parametric estimation of the odds ratios for continuous exposures using generalized additive models with an unknown link function.

    PubMed

    Cadarso-Suárez, Carmen; Roca-Pardiñas, Javier; Figueiras, Adolfo; González-Manteiga, Wenceslao

    2005-04-30

    The generalized additive, model (GAM) is a powerful and widely used tool that allows researchers to fit, non-parametrically, the effect of continuous predictors on a transformation of the mean response variable. Such a transformation is given by a so-called link function, and in GAMs this link function is assumed to be known. Nevertheless, if an incorrect choice is made for the link, the resulting GAM is misspecified and the results obtained may be misleading. In this paper, we propose a modified version of the local scoring algorithm that allows for the non-parametric estimation of the link function, by using local linear kernel smoothers. To better understand the effect that each covariate produces on the outcome, results are expressed in terms of the non-parametric odds ratio (OR) curves. Bootstrap techniques were used to correct the bias in the OR estimation and to construct point-wise confidence intervals. A simulation study was carried out to assess the behaviour of the resulting estimates. The proposed methodology was illustrated using data from the AIDS Register of Galicia (NW Spain), with a view to assessing the effect of the CD4 lymphocyte count on the probability of being AIDS-diagnosed via Tuberculosis (TB). This application shows how the link's flexibility makes it possible to obtain OR curve estimates that are less sensitive to the presence of outliers and unusual values that are often present in the extremes of the covariate distributions.

  8. Dependence of Invadopodia Function on Collagen Fiber Spacing and Cross-Linking: Computational Modeling and Experimental Evidence

    PubMed Central

    Enderling, Heiko; Alexander, Nelson R.; Clark, Emily S.; Branch, Kevin M.; Estrada, Lourdes; Crooke, Cornelia; Jourquin, Jérôme; Lobdell, Nichole; Zaman, Muhammad H.; Guelcher, Scott A.; Anderson, Alexander R. A.; Weaver, Alissa M.

    2008-01-01

    Invadopodia are subcellular organelles thought to be critical for extracellular matrix (ECM) degradation and the movement of cells through tissues. Here we examine invadopodia generation, turnover, and function in relation to two structural aspects of the ECM substrates they degrade: cross-linking and fiber density. We set up a cellular automaton computational model that simulates ECM penetration and degradation by invadopodia. Experiments with denatured collagen (gelatin) were used to calibrate the model and demonstrate the inhibitory effect of ECM cross-linking on invadopodia degradation and penetration. Incorporation of dynamic invadopodia behavior into the model amplified the effect of cross-linking on ECM degradation, and was used to model feedback from the ECM. When the model was parameterized with spatial fibrillar dimensions that closely matched the organization, in real life, of native ECM collagen into triple-helical monomers, microfibrils, and macrofibrils, little or no inhibition of invadopodia penetration was observed in simulations of sparse collagen gels, no matter how high the degree of cross-linking. Experimental validation, using live-cell imaging of invadopodia in cells plated on cross-linked gelatin, was consistent with simulations in which ECM cross-linking led to higher rates of both invadopodia retraction and formation. Analyses of invadopodia function from cells plated on cross-linked gelatin and collagen gels under standard concentrations were consistent with simulation results in which sparse collagen gels provided a weak barrier to invadopodia. These results suggest that the organization of collagen, as it may occur in stroma or in vitro collagen gels, forms gaps large enough so as to have little impact on invadopodia penetration/degradation. By contrast, dense ECM, such as gelatin or possibly basement membranes, is an effective obstacle to invadopodia penetration and degradation, particularly when cross-linked. These results provide a

  9. X-Linked Adrenoleukodystrophy: Molecular and Functional Analysis of the ABCD1 Gene in Argentinean Patients

    PubMed Central

    Amorosi, Cyntia Anabel; Myskóva, Helena; Monti, Mariela Roxana; Argaraña, Carlos Enrique; Morita, Masashi; Kemp, Stephan; de Kremer, Raquel Dodelson; Dvoráková, Lenka; de Ramírez, Ana María Oller

    2012-01-01

    X-linked adrenoleukodystrophy (X-ALD) is an inherited metabolic disease associated with mutations in the ABCD1 gene that encodes an ATP-binding cassette transporter protein, ALDP. The disease is characterized by increased concentrations of very long-chain fatty acids (VLCFAs) in plasma and in adrenal, testicular and nervous tissues, due to a defect in peroxisomal VLCFA β-oxidation. In the present study, we analyzed 10 male patients and 17 female carriers from 10 unrelated pedigrees with X-ALD from Argentina. By sequencing the ABCD1 we detected 9 different mutations, 8 of which were novel. These new mutations were verified by a combination of methods that included both functional (western blot and peroxisomal VLCFA β-oxidation) and bioinformatics analysis. The spectrum of novel mutations consists of 3 frameshift (p.Ser284fs*16, p.Glu380Argfs*21 and p.Thr254Argfs*82); a deletion (p.Ser572_Asp575del); a splicing mutation (c.1081+5G>C) and 3 missense mutations (p.Ala341Asp, p.His420Pro and p.Tyr547Cys). In one patient 2 changes were found: a known missense (p.His669Arg) and an unpublished amino acid substitution (p.Ala19Ser). In vitro studies suggest that p.Ala19Ser is a polymorphism. Moreover, we identified two novel intronic polymorphisms and two amino acid polymorphisms. In conclusion, this study extends the spectrum of mutation in X-ALD and facilitates the identification of heterozygous females. PMID:23300730

  10. X-linked adrenoleukodystrophy: molecular and functional analysis of the ABCD1 gene in Argentinean patients.

    PubMed

    Amorosi, Cyntia Anabel; Myskóva, Helena; Monti, Mariela Roxana; Argaraña, Carlos Enrique; Morita, Masashi; Kemp, Stephan; Dodelson de Kremer, Raquel; Dvoráková, Lenka; Oller de Ramírez, Ana María

    2012-01-01

    X-linked adrenoleukodystrophy (X-ALD) is an inherited metabolic disease associated with mutations in the ABCD1 gene that encodes an ATP-binding cassette transporter protein, ALDP. The disease is characterized by increased concentrations of very long-chain fatty acids (VLCFAs) in plasma and in adrenal, testicular and nervous tissues, due to a defect in peroxisomal VLCFA β-oxidation. In the present study, we analyzed 10 male patients and 17 female carriers from 10 unrelated pedigrees with X-ALD from Argentina. By sequencing the ABCD1 we detected 9 different mutations, 8 of which were novel. These new mutations were verified by a combination of methods that included both functional (western blot and peroxisomal VLCFA β-oxidation) and bioinformatics analysis. The spectrum of novel mutations consists of 3 frameshift (p.Ser284fs*16, p.Glu380Argfs*21 and p.Thr254Argfs*82); a deletion (p.Ser572_Asp575del); a splicing mutation (c.1081+5G>C) and 3 missense mutations (p.Ala341Asp, p.His420Pro and p.Tyr547Cys). In one patient 2 changes were found: a known missense (p.His669Arg) and an unpublished amino acid substitution (p.Ala19Ser). In vitro studies suggest that p.Ala19Ser is a polymorphism. Moreover, we identified two novel intronic polymorphisms and two amino acid polymorphisms. In conclusion, this study extends the spectrum of mutation in X-ALD and facilitates the identification of heterozygous females.

  11. STRESS REGULATION AS A LINK BETWEEN EXECUTIVE FUNCTION AND PRE-FRAILTY IN OLDER ADULTS

    PubMed Central

    Roiland, R.A.; Lin, F.; Phelan, C.; Chapman, B.P.

    2017-01-01

    Objectives Both pre-frailty and frailty are linked with impaired executive function (EF) but the mechanism underlying this relationship is not known. Williams and colleagues’ model posits EF affects health outcomes via stress regulation. This model was utlized to test indicators of stress regulation as mediators of the relationship between EF and pre-frailty in older adults. Design Cross-sectional. Setting Academic general clinical research centers. Participants 690 community-dwelling older adults ≥ 50 years of age. Measurements Pre-frailty was measured using a modified form of the Fried Frailty measure. EF was assessed via telephone-based neurocognitive assessments. Indicators of stress regulation included: stress exposure (measured by perceived stress), reactivity and recovery (measured by heart rate) and restoration (measured by serum interleukin-6 and sleep quality). Results 396 individuals were classified as non-frail, 277 as pre-frail, and 17 as frail. Pre-frail and non-frail individuals were included in data analyses. Compared to non-frail individuals, prefrail were older and exhibited poorer EF, higher levels of stress exposure and poorer stress restoration. Poorer EF was associated with greater stress exposure, less stress reactivity, longer stress recovery and poorer stress restoration. The total effect of the relationship between EF and pre-frailty was significant with significant indirect effects supporting stress exposure and restoration as mediators of the relationship. Conclusion Stress exposure and restoration appear to mediate the relationship between EF and pre-frailty. Longitudinal studies are needed to clarify the direction of causality and determine whether stress regulation processes are appropriate targets for interventions aiming to prevent declines in EF and the development of pre-frailty. PMID:26412287

  12. Functional analysis of the TRIB1 associated locus linked to plasma triglycerides and coronary artery disease.

    PubMed

    Douvris, Adrianna; Soubeyrand, Sébastien; Naing, Thet; Martinuk, Amy; Nikpay, Majid; Williams, Andrew; Buick, Julie; Yauk, Carole; McPherson, Ruth

    2014-06-03

    The TRIB1 locus has been linked to hepatic triglyceride metabolism in mice and to plasma triglycerides and coronary artery disease in humans. The lipid-associated single nucleotide polymorphisms (SNPs), identified by genome-wide association studies, are located ≈30 kb downstream from TRIB1, suggesting complex regulatory effects on genes or pathways relevant to hepatic triglyceride metabolism. The goal of this study was to investigate the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits. Characterization of the risk locus reveals that it encompasses a gene, TRIB1-associated locus (TRIBAL), composed of a well-conserved promoter region and an alternatively spliced transcript. Bioinformatic analysis and resequencing identified a single SNP, rs2001844, within the promoter region that associates with increased plasma triglycerides and reduced high-density lipoprotein cholesterol and coronary artery disease risk. Further, correction for triglycerides as a covariate indicated that the genome-wide association studies association is largely dependent on triglycerides. In addition, we show that rs2001844 is an expression trait locus (eQTL) for TRIB1 expression in blood and alters TRIBAL promoter activity in a reporter assay model. The TRIBAL transcript has features typical of long noncoding RNAs, including poor sequence conservation. Modulation of TRIBAL expression had limited impact on either TRIB1 or lipid regulatory genes mRNA levels in human hepatocyte models. In contrast, TRIB1 knockdown markedly increased TRIBAL expression in HepG2 cells and primary human hepatocytes. These studies demonstrate an interplay between a novel locus, TRIBAL, and TRIB1. TRIBAL is located in the genome-wide association studies identified risk locus, responds to altered expression of TRIB1, harbors a risk SNP that is an eQTL for TRIB1 expression, and associates with plasma triglyceride concentrations. © 2014 The Authors. Published on behalf of the

  13. 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

  14. Sphingosine kinase functionally links elevated transmural pressure and increased reactive oxygen species formation in resistance arteries.

    PubMed

    Keller, Matthias; Lidington, Darcy; Vogel, Lukas; Peter, Bernhard Friedrich; Sohn, Hae-Young; Pagano, Patrick J; Pitson, Stuart; Spiegel, Sarah; Pohl, Ulrich; Bolz, Steffen-Sebastian

    2006-04-01

    Myogenic vasoconstriction, an intrinsic response to elevated transmural pressure (TMP), requires the activation of sphingosine kinase (Sk1) and the generation of reactive oxygen species (ROS). We hypothesized that pressure-induced Sk1 signaling and ROS generation are functionally linked. Using a model of cannulated resistance arteries isolated from the hamster gracilis muscle, we monitored vessel diameter and smooth muscle cell (SMC) Ca2+i (Fura-2) or ROS production (dichlorodihydrofluorescein). Elevation of TMP stimulated the translocation of a GFP-tagged Sk1 fusion protein from the cytosol to the plasma membrane, indicative of enzymatic activation. Concurrently, elevation of TMP initiated a rapid and transient production of ROS, which was enhanced by expression of wild-type Sk1 (hSk(wt)) and inhibited by its dominant-negative mutant (hSk(G82D)). Exogenous sphingosine-1-phosphate (S1P) also stimulated ROS generation is isolated vessels. Chemical (1 micromol/L DPI), peptide (gp91ds-tat/gp91ds), and genetic (N17Rac) inhibition strategies indicated that NADPH oxidase was the source of the pressure-induced ROS. NADPH oxidase inhibition attenuated myogenic vasoconstriction and reduced the apparent Ca2+ sensitivity of the SMC contractile apparatus, without affecting Ca2+-independent, RhoA-mediated vasoconstriction in response to exogenous S1P. Our results indicate a mandatory role for Sk1/S1P in mediating pressure-induced, NADPH oxidase-derived ROS formation. In turn, ROS generation appears to increase Ca2+ sensitivity, necessary for full myogenic vasoconstriction.

  15. Linking epigenetic function to electrostatics: The DNMT2 structural model example.

    PubMed

    Vieira, Gilberto Cavalheiro; Vieira, Gustavo Fioravanti; Sinigaglia, Marialva; Silva Valente, Vera Lúcia da

    2017-01-01

    The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.

  16. Functional effects of a tropomyosin mutation linked to FHC contribute to maladaptation during acidosis

    PubMed Central

    Sheehan, Katherine A.; Arteaga, Grace M.; Hinken, Aaron C.; Dias, Fernando A.; Ribeiro, Cibele; Wieczorek, David F.; Solaro, R. John; Wolska, Beata M.

    2010-01-01

    Familial Hypertrophic Cardiomyopathy (FHC) is a leading cause of sudden cardiac death among young athletes but the functional effects of the myofilament mutations during FHC-associated ischemia and acidosis, due in part to increased extravascular compressive forces and microvascular dysfunction, are not well characterized. We tested the hypothesis that the FHC-linked tropomyosin (Tm) mutation Tm-E180G alters the contractile response to acidosis via increased myofilament Ca2+ sensitivity. Intact papillary muscles from transgenic (TG) mice expressing Tm-E180G and exposed to acidic conditions (pH 6.9) exhibited a significantly smaller decrease in normalized isometric tension compared to non-transgenic (NTG) preparations. Times to peak tension and to 90% of twitch force relaxation in TG papillary muscles were significantly prolonged. Intact single ventricular TG myocytes demonstrated significantly less inhibition of unloaded shortening during moderate acidosis (pH 7.1) than NTG myocytes. The peak Ca2+ transients were not different for TG or NTG at any pH tested. The time constant of re-lengthening was slower in TG myocytes, but not the rate of Ca2+ decline. TG detergent-extracted fibers demonstrated increased Ca2+ sensitivity of force and maximal tension compared to NTG at both normal and acidic pH (pH 6.5). Tm phosphorylation was not different between TG and NTG muscles at either pH. Our data indicate that acidic pH diminished developed force in hearts of TG mice less than in NTG due to their inherently increased myofilament Ca2+ sensitivity, thus potentially contributing to altered energy demands and increased propensity for contractile dysfunction. PMID:21047515

  17. 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

  18. 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…

  19. 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…

  20. 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…

  1. 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…

  2. 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…

  3. 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…

  4. Keratoconus, cross-link-induction, comparison between fitting exponential function and a fitting equation obtained by a mathematical model.

    PubMed

    Albanese, A; Urso, R; Bianciardi, L; Rigato, M; Battisti, E

    2009-11-01

    With reference to experimental data in the literature, we present a model consisting of two elastic elements, conceived to simulate resistance to stretching, at constant velocity of elongation, of corneal tissue affected by keratoconus, treated with riboflavin and ultraviolet irradiation to induce cross-linking. The function describing model behaviour adapted to stress and strain values. It was found that the Young's moduli of the two elastic elements increased in cross-linked tissues and that cross-linking treatment therefore increased corneal rigidity. It is recognized that this observation is substantially in line with the conclusion reported in the literature, obtained using an exponential fitting function. It is observed, however, that the latter function implies a condition of non-zero stresses without strain, and does not provide interpretative insights for lack of any biomechanical basis. Above all, the function fits a singular trend, inexplicably claimed to be viscoelastic, with surprising perfection. In any case, using the reported data, the study demonstrates that a fitting equation obtained by a modelling approach not only shows the evident efficacy of the treatment, but also provides orientations for studying modifications induced in cross-linked fibres.

  5. Exogenous collagen cross-linking recovers tendon functional integrity in an experimental model of partial tear.

    PubMed

    Fessel, Gion; Wernli, Jeremy; Li, Yufei; Gerber, Christian; Snedeker, Jess G

    2012-06-01

    We investigated the hypothesis that exogenous collagen cross-linking can augment intact regions of tendon to mitigate mechanical propagation of partial tears. We first screened the low toxicity collagen cross-linkers genipin, methylglyoxal and ultra-violet (UV) light for their ability to augment tendon stiffness and failure load in rat tail tendon fascicles (RTTF). We then investigated cross-linking effects in load bearing equine superficial digital flexor tendons (SDFT). Data indicated that all three cross-linking agents augmented RTTF mechanical properties but reduced native viscoelasticity. In contrast to effects observed in fascicles, methylglyoxal treatment of SDFT detrimentally affected tendon mechanical integrity, and in the case of UV did not alter tendon mechanics. As in the RTTF experiments, genipin cross-linking of SDFT resulted in increased stiffness, higher failure loads and reduced viscoelasticity. Based on this result we assessed the efficacy of genipin in arresting tendon tear propagation in cyclic loading to failure. Genipin cross-linking secondary to a mid-substance biopsy-punch significantly reduced tissue strains, increased elastic modulus and increased resistance to fatigue failure. We conclude that genipin cross-linking of injured tendons holds potential for arresting tendon tear progression, and that implications of the treatment on matrix remodeling in living tendons should now be investigated.

  6. Assembly, cross-linking and encapsulation using functionalized nanoparticles at liquid interfaces

    NASA Astrophysics Data System (ADS)

    Tangirala, Ravisubhash

    The assembly of nanoparticles at the interface of immiscible fluids holds promise for the preparation of new materials that benefit from both the physical properties of the nanoparticles and the chemistry associated with the ligands. Shaking nanoparticle solutions in organic solvents with water, results in the formation of nanoparticle-coated droplets that range in size from 10 microm to 200 microm. A strategy to control the size of these emulsions is described, by passing the droplets through commercial track-etch membranes with known pore sizes. Extrusion reduces the droplet size by breaking the droplets while passing theough the membrane pores, and reforming in the presence of excess nanoparticles in solution to form droplets as small as 1-5 microm. Crosslinking of nanoparticles at a liquid interface lends greater stability to the interfacial assembly, leading to ultrathin nanoparticle-based capsules, which possess mechanical integrity even after removal of the interface. Two approaches towards crosslinking are used in this thesis. Norbornene-functionalized CdSe/ZnS are used to afford facile capsule visualization by fluorescence confocal microscopy, as well as ease of crosslinking in mild conditions by means of ring-opening metathesis polymerization (ROMP). The crosslinked capsules can be used to encapsulate materials, and display size-selective retention capability, governed by the interstitial spaces between the nanoparticles. In a second approach to making hybrid capsules and sheets, horse spleen ferritin bionanoparticles and aldehyde-functionalized CdSe quantum dots are co-assembled at an oil-water interface. The cross-linked materials formed by reaction of the aldehyde functionality on the quantum dots with the surface-available amines on the ferritin bionanoparticles can be disrupted by addition of acid, thus leading to pH-degradable capsules and sheets. The driving force for assembly of nanoparticles at liquid interfaces is the reduction of the

  7. 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

  8. 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

  9. 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

  10. Linking the Bournemouth Questionnaire for low back pain to the International Classification of Functioning, Disability and Health.

    PubMed

    Nicol, Richard; Robinson Nicol, Meri; Hopfe, Maren; Newell, Dave

    2016-01-01

    Understanding the content of health-related quality of life (HRQOL) questionnaires can facilitate comparison and selection of the most appropriate tool in the assessment of patients with low back pain. The International Classification of Functioning, Disability and Health (ICF), as part of the WHO-FIC, can be used as a standardised method for mapping and comparing HRQOL questionnaire content. The purpose of this study was to link the Bournemouth Questionnaire (BQ) to the ICF in order to assess and compare the content of the BQ to the brief ICF core sets for low back pain. The BQ was linked to the ICF following the rules described by Cieza and Stuki. Following the linking process, the results were further linked to the brief ICF core sets for low back pain. The BQ covered 21 ICF categories within the domains of body functions and activities and participation. Only five meaningful concepts could not be linked to the ICF. The brief core sets for low back pain contain 35 categories, identified as important concepts in back pain patients. The BQ covered 10 of the categories of the brief core sets. HRQOL tools provide valuable information about the health status of patients. Content comparison based on ICF provides relevant information about the concepts covered and enables selection of the appropriate clinical tools. The BQ is easy to administer and is linked to a number of important concepts contained within the ICF and to concepts considered to be important in the assessment of patients with LBP. Selecting appropriate health-related quality of life (HRQOL) tools can prove difficult, with such a variety of them available, and each with varying content. ICF provides a standardised framework for the content assessment of HRQOL tools. Understanding the content of HRQOL tools can facilitate better tool selection and assist in the accurate assessment of patients with low back pain.

  11. Neisseria gonorrhoeae O-linked pilin glycosylation: functional analyses define both the biosynthetic pathway and glycan structure

    PubMed Central

    Aas, Finn Erik; Vik, Åshild; Vedde, John; Koomey, Michael; Egge-Jacobsen, Wolfgang

    2007-01-01

    Neisseria gonorrhoeae expresses an O-linked protein glycosylation pathway that targets PilE, the major pilin subunit protein of the Type IV pilus colonization factor. Efforts to define glycan structure and thus the functions of pilin glycosylation (Pgl) components at the molecular level have been hindered by the lack of sensitive methodologies. Here, we utilized a ‘top-down’ mass spectrometric approach to characterize glycan status using intact pilin protein from isogenic mutants. These structural data enabled us to directly infer the function of six components required for pilin glycosylation and to define the glycan repertoire of strain N400. Additionally, we found that the N. gonorrhoeae pilin glycan is O-acetylated, and identified an enzyme essential for this unique modification. We also identified the N. gonorrhoeae pilin oligosaccharyltransferase using bioinformatics and confirmed its role in pilin glycosylation by directed mutagenesis. Finally, we examined the effects of expressing the PglA glycosyltransferase from the Campylobacter jejuni N-linked glycosylation system that adds N-acetylgalactosamine onto undecaprenylpyrophosphate-linked bacillosamine. The results indicate that the C. jejuni and N. gonorrhoeae pathways can interact in the synthesis of O-linked di- and trisaccharides, and therefore provide the first experimental evidence that biosynthesis of the N. gonorrhoeae pilin glycan involves a lipid-linked oligosaccharide precursor. Together, these findings underpin more detailed studies of pilin glycosylation biology in both N. gonorrhoeae and N. meningitidis, and demonstrate how components of bacterial O- and N-linked pathways can be combined in novel glycoengineering strategies. PMID:17608667

  12. 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…

  13. 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…

  14. The Extent to Which Collaborative Teams of Educators Link the Results of Functional Assessment to Function-Based Interventions

    ERIC Educational Resources Information Center

    de Courcy-Bower, Laurie

    2010-01-01

    A promising approach to addressing challenging behavior in schools is to develop and implement "function-based interventions" (Dunlap et al., 2006; Hanley, Iwata, & McCord, 2003). Function-based interventions are individualized interventions in which five key outcomes of functional assessment (i.e., identification of challenging behavior,…

  15. Chronic cigarette smoking is linked with structural alterations in brain regions showing acute nicotinic drug-induced functional modulations.

    PubMed

    Sutherland, Matthew T; Riedel, Michael C; Flannery, Jessica S; Yanes, Julio A; Fox, Peter T; Stein, Elliot A; Laird, Angela R

    2016-06-02

    Whereas acute nicotine administration alters brain function which may, in turn, contribute to enhanced attention and performance, chronic cigarette smoking is linked with regional brain atrophy and poorer cognition. However, results from structural magnetic resonance imaging (MRI) studies comparing smokers versus nonsmokers have been inconsistent and measures of gray matter possess limited ability to inform functional relations or behavioral implications. The purpose of this study was to address these interpretational challenges through meta-analytic techniques in the service of clarifying the impact of chronic smoking on gray matter integrity and more fully contextualizing such structural alterations. We first conducted a coordinate-based meta-analysis of structural MRI studies to identify consistent structural alterations associated with chronic smoking. Subsequently, we conducted two additional meta-analytic assessments to enhance insight into potential functional and behavioral relations. Specifically, we performed a multimodal meta-analytic assessment to test the structural-functional hypothesis that smoking-related structural alterations overlapped those same regions showing acute nicotinic drug-induced functional modulations. Finally, we employed database driven tools to identify pairs of structurally impacted regions that were also functionally related via meta-analytic connectivity modeling, and then delineated behavioral phenomena associated with such functional interactions via behavioral decoding. Across studies, smoking was associated with convergent structural decreases in the left insula, right cerebellum, parahippocampus, multiple prefrontal cortex (PFC) regions, and the thalamus. Indicating a structural-functional relation, we observed that smoking-related gray matter decreases overlapped with the acute functional effects of nicotinic agonist administration in the left insula, ventromedial PFC, and mediodorsal thalamus. Suggesting structural

  16. Hydroxy-functionalized hyper-cross-linked ultra-microporous organic polymers for selective CO2 capture at room temperature.

    PubMed

    Samanta, Partha; Chandra, Priyanshu; Ghosh, Sujit K

    2016-01-01

    Two hydroxy-functionalized hyper-cross-linked ultra-microporous compounds have been synthesized by Friedel-Crafts alkylation reaction and characterised with different spectroscopic techniques. Both compounds exhibit an efficient carbon dioxide uptake over other gases like N2, H2 and O2 at room temperature. A high isosteric heat of adsorption (Qst) has been obtained for both materials because of strong interactions between polar -OH groups and CO2 molecules.

  17. Hydroxy-functionalized hyper-cross-linked ultra-microporous organic polymers for selective CO2 capture at room temperature

    PubMed Central

    Samanta, Partha; Chandra, Priyanshu

    2016-01-01

    Summary Two hydroxy-functionalized hyper-cross-linked ultra-microporous compounds have been synthesized by Friedel–Crafts alkylation reaction and characterised with different spectroscopic techniques. Both compounds exhibit an efficient carbon dioxide uptake over other gases like N2, H2 and O2 at room temperature. A high isosteric heat of adsorption (Q st) has been obtained for both materials because of strong interactions between polar –OH groups and CO2 molecules. PMID:27829902

  18. The Role of Representations in Executive Function: Investigating a Developmental Link between Flexibility and Abstraction

    PubMed Central

    Kharitonova, Maria; Munakata, Yuko

    2011-01-01

    Young children often perseverate, engaging in previously correct, but no longer appropriate behaviors. One account posits that such perseveration results from the use of stimulus-specific representations of a situation, which are distinct from abstract, generalizable representations that support flexible behavior. Previous findings supported this account, demonstrating that only children who flexibly switch between rules could generalize their behavior to novel stimuli. However, this link between flexibility and generalization might reflect general cognitive abilities, or depend upon similarities across the measures or their temporal order. The current work examined these issues by testing the specificity and generality of this link. In two experiments with 3-year-old children, flexibility was measured in terms of switching between rules in a card-sorting task, while abstraction was measured in terms of selecting which stimulus did not belong in an odd-one-out task. The link between flexibility and abstraction was general across (1) abstraction dimensions similar to or different from those in the card-sorting task and (2) abstraction tasks that preceded or followed the switching task. Good performance on abstraction and flexibility measures did not extend to all cognitive tasks, including an IQ measure, and dissociated from children’s ability to gaze at the correct stimulus in the odd-one-out task, suggesting that the link between flexibility and abstraction is specific to such measures, rather than reflecting general abilities that affect all tasks. We interpret these results in terms of the role that developing prefrontal cortical regions play in processes such as working memory, which can support both flexibility and abstraction. PMID:22144971

  19. Linking Brief Functional Analysis to Intervention Design in General Education Settings

    ERIC Educational Resources Information Center

    Ishuin, Tifanie

    2009-01-01

    This study focused on the utility and applicability of brief functional analysis in general education settings. The purpose of the study was to first identify the environmental variables maintaining noncompliance through a brief functional analysis, and then to design and implement a functionally equivalent intervention. The participant exhibited…

  20. 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.

  1. 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

  2. Improving the Understanding of the Link between Cognition and Functional Capacity in Schizophrenia and Bipolar Disorder

    PubMed Central

    Moore, Raeanne C.; Harmell, Alexandrea L.; Harvey, Philip D.; Bowie, Christopher R.; Depp, Colin A.; Pulver, Ann E.; McGrath, John A; Patterson, Thomas L.; Cardenas, Veronica; Wolyniec, Paula; Thornquist, Mary H.; Luke, James R.; Palmer, Barton W.; Jeste, Dilip V.; Mausbach, Brent T.

    2015-01-01

    OBJECTIVE Deficits in cognitive functioning are related to functional disability in people with serious mental illness. Measures of functional capacity are commonly used as a proxy for functional disabilities for cognitive remediation programs, and robust linear relationships between functional capacity and cognitive deficits are frequently observed. This study aimed to determine whether a curvilinear relationship better approximates the association between cognitive functioning and functional capacity. METHOD Two independent samples were studied. Study 1: Participants with schizophrenia (n=435) and bipolar disorder (n=390) aged 18–83 completed a neuropsychological battery and a performance-based measure of functional capacity. Study 2: 205 participants with schizophrenia (age range=39–72) completed a brief neuropsychological screening battery and a performance-based measure of functional capacity. For both studies, linear and quadratic curve estimations were conducted with cognitive performance predicting functional capacity scores. RESULTS Significant linear and quadratic trends were observed for both studies. Study 1: In both the schizophrenia and bipolar participants, when cognitive composite z-scores were >0 (indicating normal to above normal performance), cognition was not related to functional capacity. Study 2: When neuropsychological screening battery z-scores were >−1 (indicating low average to average performance), cognition was not related to functional capacity. CONCLUSIONS These results illustrate that in cognitively normal adults with serious mental illness, the relationship between cognitive function and functional capacity is relatively weak. These findings may aid clinicians and researchers determine who may optimally benefit from cognitive remediation programs, with greater benefits possibly being achieved for individuals with cognitive deficits relative to individuals with normal cognition. PMID:26427917

  3. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Adipokines in reproductive function: a link between obesity and polycystic ovary syndrome.

    PubMed

    Chen, Xinwang; Jia, Xiao; Qiao, Jie; Guan, Youfei; Kang, Jihong

    2013-04-01

    Polycystic ovary syndrome (PCOS) is the most common endocrinopathy associated with infertility and metabolic disorder in women of reproductive age. Dysfunction of adipose tissue has been implicated in the pathophysiology of PCOS. Increasing evidence shows that the dysregulated expression of adipokines, the secreted products of adipose tissue, plays an important role in the pathology of PCOS. Here, we review the role of several identified adipokines that may act as a link between obesity and PCOS. PCOS also reciprocally influences the profile of adipokines. Insight into the underlying mechanisms will help better understand the pathology of PCOS and identify new therapeutic targets of this syndrome.

  5. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 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.

  7. How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein?

    PubMed

    Li, Wei

    2017-01-01

    Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease with dysfunctional α-motor neurons in the anterior horn of the spinal cord. SMA is caused by loss (∼95% of SMA cases) or mutation (∼5% of SMA cases) of the survival motor neuron 1 gene SMN1. As the product of SMN1, SMN is a component of the SMN complex, and is also involved in the biosynthesis of the small nuclear ribonucleoproteins (snRNPs), which play critical roles in pre-mRNA splicing in the pathogenesis of SMA. To investigate how SMA-linked mutations of SMN1 lead to structural/functional deficiency of SMN, a set of computational analysis of SMN-related structures were conducted and are described in this article. Of extraordinary interest, the structural analysis highlights three SMN residues (Asp44, Glu134 and Gln136) with SMA-linked missense mutations, which cause disruptions of electrostatic interactions for Asp44, Glu134 and Gln136, and result in three functionally deficient SMA-linked SMN mutants, Asp44Val, Glu134Lys and Gln136Glu. From the computational analysis, it is also possible that SMN's Lys45 and Asp36 act as two electrostatic clips at the SMN-Gemin2 complex structure interface.

  8. School Functioning in Early Adolescence: Gender-Linked Responses to Peer Victimization

    ERIC Educational Resources Information Center

    Hoglund, Wendy L. G.

    2007-01-01

    Research indicates that peer victimization contributes to poor school functioning in childhood and adolescence, yet the processes by which victimization interferes with school functioning are unclear. This study examined internalizing and externalizing problems as domain-specific mediators of the association between subtypes of peer victimization…

  9. School Functioning in Early Adolescence: Gender-Linked Responses to Peer Victimization

    ERIC Educational Resources Information Center

    Hoglund, Wendy L. G.

    2007-01-01

    Research indicates that peer victimization contributes to poor school functioning in childhood and adolescence, yet the processes by which victimization interferes with school functioning are unclear. This study examined internalizing and externalizing problems as domain-specific mediators of the association between subtypes of peer victimization…

  10. Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

    USDA-ARS?s Scientific Manuscript database

    Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...

  11. OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function

    SciTech Connect

    Juang, Yu-Chi; Landry, Marie-Claude; Sanches, Mario; Vittal, Vinayak; Leung, Charles C.Y.; Ceccarelli, Derek F.; Mateo, Abigail-Rachele F.; Pruneda, Jonathan N.; Mao, Daniel Y.L.; Szilard, Rachel K.; Orlicky, Stephen; Munro, Meagan; Brzovic, Peter S.; Klevit, Rachel E.; Sicheri, Frank; Durocher, Daniel

    2012-03-26

    Ubiquitylation entails the concerted action of E1, E2, and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response.

  12. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis.

    PubMed

    Jarrell, Ken F; Ding, Yan; Meyer, Benjamin H; Albers, Sonja-Verena; Kaminski, Lina; Eichler, Jerry

    2014-06-01

    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.

  13. OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function

    PubMed Central

    Juang, Yu-Chi; Landry, Marie-Claude; Sanches, Mario; Vittal, Vinayak; Leung, Charles; Ceccarelli, Derek F.; Mateo, Abigail-Rachele F.; Pruneda, Jonathan N.; Mao, Dan; Szilard, Rachel K.; Orlicky, Stephen; Munro, Meagan; Brzovic, Peter S.; Klevit, Rachel E.; Sicheri, Frank; Durocher, Daniel

    2012-01-01

    SUMMARY Ubiquitylation entails the concerted action of E1, E2 and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C-terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response. PMID:22325355

  14. Prm1 Functions as a Disulfide-linked Complex in Yeast Mating*

    PubMed Central

    Olmo, Valerie N.; Grote, Eric

    2010-01-01

    Prm1 is a pheromone-induced membrane glycoprotein that promotes plasma membrane fusion in yeast mating pairs. HA-Prm1 migrates at twice its expected molecular weight on non-reducing SDS-PAGE gels and coprecipitates with Prm1-TAP, indicating that Prm1 is a disulfide-linked homodimer. The N terminus of a plasma membrane-localized GFP-Prm1 endocytic mutant projects into the cytoplasm, where it is protected from low pH quenching in live cells and from external protease in spheroplasts. In a revised topological map, Prm1 has four transmembrane domains and two large extracellular loops. Mutation of all four cysteines in the extracellular loops blocked disulfide bond formation and destabilized the Prm1 homodimer without preventing Prm1 transport to contact sites in mating pairs. Cys120 in loop 1 and Cys545 in loop 2 form disulfide cross-links in the Prm1 homodimer and are required for fusion activity. Cys120 lies between a hydrophobic segment formerly thought to be a transmembrane domain and an amphipathic helix. An interaction between either of these regions and the opposing membrane could promote fusion. PMID:19933274

  15. Growth inhibition of MCF-7 tumor cell line by phenylacetate linked to functionalized dextran.

    PubMed

    Frank, L; Avramoglou, T; Sainte-Catherine, O; Jozefonvicz, J; Kraemer, M

    2004-01-01

    We investigated the antiproliferative effect of phenylacetate covalently linked to dextran derivatives (DMCBPA conjugates) on human breast cancer MCF-7 cells. We show that free sodium phenylacetate (NaPA) inhibits the cell growth (IC50 = 14 mM), while an important inhibitory effect is observed for DMCBPA conjugates. The IC50 dose of these conjugates is as low as 1.0 mg/ml, corresponding to 1.3 mM of phenylacetate. The precursors, dextran substituted with methylcarboxylate and benzylamide groups, did not affect the growth of MCF-7 tumor cells. We have observed that MCF-7 cell growth inhibition depends on amount of phenylacetate linked to the conjugate. The data indicated that an optimum antiproliferative effect is more significant when the amount of phenylacetate groups present on the dextran backbone is high. Analysis of doubling time by growth kinetics study shows that conjugates have more time-sustained effect than free NaPA. It is noteworthy that the inhibitory effect is observed at non-toxic concentration. Theses conjugates could be considered as acceptable derivatives to prevent tumor progression.

  16. 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

  17. Integrin-linked kinase mediates force transduction in cardiomyocytes by modulating SERCA2a/PLN function.

    PubMed

    Traister, Alexandra; Li, Mark; Aafaqi, Shabana; Lu, Mingliang; Arab, Sara; Radisic, Milica; Gross, Gil; Guido, Fiorella; Sherret, John; Verma, Subodh; Slorach, Cameron; Mertens, Luc; Hui, Wei; Roy, Anna; Delgado-Olguín, Paul; Hannigan, Gregory; Maynes, Jason T; Coles, John G

    2014-09-11

    Human dilated cardiomyopathy (DCM) manifests as a profound reduction in biventricular cardiac function that typically progresses to death or cardiac transplantation. There is no effective mechanism-based therapy currently available for DCM, in part because the transduction of mechanical load into dynamic changes in cardiac contractility (termed mechanotransduction) remains an incompletely understood process during both normal cardiac function and in disease states. Here we show that the mechanoreceptor protein integrin-linked kinase (ILK) mediates cardiomyocyte force transduction through regulation of the key calcium regulatory protein sarcoplasmic/endoplasmic reticulum Ca(2+)ATPase isoform 2a (SERCA-2a) and phosphorylation of phospholamban (PLN) in the human heart. A non-oncogenic ILK mutation with a synthetic point mutation in the pleckstrin homology-like domain (ILK(R211A)) is shown to enhance global cardiac function through SERCA-2a/PLN. Thus, ILK serves to link mechanoreception to the dynamic modulation of cardiac contractility through a previously undiscovered interaction with the functional SERCA-2a/PLN module that can be exploited to rescue impaired mechanotransduction in DCM.

  18. Functional characterization of neotropical snakes peripheral blood leukocytes subsets: Linking flow cytometry cell features, microscopy images and serum corticosterone levels.

    PubMed

    de Carvalho, Marcelo Pires Nogueira; Queiroz-Hazarbassanov, Nicolle Gilda Teixeira; de Oliveira Massoco, Cristina; Sant'Anna, Sávio Stefanini; Lourenço, Mariana Mathias; Levin, Gabriel; Sogayar, Mari Cleide; Grego, Kathleen Fernandes; Catão-Dias, José Luiz

    2017-09-01

    Reptiles are the unique ectothermic amniotes, providing the key link between ectothermic anamniotes fish and amphibians, and endothermic birds and mammals; becoming an important group to study with the aim of providing significant knowledge into the evolutionary history of vertebrate immunity. Classification systems for reptiles' leukocytes have been described by their appearance rather than function, being still inconsistent. With the advent of modern techniques and the establishment of analytical protocols for snakes' blood by flow cytometry, we bring a qualitative and quantitative assessment of innate activities presented by snakes' peripheral blood leukocytes, thereby linking flow cytometric features with fluorescent and light microscopy images. Moreover, since corticosterone is an important immunomodulator in reptiles, hormone levels of all blood samples were measured. We provide novel and additional information which should contribute to better understanding of the development of the immune system of reptiles and vertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    PubMed

    Heck, Angela; Fastenrath, Matthias; Ackermann, Sandra; Auschra, Bianca; Bickel, Horst; Coynel, David; Gschwind, Leo; Jessen, Frank; Kaduszkiewicz, Hanna; Maier, Wolfgang; Milnik, Annette; Pentzek, Michael; Riedel-Heller, Steffi G; Ripke, Stephan; Spalek, Klara; Sullivan, Patrick; Vogler, Christian; Wagner, Michael; Weyerer, Siegfried; Wolfsgruber, Steffen; de Quervain, Dominique J-F; Papassotiropoulos, Andreas

    2014-03-05

    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.

  20. Fast solid-phase extraction of N-linked glycopeptides by amine-functionalized mesoporous silica nanoparticles.

    PubMed

    Miao, Weili; Zhang, Cheng; Cai, Yan; Zhang, Ying; Lu, Haojie

    2016-04-21

    Selective enrichment is a crucial step before the mass spectrometric analysis of glycoproteins. A new approach using 3-aminopropyltriethoxysilane (APTES)-functionalized mesoporous silica materials (SBA-15) was reported to enrich the glycoproteins. Selective extraction of glycopeptides was achieved through coupling the oxidized glycan chains on the glycopeptides with the amine groups on SBA-15 through a reductive amination reaction, then the captured glycopeptides were detached from the SBA-15 for the following MS analysis using the enzyme PNGase F. Because the mesoporous material has a confinement effect, the efficiency of enrichment and enzymatic deglycosylation was improved dramatically. The coupling time was shortened from 4 hours to 1 hour, and the deglycosylation time was greatly shortened from 6 hours to 3 hours. This approach was successfully applied to profile the N-glycoproteome of human colorectal cancer serum. 84 N-linked glycosylation sites from 56 N-linked glycoproteins were identified from as little as 5 μL serum.

  1. Heterogeneity of Igh-linked allotypic determinants expressed on functional T cell subsets as detected by monoclonal antibodies.

    PubMed

    Karasuyama, H; Kim, M; Okumura, K; Tada, T

    1984-05-01

    Hybridomas producing monoclonal antibodies (mAb) specific for immunoglobulin heavy chain (Igh) allotype-linked gene products expressed only on functional T cells but not on B cells and macrophages were established by fusion of allotype congenic SJL (Igh-1b) and SJA /9 (Igh-1a) B cells immunized reciprocally with partner spleen cells with a myeloma P3-X63-Ag8-653 of BALB/c origin. Nine mAb have been selected on the criteria that they can specifically block various antigen-dependent functions of known T cell subsets in in vitro immune responses of mouse strains having the corresponding Igh allotype, but not the other one. These included (a) four mAb that augment the in vitro secondary antibody response of either Igh-1a or Igh-1b strains and thus are considered to react with the Igh-linked allotypic determinant expressed on suppressor T cells, (b) one mAb that inhibits the helper T cell activity of Igh-1b but not of Igh-1a strains, (c) two mAb that inhibit the antigen-induced proliferative response of Igh-1a but not Igh-1b strains, and (d) two mAb that block the cytotoxicity of alloreactive cytotoxic T cells of Igh-1a strains. The linkage to Igh-1 allotype of the T cell products was established by testing with Igh-1-congenic strains with different backgrounds including the H-2 complex. Some of the mAb were able to react with cloned hybridomas and a continuous cell line of the given allotype and functions. Each mAb was able to block one of the known functions of T cell subsets, but not others, indicating the existence of the heterogeneity and multiplicity of the Igh allotype-linked products on T cells.

  2. A Three-way Parallel ICA Approach to Analyze Links among Genetics, Brain Structure and Brain Function

    PubMed Central

    Vergara, Victor M.; Ulloa, Alvaro; Calhoun, Vince D.; Boutte, David; Chen, Jiayu; Liu, Jingyu

    2014-01-01

    Multi-modal data analysis techniques, such as the Parallel Independent Component Analysis (pICA), are essential in neuroscience, medical imaging and genetic studies. The pICA algorithm allows the simultaneous decomposition of up to two data modalities achieving better performance than separate ICA decompositions and enabling the discovery of links between modalities. However, advances in data acquisition techniques facilitate the collection of more than two data modalities from each subject. Examples of commonly measured modalities include genetic information, structural magnetic resonance imaging (MRI) and functional MRI. In order to take full advantage of the available data, this work extends the pICA approach to incorporate three modalities in one comprehensive analysis. Simulations demonstrate the three-way pICA performance in identifying pairwise links between modalities and estimating independent components which more closely resemble the true sources than components found by pICA or separate ICA analyses. In addition, the three-way pICA algorithm is applied to real experimental data obtained from a study that investigate genetic effects on alcohol dependence. Considered data modalities include functional MRI (contrast images during alcohol exposure paradigm), gray matter concentration images from structural MRI and genetic single nucleotide polymorphism (SNP). The three-way pICA approach identified links between a SNP component (pointing to brain function and mental disorder associated genes, including BDNF, GRIN2B and NRG1), a functional component related to increased activation in the precuneus area, and a gray matter component comprising part of the default mode network and the caudate. Although such findings need further verification, the simulation and in-vivo results validate the three-way pICA algorithm presented here as a useful tool in biomedical data fusion applications. PMID:24795156

  3. A three-way parallel ICA approach to analyze links among genetics, brain structure and brain function.

    PubMed

    Vergara, Victor M; Ulloa, Alvaro; Calhoun, Vince D; Boutte, David; Chen, Jiayu; Liu, Jingyu

    2014-09-01

    Multi-modal data analysis techniques, such as the Parallel Independent Component Analysis (pICA), are essential in neuroscience, medical imaging and genetic studies. The pICA algorithm allows the simultaneous decomposition of up to two data modalities achieving better performance than separate ICA decompositions and enabling the discovery of links between modalities. However, advances in data acquisition techniques facilitate the collection of more than two data modalities from each subject. Examples of commonly measured modalities include genetic information, structural magnetic resonance imaging (MRI) and functional MRI. In order to take full advantage of the available data, this work extends the pICA approach to incorporate three modalities in one comprehensive analysis. Simulations demonstrate the three-way pICA performance in identifying pairwise links between modalities and estimating independent components which more closely resemble the true sources than components found by pICA or separate ICA analyses. In addition, the three-way pICA algorithm is applied to real experimental data obtained from a study that investigate genetic effects on alcohol dependence. Considered data modalities include functional MRI (contrast images during alcohol exposure paradigm), gray matter concentration images from structural MRI and genetic single nucleotide polymorphism (SNP). The three-way pICA approach identified links between a SNP component (pointing to brain function and mental disorder associated genes, including BDNF, GRIN2B and NRG1), a functional component related to increased activation in the precuneus area, and a gray matter component comprising part of the default mode network and the caudate. Although such findings need further verification, the simulation and in-vivo results validate the three-way pICA algorithm presented here as a useful tool in biomedical data fusion applications.

  4. 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.

  5. 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

  6. 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...

  7. 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.

  8. 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

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

    PubMed

    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

    2015-01-20

    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.

  10. 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...

  11. Linking variability in brain chemistry and circuit function through multimodal human neuroimaging.

    PubMed

    Fisher, P M; Hariri, A R

    2012-08-01

    Identifying neurobiological mechanisms mediating the emergence of individual differences in behavior is critical for advancing our understanding of relative risk for psychopathology. Neuroreceptor positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) can be used to assay in vivo regional brain chemistry and function, respectively. Typically, these neuroimaging modalities are implemented independently despite the capacity for integrated data sets to offer unique insight into molecular mechanisms associated with brain function. Through examples from the serotonin and dopamine system and its effects on threat- and reward-related brain function, we review evidence for how such a multimodal neuroimaging strategy can be successfully implemented. Furthermore, we discuss how multimodal PET-fMRI can be integrated with techniques such as imaging genetics, pharmacological challenge paradigms and gene-environment interaction models to more completely map biological pathways mediating individual differences in behavior and related risk for psychopathology and inform the development of novel therapeutic targets.

  12. Linking plat traits at ecosystem scale to ecosystem functions as observed by eddy covariance measurements

    NASA Astrophysics Data System (ADS)

    Sadat Musavi, Talie; Kattge, Jens; Mahecha, Miguel; Reichstein, Markus; Van de Weg, Marjan; Van Bodegom, Peter; Bahn, Michael

    2013-04-01

    In this study we analyze the correlation structure among plant traits, ecosystem functional properties, characteristics of climate, soil and vegetation at 253 FLUXNET sites. This correlation structure may provide a basis for assessing vegetation functioning and its vulnerability under climate change. Until now, analyses of the FLUXNET dataset have shown that much of the observed spatial and temporal variation of ecosystem fluxes can be explained and scaled by information on soil, climate and vegetation structure, without considering the variation in the functional characteristics of the vegetation occurring at the FLUXNET sites. Instead, these studies have used plant functional types (PFT) as a parameter representing the vegetation influence on fluxes. However, provided the variability in traits that exists within an individual PFT at different sites, we analyze in this study how traits additionally influence ecosystem functional properties. We use community mean trait values to understand how vegetation characteristics relate to ecosystem functional properties, like maximum GPP at light saturation, or photosynthetic water use efficiency. These functional properties are derived from the combination of ecosystem level flux observation and information of spatial meteorology and vegetation remote sensing covariates. In addition, we investigate whether vegetation characteristics have an influence on ecosystem fluxes when combined with climate and soil information. So far analyses of this kind were impossible due to a lack of plant trait information. But the plant trait dataset TRY has been growing for years and in combination with novel methods in machine learning. We now have the opportunity to predict plant trait values for individual sites. We will present first results focusing on the relationship of ecosystem functional properties to leaf traits like specific leaf area and leaf carbon, nitrogen and phosphorus concentration scaled to canopy level.

  13. Test–Retest Intervisit Variability of Functional and Structural Parameters in X-Linked Retinoschisis

    PubMed Central

    Jeffrey, Brett G.; Cukras, Catherine A.; Vitale, Susan; Turriff, Amy; Bowles, Kristin; Sieving, Paul A.

    2014-01-01

    Purpose To examine the variability of four outcome measures that could be used to address safety and efficacy in therapeutic trials with X-linked juvenile retinoschisis. Methods Seven men with confirmed mutations in the RS1 gene were evaluated over four visits spanning 6 months. Assessments included visual acuity, full-field electroretinograms (ERG), microperimetric macular sensitivity, and retinal thickness measured by optical coherence tomography (OCT). Eyes were separated into Better or Worse Eye groups based on acuity at baseline. Repeatability coefficients were calculated for each parameter and jackknife resampling used to derive 95% confidence intervals (CIs). Results The threshold for statistically significant change in visual acuity ranged from three to eight letters. For ERG a-wave, an amplitude reduction greater than 56% would be considered significant. For other parameters, variabilities were lower in the Worse Eye group, likely a result of floor effects due to collapse of the schisis pockets and/or retinal atrophy. The criteria for significant change (Better/Worse Eye) for three important parameters were: ERG b/a-wave ratio (0.44/0.23), point wise sensitivity (10.4/7.0 dB), and central retinal thickness (31%/18%). Conclusions The 95% CI range for visual acuity, ERG, retinal sensitivity, and central retinal thickness relative to baseline are described for this cohort of participants with X-linked juvenile retinoschisis (XLRS). Translational Relevance A quantitative understanding of the variability of outcome measures is vital to establishing the safety and efficacy limits for therapeutic trials of XLRS patients. PMID:25346871

  14. Application of the Principle of Linked Functions to ATP-Driven Ion Pumps: Kinetics of Activation by ATP

    NASA Astrophysics Data System (ADS)

    Reynolds, Jacqueline A.; Johnson, Edward A.; Tanford, Charles

    1985-06-01

    If a ligand binds with unequal affinity to two distinct states of a protein, then the equilibrium between the two states becomes a function of the concentration of the ligand. A necessary consequence is that the ligand must also affect the forward and/or reverse rate constants for transition between the two states. For an enzyme or transport protein with such a transition as a slow step in the catalytic cycle, the overall rate also becomes a function of ligand concentration. These conclusions are independent of whether or not the ligand is a direct participant in the reaction. If it is a direct partitipant, then the kinetic effect arising from the principle of linked functions is distinct from the direct catalytic effect. These principles suffice to account for the biphasic response of the hydrolytic activity of ATP-driven ion pumps to the concentration of ATP, without the need to invoke more than one ATP binding site per catalytic center.

  15. Reflective Functioning, Physiological Reactivity, and Overcontrol in Mothers: Links with School-Aged Children's Reflective Functioning

    ERIC Educational Resources Information Center

    Borelli, Jessica L.; Hong, Kajung; Rasmussen, Hannah F.; Smiley, Patricia A.

    2017-01-01

    Theorists argue that parental reflective functioning (PRF) is activated in response to emotions, potentially supporting parenting sensitivity even when arousal is high. That is, when parents become emotionally reactive when interacting with their children, those who can use PRF to understand their children's mental states should be able to parent…

  16. 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

  17. 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). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  18. Functional limitations linked to high body mass index, age and current pain in obese women.

    PubMed

    Evers Larsson, U; Mattsson, E

    2001-06-01

    To describe functional limitations in obese women. Comparisons of functional limitations in obese women and in a normal-weight reference group regarding mobility, balance and housework transport. A large room with a corridor and staircase nearby. Fifty-seven consecutively selected obese female outpatients, mean age 44 y, body mass index (BMI) 37 kg.m(-2), and 22 voluntary references, mean age 49 y, BMI 22 kg.m(-2). Pain questionnaire (for background data); a new valid and reliable test protocol measuring activities of daily life (ADL), pain and exertion, heart rate, balance and speed. The patients had problems in performing 13 of 16 actions compared with the references (P-values between 0.05 and 0.001). They moved more slowly and had difficulties and /or pain and exertion in flexibility tasks, balancing, activities at floor level (bending and kneeling), climbing stairs and carrying groceries. BMI (P=0.002), age (P=0.02) and current pain (P=0.02) from the lower body predicted functional limitation. The functional test reflected functional limitations in obese women, revealing difficulties and perceived pain in ADL. The test protocol can be used to evaluate the effects of training or dieting. For clinical use we recommend considering BMI, age and current pain for use when individualizing advice on training.

  19. Psychological Symptoms Linking Exposure to Community Violence and Academic Functioning in African American Adolescents

    PubMed Central

    Busby, Danielle R.; Lambert, Sharon F.; Ialongo, Nicholas S.

    2013-01-01

    African American adolescents are exposed disproportionately to community violence, increasing their risk for emotional and behavioral symptoms that can detract from learning and undermine academic outcomes. The present study examined whether aggressive behavior and depressive and anxious symptoms mediated the association between exposure to community violence and academic functioning, and if the indirect effects of community violence on academic functioning differed for boys and girls, in a community sample of urban African American adolescents (N = 491; 46.6% female). Structural equation modeling was used to examine the indirect effect of exposure to community violence in grade 6 on grade 8 academic functioning. Results revealed that aggression in grade 7 mediated the association between grade 6 exposure to community violence and grade 8 academic functioning. There were no indirect effects through depressive and anxious symptoms, and gender did not moderate the indirect effect. Findings highlight the importance of targeting aggressive behavior for youth exposed to community violence to not only improve their behavioral adjustment but also their academic functioning. Implications for future research are discussed. PMID:23277294

  20. Psychological symptoms linking exposure to community violence and academic functioning in African American adolescents.

    PubMed

    Busby, Danielle R; Lambert, Sharon F; Ialongo, Nicholas S

    2013-02-01

    African American adolescents are exposed disproportionately to community violence, increasing their risk for emotional and behavioral symptoms that can detract from learning and undermine academic outcomes. The present study examined whether aggressive behavior and depressive and anxious symptoms mediated the association between exposure to community violence and academic functioning, and if the indirect effects of community violence on academic functioning differed for boys and girls, in a community sample of urban African American adolescents (N = 491; 46.6 % female). Structural equation modeling was used to examine the indirect effect of exposure to community violence in grade 6 on grade 8 academic functioning. Results revealed that aggression in grade 7 mediated the association between grade 6 exposure to community violence and grade 8 academic functioning. There were no indirect effects through depressive and anxious symptoms, and gender did not moderate the indirect effect. Findings highlight the importance of targeting aggressive behavior for youth exposed to community violence to not only improve their behavioral adjustment but also their academic functioning. Implications for future research are discussed.

  1. 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.

  2. The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.

    PubMed

    Gough, Julian; Chothia, Cyrus

    2004-06-01

    The monomeric cupredoxins are a highly divergent family of copper binding electron transport proteins that function in photosynthesis and respiration. To determine how function and structure are conserved in the context of large sequence differences, we have carried out a detailed analysis of the cupredoxins of known structure and their sequence homologs. The common structure of the cupredoxins is formed by a sandwich of two beta sheets which support a copper binding site. The structure of the deeply buried core is intimately coupled to the binding site on the surface of the protein; in each protein the conserved regions form one continuous substructure that extends from the surface active site and through the center of the molecule. Residues around the active site are conserved for functional reasons, while those deeper in the structure will be conserved for structural reasons. Together the two sets support each other.

  3. Neuroligins and neurexins: linking cell adhesion, synapse formation and cognitive function.

    PubMed

    Dean, Camin; Dresbach, Thomas

    2006-01-01

    Cell adhesion represents the most direct way of coordinating synaptic connectivity in the brain. Recent evidence highlights the importance of a trans-synaptic interaction between postsynaptic neuroligins and presynaptic neurexins. These transmembrane molecules bind each other extracellularly to promote adhesion between dendrites and axons. This signals the recruitment of presynaptic and postsynaptic molecules to form a functional synapse. Remarkably, neuroligins alone can induce the formation of fully functional presynaptic terminals in contacting axons. Conversely, neurexins alone can induce postsynaptic differentiation and clustering of receptors in dendrites. Therefore, the neuroligin-neurexin interaction has the unique ability to act as a bi-directional trigger of synapse formation. Here, we review several recent studies that offer clues as to how these proteins form synapses and how they might function in the brain to establish and modify neuronal network properties and cognition.

  4. 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

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

    PubMed

    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; Thompson, Paul M; Asarnow, Robert F

    2015-07-15

    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. 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 variance, as diffusion weighted

  6. Functional deregulation of KIT: link to mast cell proliferative diseases and other neoplasms.

    PubMed

    Cruse, Glenn; Metcalfe, Dean D; Olivera, Ana

    2014-05-01

    In this review, the authors discuss common gain-of-function mutations in the stem cell factor receptor KIT found in mast cell proliferation disorders and summarize the current understanding of the molecular mechanisms by which these transforming mutations may affect KIT structure and function leading to altered downstream signaling and cellular transformation. Drugs targeting KIT have shown mixed success in the treatment of mastocytosis and other hyperproliferative diseases. A brief overview of the most common KIT inhibitors currently used, the reasons for the varied clinical results of such inhibitors and a discussion of potential new strategies are provided.

  7. 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

  8. Ogt-dependent X-chromosome-linked protein glycosylation is a requisite modification in somatic cell function and embryo viability.

    PubMed

    O'Donnell, Niall; Zachara, Natasha E; Hart, Gerald W; Marth, Jamey D

    2004-02-01

    The Ogt gene encodes a glycosyltransferase that links N-acetylglucosamine to serine and threonine residues (O-GlcNAc) on nuclear and cytosolic proteins. Efforts to study a mammalian model of Ogt deficiency have been hindered by the requirement for this X-linked gene in embryonic stem cell viability, necessitating the use of conditional mutagenesis in vivo. We have extended these observations by segregating Ogt mutation to distinct somatic cell types, including neurons, thymocytes, and fibroblasts, the latter by an approach developed for inducible Ogt mutagenesis. We show that Ogt mutation results in the loss of O-GlcNAc and causes T-cell apoptosis, neuronal tau hyperphosphorylation, and fibroblast growth arrest with altered expression of c-Fos, c-Jun, c-Myc, Sp1, and p27. We further segregated the mutant Ogt allele to parental gametes by oocyte- and spermatid-specific Cre-loxP mutagenesis. By this we established an in vivo genetic approach that supports the ontogeny of female heterozygotes bearing mutant X-linked genes required during embryogenesis. Successful production and characterization of such female heterozygotes further indicates that mammalian cells commonly require a functional Ogt allele. We find that O-GlcNAc modulates protein phosphorylation and expression among essential and conserved cell signaling pathways.

  9. 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.

  10. Biomechanical variation of silk links spinning plasticity to spider web function.

    PubMed

    Boutry, Cecilia; Blackledge, Todd A

    2009-01-01

    Spider silk is renowned for its high tensile strength, extensibility and toughness. However, the variability of these material properties has largely been ignored, especially at the intra-specific level. Yet, this variation could help us understand the function of spider webs. It may also point to the mechanisms used by spiders to control their silk production, which could be exploited to expand the potential range of applications for silk. In this study, we focus on variation of silk properties within different regions of cobwebs spun by the common house spider, Achaearanea tepidariorum. The cobweb is composed of supporting threads that function to maintain the web shape and hold spiders and prey, and of sticky gumfooted threads that adhere to insects during prey capture. Overall, structural properties, especially thread diameter, are more variable than intrinsic material properties, which may reflect past directional selection on certain silk performance. Supporting threads are thicker and able to bear higher loads, both before deforming permanently and before breaking, compared with sticky gumfooted threads. This may facilitate the function of supporting threads through sustained periods of time. In contrast, sticky gumfooted threads are more elastic, which may reduce the forces that prey apply to webs and allow them to contact multiple sticky capture threads. Therefore, our study suggests that spiders actively modify silk material properties during spinning in ways that enhance web function.

  11. 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, ...

  12. 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, ...

  13. 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.

  14. “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

  15. 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…

  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…

  17. The Link between Preschoolers' Executive Function and Theory of Mind and the Role of Epistemic States

    ERIC Educational Resources Information Center

    Henning, Anne; Spinath, Frank M.; Aschersleben, Gisa

    2011-01-01

    The aim of this study was to assess the specific relation between 3- to 6-year-olds' performance on a task measuring executive function (EF), the Dimensional Change Card Sort task (DCCS), and different developmental attainments in their theory of mind (ToM) by employing a battery of scaled ToM tasks that were comparable in task format and task…

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

    PubMed Central

    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

  19. 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…

  20. 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.

  1. "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.

  2. 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…

  3. 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

  4. LECT2 functions as a hepatokine that links obesity to skeletal muscle insulin resistance.

    PubMed

    Lan, Fei; Misu, Hirofumi; Chikamoto, Keita; Takayama, Hiroaki; Kikuchi, Akihiro; Mohri, Kensuke; Takata, Noboru; Hayashi, Hiroto; Matsuzawa-Nagata, Naoto; Takeshita, Yumie; Noda, Hiroyo; Matsumoto, Yukako; Ota, Tsuguhito; Nagano, Toru; Nakagen, Masatoshi; Miyamoto, Ken-ichi; Takatsuki, Kanako; Seo, Toru; Iwayama, Kaito; Tokuyama, Kunpei; Matsugo, Seiichi; Tang, Hong; Saito, Yoshiro; Yamagoe, Satoshi; Kaneko, Shuichi; Takamura, Toshinari

    2014-05-01

    Recent articles have reported an association between fatty liver disease and systemic insulin resistance in humans, but the causal relationship remains unclear. The liver may contribute to muscle insulin resistance by releasing secretory proteins called hepatokines. Here we demonstrate that leukocyte cell-derived chemotaxin 2 (LECT2), an energy-sensing hepatokine, is a link between obesity and skeletal muscle insulin resistance. Circulating LECT2 positively correlated with the severity of both obesity and insulin resistance in humans. LECT2 expression was negatively regulated by starvation-sensing kinase adenosine monophosphate-activated protein kinase in H4IIEC hepatocytes. Genetic deletion of LECT2 in mice increased insulin sensitivity in the skeletal muscle. Treatment with recombinant LECT2 protein impaired insulin signaling via phosphorylation of Jun NH2-terminal kinase in C2C12 myocytes. These results demonstrate the involvement of LECT2 in glucose metabolism and suggest that LECT2 may be a therapeutic target for obesity-associated insulin resistance.

  5. 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.

  6. IKKbeta suppression of TSC1 function links the mTOR pathway with insulin resistance.

    PubMed

    Lee, Dung-Fang; Kuo, Hsu-Ping; Chen, Chun-Te; Wei, Yongkun; Chou, Chao-Kai; Hung, Jen-Yu; Yen, Chia-Jui; Hung, Mien-Chie

    2008-11-01

    The proinflammatory cytokine TNFalpha is one of the factors that links obesity-derived chronic inflammation with insulin resistance. Activation of mTOR signaling pathway has been found to suppress insulin sensitivity through serine phosphorylation and the inhibition of IRS1 by mTOR and its downstream effector, S6K1. It remains elusive that whether the mTOR pathway has a role in TNFalpha-mediated insulin resistance. In the present study, we demonstrated that TNFalpha-IKKbeta-mediated inactivation of TSC1 resulted in increasing phosphorylation of IRS1 serine 307 and serine 636/639, impaired insulin-induced glucose uptake, tyrosine phosphorylation of IRS1, and the association between IRS1 and PI3K p85. Furthermore, a higher expression of pIKKbeta (S181), pTSC1(S511), and pS6(S240/244) was found in livers obtained from both C57BL/6J mice on a high-fat diet and B6.V-Lepob/J mice. Collectively, dysregulation of the TSC1/ TSC2/mTOR signaling pathway by IKKbeta is a common molecular switch for both cancer pathogenesis and diet- and obesity-induced insulin resistance.

  7. 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.

  8. 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

  9. A functional link between Wnt signaling and SKP2-independent p27 turnover in mammary tumors

    PubMed Central

    Miranda-Carboni, Gustavo A.; Krum, Susan A.; Yee, Kathleen; Nava, Miguel; Deng, Qiming E.; Pervin, Shehla; Collado-Hidalgo, Alicia; Galić, Zoran; Zack, Jerome A.; Nakayama, Keiko; Nakayama, Keiichi I.; Lane, Timothy F.

    2008-01-01

    Loss of the CDK inhibitor p27KIP1 is widely linked with poor prognosis in human cancer. In Wnt10b-expressing mammary tumors, levels of p27KIP1 were extremely low; conversely, Wnt10b-null mammary cells expressed high levels of this protein, suggesting Wnt-dependent regulation of p27KIP1. Interestingly we found that Wnt-induced turnover of p27KIP1 was independent from classical SCFSKP2-mediated degradation in both mouse and human cells. Instead, turnover required Cullin 4A and Cullin 4B, components of an alternative E3 ubiquitin ligase induced in response to active Wnt signaling. We found that CUL4A was a novel Wnt target gene in both mouse and human cells and that CUL4A physically interacted with p27KIP1 in Wnt-responding cells. We further demonstrated that both Cul4A and Cul4B were required for Wnt-induced p27KIP1 degradation and S-phase progression. CUL4A and CUL4B are therefore components of a conserved Wnt-induced proteasome targeting (WIPT) complex that regulates p27KIP1 levels and cell cycle progression in mammalian cells. PMID:19056892

  10. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.

    PubMed

    Dávila López, Marcela; Martínez Guerra, Juan José; Samuelsson, Tore

    2010-05-14

    The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.

  11. Analysis of Gene Order Conservation in Eukaryotes Identifies Transcriptionally and Functionally Linked Genes

    PubMed Central

    Dávila López, Marcela; Martínez Guerra, Juan José; Samuelsson, Tore

    2010-01-01

    The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control. PMID:20498846

  12. LINKING LUNG AIRWAY STRUCTURE TO PULMONARY FUNCTION VIA COMPOSITE BRIDGE REGRESSION

    PubMed Central

    Chen, Kun; Hoffman, Eric A.; Seetharaman, Indu; Jiao, Feiran; Lin, Ching-Long; Chan, Kung-Sik

    2017-01-01

    The human lung airway is a complex inverted tree-like structure. Detailed airway measurements can be extracted from MDCT-scanned lung images, such as segmental wall thickness, airway diameter, parent-child branch angles, etc. The wealth of lung airway data provides a unique opportunity for advancing our understanding of the fundamental structure-function relationships within the lung. An important problem is to construct and identify important lung airway features in normal subjects and connect these to standardized pulmonary function test results such as FEV1%. Among other things, the problem is complicated by the fact that a particular airway feature may be an important (relevant) predictor only when it pertains to segments of certain generations. Thus, the key is an efficient, consistent method for simultaneously conducting group selection (lung airway feature types) and within-group variable selection (airway generations), i.e., bi-level selection. Here we streamline a comprehensive procedure to process the lung airway data via imputation, normalization, transformation and groupwise principal component analysis, and then adopt a new composite penalized regression approach for conducting bi-level feature selection. As a prototype of composite penalization, the proposed composite bridge regression method is shown to admit an efficient algorithm, enjoy bi-level oracle properties, and outperform several existing methods. We analyze the MDCT lung image data from a cohort of 132 subjects with normal lung function. Our results show that, lung function in terms of FEV1% is promoted by having a less dense and more homogeneous lung comprising an airway whose segments enjoy more heterogeneity in wall thicknesses, larger mean diameters, lumen areas and branch angles. These data hold the potential of defining more accurately the “normal” subject population with borderline atypical lung functions that are clearly influenced by many genetic and environmental factors. PMID

  13. Linking the biology and physics of multifunctional grasses and soil hydrological function

    NASA Astrophysics Data System (ADS)

    MacLeod, C. J. A.; Binley, A.; Haygarth, P. M.; Humphreys, M. W.; Joynes, A.; Papadopoulos, A.; Skot, L.; Turner, L. B.; Watts, C.; Whalley, W. R.

    2009-04-01

    Sustainable grassland systems need to function during periods of water deficit and excess. Traditionally, forage grasses have been bred for drought resistance and winter hardiness traits. There is a need to select for and grow grass cultivars under drought and water logged conditions, whilst delivering environmental services. A limited number of studies have been carried out on inter-species variability of plant water status and growth during periods of water deficit. However, little is known about how different grasses influence soil profile hydraulic properties. We have established and monitored the influence of grass type on soil hydrological properties and rainfall-runoff relationships. Changes in soil hydrological properties have been monitored using a range of soil physical and geophysical methods. In this paper we report on a large interdisciplinary project that is advancing our understanding of how grass selection may benefit soil hydraulic functioning during periods of water excess.

  14. Functional connectivity of the striatum links motivation to action control in humans.

    PubMed

    Harsay, Helga A; Cohen, Michael X; Oosterhof, Nikolaas N; Forstmann, Birte U; Mars, Rogier B; Ridderinkhof, K Richard

    2011-07-20

    Motivation improves the efficiency of intentional behavior, but how this performance modulation is instantiated in the human brain remains unclear. We used a reward-cued antisaccade paradigm to investigate how motivational goals (the expectation of a reward for good performance) modulate patterns of neural activation and functional connectivity to improve preparation for antisaccade performance. Behaviorally, subjects performed better (faster and more accurate antisaccades) when they knew they would be rewarded for good performance. Reward anticipation was associated with increased activation in the ventral and dorsal striatum, and cortical oculomotor regions. Functional connectivity between the caudate nucleus and cortical oculomotor control structures predicted individual differences in the behavioral benefit of reward anticipation. We conclude that although both dorsal and ventral striatal circuitry are involved in the anticipation of reward, only the dorsal striatum and its connected cortical network is involved in the direct modulation of oculomotor behavior by motivational incentive.

  15. An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles

    PubMed Central

    Kotaru, Appala Raju; Shameer, Khader; Sundaramurthy, Pandurangan; Joshi, Ramesh Chandra

    2013-01-01

    Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes. PMID:23750082

  16. 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. © 2014 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles.

    PubMed

    Kotaru, Appala Raju; Shameer, Khader; Sundaramurthy, Pandurangan; Joshi, Ramesh Chandra

    2013-01-01

    Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.

  18. Is There a Link Between Cognitive Reserve and Cognitive Function in the Oldest-Old?

    PubMed

    Lavrencic, Louise M; Richardson, Connor; Harrison, Stephanie L; Muniz-Terrera, Graciela; Keage, Hannah A D; Brittain, Katie; Kirkwood, Thomas B L; Jagger, Carol; Robinson, Louise; Stephan, Blossom C M

    2017-07-22

    The oldest-old (aged ≥85 years) are the fastest growing age group, with the highest risk of cognitive impairment and dementia. This study investigated whether cognitive reserve applies to the oldest-old. This has implications for cognitive interventions in this age group. Baseline and 5-year follow-up data from the Newcastle 85+ Study were used (N = 845, mean age = 85.5, 38% male). A Cognitive Reserve Index (CRI) was created, including: education, social class, marital status, engagement in mental activities, social participation, and physical activity. Global (Mini-Mental State Examination) and domain specific (Cognitive Drug Research Battery subtests assessing memory, attention, and speed) cognitive functions were assessed. Dementia diagnosis was determined by health records. Logistic regression analysis examined the association between CRI scores and incident dementia. Mixed effects models investigated baseline and longitudinal associations between the CRI scores and cognitive function. Analyses controlled for sex, age, depression, and cardiovascular disease history. Higher reserve associated with better cognitive performance on all baseline measures, but not 5-year rate of change. The CRI associated with prevalent, but not incident dementia. In the oldest-old, higher reserve associated with better baseline global and domain-specific cognitive function and reduced risk of prevalent dementia; but not cognitive decline or incident dementia. Increasing reserve could promote cognitive function in the oldest-old. The results suggest there would be little impact on trajectories, but replication is needed. Development of preventative strategies would benefit from identifying the role of each factor in building reserve and why rate of change is not affected.

  19. Reproductive function in men affected by X-linked adrenoleukodystrophy/adrenomyeloneuropathy.

    PubMed

    Stradomska, T J; Kubalska, J; Janas, R; Tylki-Szymanska, A

    2012-02-01

    X-linked adrenoleukodystrophy (X-ALD) is the most frequent, severely neurodegenerative, clinically heterogeneous peroxisomal disorder, the signs of which are a consequence of myelin, adrenal cortex, and testes impairment. We studied testosterone, LH, and FSH levels in X-ALD/adrenomyeloneuropathy (AMN) patients. We evaluate the ability to procreate of these patients by analysis of pedigree and family screening by detection of very long-chain fatty acid (VLCFA) levels. Seventeen patients with X-ALD/AMN (16 with AMN and one asymptomatic) aged 24-48 (mean±S.D., 34.7±5.9) years, were identified based on the clinical picture, magnetic resonance imaging, and the presence of increased serum VLCFA levels. Nine X-ALD/AMN patients' daughters, mean ages ±S.D.=7.7±3.8 years, were identified as heterozygote by elevated VLCFA levels. Serum VLCFA levels were determined as ester derivatives by a gas chromatography method. Serum testosterone, LH, and FSH levels in X-ALD/AMN patients were detected by IRMAs. Serum testosterone levels were at the lowest levels of normal range but serum LH and FSH concentrations were increased in 57.1 and in 42.9% of X-ALD/AMN patients respectively. Among the 11 investigated of X-ALD/AMN married adult men, nine had produced offspring, a total of 13 children. All patients' daughters showed elevated serum VLCFA at heterozygote levels. In this study, we report that in a group of X-ALD/AMN married adult men, we did not find a significant decrease in fertility compared with the Polish population (18.2 vs 15%).

  20. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity.

    PubMed

    Hernández, Ester; Bargiela, Rafael; Diez, María Suárez; Friedrichs, Anette; Pérez-Cobas, Ana Elena; Gosalbes, María José; Knecht, Henrik; Martínez-Martínez, Mónica; Seifert, Jana; von Bergen, Martin; Artacho, Alejandro; Ruiz, Alicia; Campoy, Cristina; Latorre, Amparo; Ott, Stephan J; Moya, Andrés; Suárez, Antonio; Martins dos Santos, Vitor A P; Ferrer, Manuel

    2013-01-01

    The microbiomes in the gastrointestinal tract (GIT) of individuals receiving antibiotics and those in obese subjects undergo compositional shifts, the metabolic effects and linkages of which are not clearly understood. Herein, we set to gain insight into these effects, particularly with regard to carbohydrate metabolism, and to contribute to unravel the underlying mechanisms and consequences for health conditions. We measured the activity level of GIT carbohydrate-active enzymes toward 23 distinct sugars in adults patients (n = 2) receiving 14-d β-lactam therapy and in obese (n = 7) and lean (n = 5) adolescents. We observed that both 14 d antibiotic-treated and obese subjects showed higher and less balanced sugar anabolic capacities, with 40% carbohydrates being preferentially processed as compared with non-treated and lean patients. Metaproteome-wide metabolic reconstructions confirmed that the impaired utilization of sugars propagated throughout the pentose phosphate metabolism, which had adverse consequences for the metabolic status of the GIT microbiota. The results point to an age-independent positive association between GIT glycosidase activity and the body mass index, fasting blood glucose and insulin resistance (r ( 2) ≥ 0.95). Moreover, antibiotics altered the active fraction of enzymes controlling the thickness, composition and consistency of the mucin glycans. Our data and analyses provide biochemical insights into the effects of antibiotic usage on the dynamics of the GIT microbiota and pin-point presumptive links to obesity. The knowledge and the hypotheses generated herein lay a foundation for subsequent, systematic research that will be paramount for the design of "smart" dietary and therapeutic interventions to modulate host-microbe metabolic co-regulation in intestinal homeostasis.

  1. 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

  2. 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.

  3. Oxygenation-linked subunit interactions in human hemoglobin: analysis of linkage functions for constituent energy terms.

    PubMed

    Johnson, M L; Halvorson, H R; Ackers, G K

    1976-11-30

    Resolution of the linkage functions between oxygenation and subunit association-dissociation equilibria in human hemoglobin into the constituent microscopic terms has been explored by numerical simulation and least-squares analysis. The correlation properties between parameters has been studied using several choices of parameter sets in order to optimize resolution. It is found that, with currently available levels of experimental precision and ranges of variables, neither linkage function can provide sufficient resolution of all the desired energy terms. The most difficult quantities to resolve always include the dimer-tetramer association constant for unliganded hemoglobin and the oxygen binding constants to alphabeta dimers. A feasible experimental strategy for overcoming these difficulties lies in independent determination of the dimer-tetramer association constants for unliganded and fully oxygenated hemoglobin. These constants, in combination with the median lignad concentration, provide an estimate of the energy for total oxygenation of tetramers which is essentially independent of the other constituent energies. It is shown that if these separately determinable parameters are fixed, the remaining terms may be estimated to good accuracy using data which represents either linkage function. In general it is desirable to combine information from both types of experimental quantities. A previous paper (Mills, F.C., Johnson, M.L., and Ackers, G.K. (1976), Biochemestry, 15, the preceding paper in this issue) describes the experimental implementation of this strategy.

  4. Rab6-interacting protein 1 links Rab6 and Rab11 function.

    PubMed

    Miserey-Lenkei, Stéphanie; Waharte, François; Boulet, Annick; Cuif, Marie-Hélène; Tenza, Danielle; El Marjou, Amed; Raposo, Graça; Salamero, Jean; Héliot, Laurent; Goud, Bruno; Monier, Solange

    2007-10-01

    Rab11 and Rab6 guanosine triphosphatases are associated with membranes of the recycling endosomes (REs) and Golgi complex, respectively. Evidence indicates that they sequentially regulate a retrograde transport pathway between these two compartments, suggesting the existence of proteins that must co-ordinate their functions. Here, we report the characterization of two isoforms of a protein, Rab6-interacting protein 1 (R6IP1), originally identified as a Rab6-binding protein. R6IP1 also binds to Rab11A in its GTP-bound conformation. In interphase cells, R6IP1 is targeted to the Golgi in a Rab6-dependent manner but can associate with Rab11-positive compartments when the level of Rab11A is increased within the cells. Fluorescence resonance energy transfer analysis using fluorescence lifetime imaging shows that the overexpression of R6IP1 promotes an interaction between Rab11A and Rab6 in living cells. Accordingly, the REs marked by Rab11 and transferrin receptor are depleted from the cell periphery and accumulate in the pericentriolar area. However, endosomal and Golgi membranes do not appear to fuse with each other. We also show that R6IP1 function is required during metaphase and cytokinesis, two mitotic steps in which a role of Rab6 and Rab11 has been previously documented. We propose that R6IP1 may couple Rab6 and Rab11 function throughout the cell cycle.

  5. 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.

  6. Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

    PubMed Central

    Hensen, Ulf; Meyer, Tim; Haas, Jürgen; Rex, René; Vriend, Gert; Grubmüller, Helmut

    2012-01-01

    Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics. PMID:22606222

  7. 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.

  8. 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

  9. 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.

  10. A functional comparison of cardiac troponin C from representatives of three vertebrate taxa: Linking phylogeny and protein function.

    PubMed

    Sears, Elizabeth J; Gillis, Todd E

    2016-12-01

    The Ca(2+) affinity of cardiac troponin C (cTnC) from rainbow trout is significantly greater than that of cTnC from mammalian species. This high affinity is thought to enable cardiac function in trout at low physiological temperatures and is due to residues Asn(2), Ile(28), Gln(29), and Asp(30) (Gillis et al., 2005, Physiol Genomics, 22, 1-7). Interestingly, the cTnC of the African clawed frog Xenopus laevis (frog cTnC) contains Gln(29) and Asp(30) but the residues at positions 2 and 28 are those found in all mammalian cTnC isoforms (Asp(2) and Val(28)). The purpose of this study was to determine the Ca(2+) affinity of frog cTnC, and to determine how these three protein orthologs influence the function of complete troponin complexes. Measurements of Ca(2+) affinity and the rate of Ca(2+) dissociation from the cTnC isoforms and cTn complexes were made by monitoring the fluorescence of anilinonapthalenesulfote iodoacetamide (IAANS) engineered into the cTnC isoforms to report changes in protein conformation. The results demonstrate that the Ca(2+) affinity of frog cTnC is greater than that of trout cTnC and human cTnC. We also found that replacing human cTnC with frog cTnC in a mammalian cTn complex increased the Ca(2+) affinity of the complex by 5-fold, which is also greater than complexes containing trout cTnC. Together these results suggest that frog cTnC has the potential to increase the Ca(2+) sensitivity of force generation by the mammalian heart.

  11. Pink1 forms a multiprotein complex with Miro and Milton, linking Pink1 function to mitochondrial trafficking.

    PubMed

    Weihofen, Andreas; Thomas, Kelly Jean; Ostaszewski, Beth L; Cookson, Mark R; Selkoe, Dennis J

    2009-03-10

    Recessive mutations in Pink1 lead to a selective degeneration of dopaminergic neurons in the substantia nigra that is characteristic of Parkinson disease. Pink1 is a kinase that is targeted in part to mitochondria, and loss of Pink1 function can alter mitochondrial morphology and dynamics, thus supporting a link between mitochondrial dysfunction and Parkinson disease etiology. Here, we report the unbiased identification and confirmation of a mitochondrial multiprotein complex that contains Pink1, the atypical GTPase Miro, and the adaptor protein Milton. Our screen also identified an interaction between Pink1 and Mitofilin. Based on previously established functions for Miro and Milton in the trafficking of mitochondria along microtubules, we postulate here a role for Pink1 in mitochondrial trafficking. Using subcellular fractionation, we show that the overexpression of Miro and Milton, both of which are known to reside at the outer mitochondrial membrane, increases the mitochondrial Pink1 pool, suggesting a function of Pink1 at the outer membrane. Further, we document that Pink1 expressed without a mitochondrial targeting sequence can still be targeted to a mitochondria-enriched subcellular fraction via Miro and Milton. The latter finding is important for the interpretation of a previously reported protective effect of Pink1 expressed without a mitochondrial targeting sequence. Finally, we find that Miro and Milton expression suppresses altered mitochondrial morphology induced by loss of Pink1 function in cell culture. Our findings suggest that Pink1 functions in the trafficking of mitochondria in cells.

  12. Imbalanced functional link between reward circuits and the cognitive control system in patients with obsessive-compulsive disorder.

    PubMed

    Xie, Chunming; Ma, Lisha; Jiang, Nan; Huang, Ruyan; Li, Li; Gong, Liang; He, Cancan; Xiao, Chaoyong; Liu, Wen; Xu, Shu; Zhang, Zhijun

    2016-08-23

    Altered reward processing and cognitive deficits are often observed in patients with obsessive-compulsive disorder (OCD); however, whether the imbalance in activity between reward circuits and the cognitive control (CC) system is associated with compulsive behavior remains unknown. Sixty-eight OCD patients and 33 cognitively normal (CN) healthy subjects participated in this resting-state functional magnetic resonance imaging study. Alterations in the functional connectivity between reward circuits and the CC system were quantitatively assessed and compared between the groups. A Granger causality analysis was used to determine the causal informational influence between and within reward circuits and the CC system across all subjects. OCD patients showed a dichotomous pattern of enhanced functional coupling in their reward circuits and a weakened functional coupling in their CC system when compared to CN subjects. Neural correlates of compulsive behavior were primarily located in the reward circuits and CC system in OCD patients. Importantly, the CC system exerted a reduced interregional causal influence over the reward system in OCD patients relative to its effect in CN subjects. The limitations of this study are that it was a cross-sectional study and the potential effects of environmental and genetic factors were not explored. OCD patients showed an imbalance in the functional link between reward circuits and the CC system at rest. This bias toward a loss of control may define a pathological state in which subjects are more vulnerable to engaging in compulsive behaviors.

  13. The Final Link: Tapping the Power of Chemical Genetics to Connect the Molecular and Biologic Functions of Mitotic Protein Kinases

    PubMed Central

    Lera, Robert F.; Burkard, Mark E.

    2013-01-01

    During mitosis, protein kinases coordinate cellular reorganization and chromosome segregation to ensure accurate distribution of genetic information into daughter cells. Multiple protein kinases contribute to mitotic regulation, modulating molecular signaling more rapidly than possible with gene expression. However, a comprehensive understanding of how kinases regulate mitotic progression remains elusive. The challenge arises from multiple functions and substrates, a large number of “bystander” phosphorylation events, and the brief window in which all mitotic events transpire. Analog-sensitive alleles of protein kinases are powerful chemical genetic tools for rapid and specific interrogation of kinase function. Moreover, combining these tools with advanced proteomics and substrate labeling has identified phosphorylation sites on numerous protein targets. Here, we review the chemical genetic tools available to study kinase function and identify substrates. We describe how chemical genetics can also be used to link kinase function with cognate phosphorylation events to provide mechanistic detail. This can be accomplished by dissecting subsets of kinase functions and chemical genetic complementation. We believe a complete “chemical genetic toolbox” will ultimately allow a comprehensive understanding of how protein kinases regulate mitosis. PMID:23075814

  14. Functional asymmetry for the active sites of linked 5-aminolevulinate synthase and 8-amino-7-oxononanoate synthase.

    PubMed

    Turbeville, Tracy D; Zhang, Junshun; Adams, W Christopher; Hunter, Gregory A; Ferreira, Gloria C

    2011-07-01

    5-Aminolevulinate synthase (ALAS) and 8-amino-7-oxononanoate synthase (AONS) are homodimeric members of the α-oxoamine synthase family of pyridoxal 5'-phosphate (PLP)-dependent enzymes. Previously, linking two ALAS subunits into a single polypeptide chain dimer yielded an enzyme (ALAS/ALAS) with a significantly greater turnover number than that of wild-type ALAS. To examine the contribution of each active site to the enzymatic activity of ALAS/ALAS, the catalytic lysine, which also covalently binds the PLP cofactor, was substituted with alanine in one of the active sites. Albeit the chemical rate for the pre-steady-state burst of ALA formation was identical in both active sites of ALAS/ALAS, the k(cat) values of the variants differed significantly (4.4±0.2 vs. 21.6±0.7 min(-1)) depending on which of the two active sites harbored the mutation. We propose that the functional asymmetry for the active sites of ALAS/ALAS stems from linking the enzyme subunits and the introduced intermolecular strain alters the protein conformational flexibility and rates of product release. Moreover, active site functional asymmetry extends to chimeric ALAS/AONS proteins, which while having a different oligomeric state, exhibit different rates of product release from the two ALAS and two AONS active sites due to the created intermolecular strain. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. pH effects on the binding of oxygen to non-vertebrate monomeric hemoglobins. A linked function model.

    PubMed

    Saroff, Harry A

    2004-07-07

    Monomeric invertabrate hemoglobins with high oxygen affinity usually contain a tyrosine in the distal region of the heme. This feature has stimulated investigations revealing that one of the properties resulting from the presence of the distal tyrosines is a decreased off rate on the binding of oxygen, thus developing the high affinity. Despite that fact that the pK value of the tyrosine group differs significantly from the groups it replaces little attention has been paid to the pH dependence of the binding of oxygen to the high affinity hemoglobins. Such a pH dependence has been reported on two of the monomeric hemoglobins with relatively low oxygen affinity and one monomeric hemoglobin of intermediate affinity. The pH data of these hemoglobins has been analysed with a linked function model involving the hydrogen ion. pK values required for the low-affinity hemoglobins vary from 4.5 to 7.5. When applied to the high-affinity hemoglobins, the linked function model provides reasonable values for the binding parameters. These pK values vary from 3.0 to 9.0.

  16. Raf-1 Physically Interacts with Rb and Regulates Its Function: a Link between Mitogenic Signaling and Cell Cycle Regulation

    PubMed Central

    Wang, Sheng; Ghosh, Richik N.; Chellappan, Srikumar P.

    1998-01-01

    Cells initiate proliferation in response to growth factor stimulation, but the biochemical mechanisms linking signals received at the cell surface receptors to the cell cycle regulatory molecules are not yet clear. In this study, we show that the signaling molecule Raf-1 can physically interact with Rb and p130 proteins in vitro and in vivo and that this interaction can be detected in mammalian cells without overexpressing any component. The binding of Raf-1 to Rb occurs subsequent to mitogen stimulation, and this interaction can be detected only in proliferating cells. Raf-1 can inactivate Rb function and can reverse Rb-mediated repression of E2F1 transcription and cell proliferation efficiently. The region of Raf-1 involved in Rb binding spanned residues 1 to 28 at the N terminus, and functional inactivation of Rb required a direct interaction. Serum stimulation of quiescent human fibroblast HSF8 cells led to a partial translocation of Raf-1 into the nucleus, where it colocalized with Rb. Further, Raf-1 was able to phosphorylate Rb in vitro quite efficiently. We believe that the physical interaction of Raf-1 with Rb is a vital step in the growth factor-mediated induction of cell proliferation and that Raf-1 acts as a direct link between cell surface signaling cascades and the cell cycle machinery. PMID:9819434

  17. 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.

  18. Corticolimbic structural alterations linked to health status and trait anxiety in functional neurological disorder.

    PubMed

    Perez, David L; Williams, Benjamin; Matin, Nassim; LaFrance, W Curt; Costumero-Ramos, Victor; Fricchione, Gregory L; Sepulcre, Jorge; Keshavan, Matcheri S; Dickerson, Bradford C

    2017-08-26

    Affective symptoms influence health status (health-related quality of life) in functional neurological disorder (FND), and the salience network is implicated in the pathophysiology of FND and mood/anxiety disorders. We hypothesised that self-reported health status and affective symptoms would map onto salience network regions and that patients with FND would show decreased insular volumes compared with controls. This voxel-based morphometry study investigated volumetric differences in 26 patients with FND (21 women, 5 men; mean age=40.3±11.5) compared with 27 healthy controls (22 women, 5 men; mean age=40.5±10.8). Post hoc analyses stratified patients with FND by mental and physical health scores (Short Form Health Survey-36). Within-group analyses investigated associations with mental health, physical health, trait anxiety and depression in patients with FND. There were no volumetric differences between the complete FND cohort and controls. In stratified analyses, however, patients with FND reporting the most severe physical health impairments showed reduced left anterior insular volume compared with controls. In within-group analyses, impaired mental health and elevated trait anxiety were associated with increased right amygdalar volumes in patients with FND. The relationship between amygdalar volume and mental health, driven by emotional well-being deficits and role limitations due to emotional problems, was independent of sensorimotor functional neurological symptom severity and motor FND subtype. In secondary within-group analyses, increased periaqueductal grey volume was associated with role limitations due to emotional problems. Impaired physical functioning correlated with decreased left anterior insular volumes. These findings support roles for several regions of the salience network in the pathophysiology of FND. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is

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

    PubMed

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

    2014-04-03

    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. Both the two null mutants (I30A and L43A) were less stable to temperature-induced unfolding in vitro than wild type (WT) 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 WT. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. 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

  1. 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.

  2. [The effect of normobaric hypoxia on the functioning of links in the endocrine system].

    PubMed

    Shakhtarin, V V; Kiriachkov, Iu Iu; Palyga, G F; Khmelevskiĭ, Ia M; Sloventantor, V Iu; Simakova, G M; Kruglikov, A P

    1990-01-01

    The paper is concerned with the data on change in the blood level of ACTH, STH, TSH, cortisol, T3, insulin, C-peptide during a 25-minute session of respiration using a gaseous hypoxic mixture with 10% oxygen (GHM-10). The investigation was performed in 23 healthy volunteers. Change in the hormonal status, characteristic of a moderate stress-reaction, was observed in 60% of the examinees. It was found out that during a GHM-10 session a degree of change in function of the studied factors of the endocrine system showed correlation with change in the activity of the autonomic nervous system.

  3. Linking plant functional traits and forest carbon stocks in the Congo Basin

    NASA Astrophysics Data System (ADS)

    Kearsley, Elizabeth; Verbeeck, Hans; Hufkens, Koen; Lewis, Simon; Huygens, Dries; Beeckman, Hans; Steppe, Kathy; Boeckx, Pascal

    2013-04-01

    Accurate estimates of the amount of carbon stored in tropical forests represent crucial baseline data for recent climate change mitigation policies. Such data are needed to quantify possible emissions due to deforestation and forest degradation, and to evaluate the potential of these forests to act as carbon sinks. Currently, only rough estimates of the carbon stocks for Central African tropical forests are available due to a lack of field data, and little is known about the response of these stocks to climate change. We present the first ground-based carbon stock data for the central Congo Basin in Yangambi, D. R. Congo, based on data of 20 inventory plots of 1 ha covering different forest types. We found an average aboveground carbon stock of 163 ± 19 Mg C ha-1 for intact old-growth forest, which is significantly lower than the stocks recorded in the outer regions of the Congo Basin. Commonly studied drivers for variations of carbon stocks include climatic and edaphic factors, but detailed trait-based studies are lacking. We identified a significant difference in height-diameter relations across the Congo Basin as a driver for spatial differences in carbon stocks. The study of a more detailed interaction of the environment and the available tree species pool as drivers for differences in carbon storage could have large implications. The effect of the species pool on carbon storage can be large since species differ in their ability to sequester carbon, and the collective functional characteristics of plant communities could be a major driver of carbon accumulation. The use of a trait-based approach shows high potential for identifying and quantifying carbon stocks as an ecosystem service. We test for associations between functional trait values and carbon storage across multiple regrowth and old-growth forests types in the Yangambi study area, with soil properties and climate similar for all plots. A selection of traits associated with carbon dynamics is made

  4. A methodological framework for linking bioreactor function to microbial communities and environmental conditions.

    PubMed

    de los Reyes, Francis L; Weaver, Joseph E; Wang, Ling

    2015-06-01

    In the continuing quest to relate microbial communities in bioreactors to function and environmental and operational conditions, engineers and biotechnologists have adopted the latest molecular and 'omic methods. Despite the large amounts of data generated, gaining mechanistic insights and using the data for predictive and practical purposes is still a huge challenge. We present a methodological framework that can guide experimental design, and discuss specific issues that can affect how researchers generate and use data to elucidate the relationships. We also identify, in general terms, bioreactor research opportunities that appear promising. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Patient perceptions of caregiver criticism in psychosis: links with patient and caregiver functioning.

    PubMed

    Onwumere, Juliana; Kuipers, Elizabeth; Bebbington, Paul; Dunn, Graham; Freeman, Daniel; Fowler, David; Garety, Philippa

    2009-02-01

    Expressed emotion (EE) has been described as a measure of caregivers' appraisals of the quality of their relationship with patients. However, far less is known about how the perception of their caregivers by patients with psychosis is shaped by caregivers' EE, and nothing about the clinical correlates of perceived EE. The current study examines the association of patient ratings of carer criticism with patient and carer characteristics. Patient ratings of carer criticism were also compared with the ratings of the carer derived from the Camberwell Family Interview. Sixty-seven patient-carer dyads participated in the cross-sectional study. Perceived carer criticism was associated with general psychopathology in patients, but not with overall levels of positive or negative symptoms of psychosis. Patients with lower levels of social functioning, higher levels of negative affect, and negative schematic beliefs about other people, tended to perceive greater criticism. Perceptions of carer criticism were associated with Camberwell Family Interview ratings of carer criticism, hostility, and high EE independently of affect, and poorer functioning. High EE was a significant predictor of perceived carer criticism. This study supports the validity of using feedback from patients to assess the emotional climate of the family environment.

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

    PubMed

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

    2013-09-15

    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.

  7. 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

  8. 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.

  9. The Structural and Functional Implications of Linked SNARE Motifs in SNAP25

    PubMed Central

    Wang, Li; Bittner, Mary A.; Axelrod, Daniel

    2008-01-01

    We investigated the functional and structural implications of SNAP25 having two SNARE motifs (SN1 and SN2). A membrane-bound, intramolecular FRET probe was constructed to report on the folding of N-terminal SN1 and C-terminal SN2 in living cells. Membrane-bound constructs containing either or both SNARE motifs were also singly labeled with donor or acceptor fluorophores. Interaction of probes with other SNAREs was monitored by the formation of SDS-resistant complexes and by changes in FRET measured in vitro using spectroscopy and in the plasma membrane of living cells using TIRF microscopy. The probes formed the predicted SDS-resistant SNARE complexes. FRET measurements revealed that syntaxin induced a close association of the N-termini of SN1 and SN2. This association required that the SNARE motifs reside in the same molecule. Unexpectedly, the syntaxin-induced FRET was prevented by VAMP. Both full-length SNAP25 constructs and the combination of its separated, membrane-bound constituent chains supported secretion in permeabilized chromaffin cells that had been allowed to rundown. However, only full-length SNAP25 constructs enabled robust secretion from intact cells or permeabilized cells before rundown. The experiments suggest that the bidentate structure permits specific conformations in complexes with syntaxin and VAMP and facilitates the function of SN1 and SN2 in exocytosis. PMID:18596234

  10. 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.

  11. Intraoperative Pleth Variability Index Is Linked to Delayed Graft Function After Kidney Transplantation.

    PubMed

    Collange, O; Jazaerli, L; Lejay, A; Biermann, C; Caillard, S; Moulin, B; Chakfe, N; Severac, F; Schaeffer, M; Mertes, P-M; Steib, A

    2016-10-01

    Delayed graft function (DGF) is an early postoperative complication of kidney transplantation (KT) predisposing to acute rejection and lower graft survival. Intraoperative arterial hypotension and hypovolemia are associated with DGF. Central venous pressure (CVP) is used to estimate volemia but its reliability has been criticized. Pleth variability index (PVI) is a hemodynamic parameter predicting fluid responsiveness. The aim of this study was to examine the relationship between intraoperative PVI and CVP values and the occurrence of DGF. This was a prospective, noninterventional, observational, single-center study. All consecutive patients with KT from deceased donors were included. Recipients received standard, CVP, and PVI monitoring. Intraoperative hemodynamic parameters were recorded from recipients at 5 time points during KT. Forty patients were enrolled. There was a poor correlation between PVI and CVP values (r(2) = 0.003; P = .44). Immediate graft function and DGF patients had similar hemodynamic values during KT, with the exception of PVI values, which were significantly higher in the DGF group. In particular, a PVI >9% before unclamping of the renal artery was the only predictive parameter of DGF in our multivariate analysis (P = .02). This study suggests that PVI values >9% during KT are associated with the occurrence of DGF. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. 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

  13. The Diabetes-Linked Transcription Factor PAX4: From Gene to Functional Consequences

    PubMed Central

    Lorenzo, Petra I.; Juárez-Vicente, Francisco; Cobo-Vuilleumier, Nadia; García-Domínguez, Mario; Gauthier, Benoit R.

    2017-01-01

    Paired box 4 (PAX4) is a key factor in the generation of insulin producing β-cells during embryonic development. In adult islets, PAX4 expression is sequestered to a subset of β-cells that are prone to proliferation and more resistant to stress-induced apoptosis. The importance of this transcription factor for adequate pancreatic islets functionality has been manifested by the association of mutations in PAX4 with the development of diabetes, independently of its etiology. Overexpression of this factor in adult islets stimulates β-cell proliferation and increases their resistance to apoptosis. Additionally, in an experimental model of autoimmune diabetes, a novel immunomodulatory function for this factor has been suggested. Altogether these data pinpoint at PAX4 as an important target for novel regenerative therapies for diabetes treatment, aiming at the preservation of the remaining β-cells in parallel to the stimulation of their proliferation to replenish the β-cell mass lost during the progression of the disease. However, the adequate development of such therapies requires the knowledge of the molecular mechanisms controlling the expression of PAX4 as well as the downstream effectors that could account for PAX4 action. PMID:28282933

  14. Genetic studies in mice directly link oocytes produced during adulthood to ovarian function and natural fertility.

    PubMed

    Wang, Ning; Satirapod, Chonthicha; Ohguchi, Yasuyo; Park, Eun-Sil; Woods, Dori C; Tilly, Jonathan L

    2017-08-30

    Multiple labs have reported that mammalian ovaries contain oogonial stem cells (OSCs), which can differentiate into oocytes that fertilize to produce offspring. However, the physiological relevance of these observations to adult ovarian function is unknown. Here we performed targeted and reversible ablation of premeiotic germ cells undergoing differentiation into oocytes in transgenic mice expressing the suicide gene, herpes simplex virus thymidine kinase (HSVtk), driven by the promoter of stimulated by retinoic acid gene 8 (Stra8), a germ cell-specific gene activated during meiotic commitment. Over a 21-day ablation phase induced by the HSVtk pro-drug, ganciclovir (GCV), oocyte numbers declined due to a disruption of new oocyte input. However, germ cell differentiation resumed after ceasing the ablation protocol, enabling complete regeneration of the oocyte pool. We next employed inducible lineage tracing to fate map, through Cre recombinase-mediated fluorescent reporter gene activation only in Stra8-expressing cells, newly-formed oocytes. Induction of the system during adulthood yielded a mosaic pool of unmarked (pre-existing) and marked (newly-formed) oocytes. Marked oocytes matured and fertilized to produce offspring, which grew normally to adulthood and transmitted the reporter to second-generation offspring. These findings establish that oocytes generated during adulthood contribute directly to ovarian function and natural fertility in mammals.

  15. A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock.

    PubMed

    Perales, Mariano; Más, Paloma

    2007-07-01

    Circadian clocks rhythmically coordinate biological processes in resonance with the environmental cycle. The clock function relies on negative feedback loops that generate 24-h rhythms in multiple outputs. In Arabidopsis thaliana, the clock component TIMING OF CAB EXPRESSION1 (TOC1) integrates the environmental information to coordinate circadian responses. Here, we use chromatin immunoprecipitation as well as physiological and luminescence assays to demonstrate that proper photoperiodic phase of TOC1 expression is important for clock synchronization of plant development with the environment. Our studies show that TOC1 circadian induction is accompanied by clock-controlled cycles of histone acetylation that favor transcriptionally permissive chromatin structures at the TOC1 locus. At dawn, TOC1 repression relies on the in vivo circadian binding of the clock component CIRCADIAN CLOCK ASSOCIATED1 (CCA1), while histone deacetylase activities facilitate the switch to repressive chromatin structures and contribute to the declining phase of TOC1 waveform around dusk. The use of cca1 late elongated hypocotyl double mutant and CCA1-overexpressing plants suggests a highly repressing function of CCA1, antagonizing H3 acetylation to regulate TOC1 mRNA abundance. The chromatin remodeling activities relevant at the TOC1 locus are distinctively modulated by photoperiod, suggesting a mechanism by which the clock sets the phase of physiological and developmental outputs.

  16. From Early Childhood to Adolescence: Linking Family Functioning and School Behavior

    PubMed Central

    Johnson, Vanessa K.

    2010-01-01

    The present study uses observational assessment of 66 two-parent families working and playing together when their eldest child is in kindergarten and again in 9th grade to identify distinct patterns of family functioning derived from structural family systems theory. Whereas concurrent assessment of the relationship between family type and adolescents' school behavior were not significant, significant prospective longitudinal relationships between family type assessed in early childhood and 9th grade school behavior were indicated. Kindergarteners whose families were primarily characterized by a strong mother-child alliance were less academically competent, more aggressive/inattentive, and more anxious/depressed/withdrawn at school nine years later when they were in 9th grade, than their peers in more cohesive or father-child allied families. PMID:21258653

  17. 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.

  18. [Potential protective role of nitric oxide and Hsp70 linked to functional foods in the atherosclerosis].

    PubMed

    Camargo, Alejandra B; Manucha, Walter

    Atherosclerosis, one of the main pathologic entities considered epidemic and a worldwide public health problem, is currently under constant review as regards its basic determining mechanisms and therapeutic possibilities. In this regard, all patients afflicted with the disease exhibit mitochondrial dysfunction, oxidative stress and inflammation. Interestingly, nitric oxide - a known vasoactive messenger gas - has been closely related to the inflammatory, oxidative and mitochondrial dysfunctional process that characterizes atherosclerosis. In addition, it has recently been demonstrated that alterations in the bioavailability of nitric oxide would induce the expression of heat shock proteins. This agrees with the use of functional foods as a strategy to prevent both vascular aging and the development of atherosclerosis. Finally, a greater knowledge regarding the mechanisms implied in the development of atherosclerosis will enable proposing new and possible hygiene, health and therapeutic interventions. Copyright © 2016 Sociedad Española de Arteriosclerosis. Publicado por Elsevier España, S.L.U. All rights reserved.

  19. 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

  20. Identical expression profiling of human and murine TIPE3 protein reveals links to its functions.

    PubMed

    Cui, Jian; Hao, Chunyan; Zhang, Wenqian; Shao, Jie; Zhang, Na; Zhang, Guizhong; Liu, Suxia

    2015-03-01

    Tumor necrosis factor-alpha-induced protein-8 like-3 (TNFAIP8L3, TIPE3) is a newly discovered member of TNFAIP8 family and regarded as a lipid second messenger transfer protein that promotes cancer. Yet the nature of the cells and tissues that express TIPE3 protein has not been determined. In this study, we examined TIPE3 expression in various murine and human tissues by immunohistochemistry and quantitative PCR. We found that TIPE3 expression was almost identical in most organs from human and mice. TIPE3 is a cytoplasmic protein expressed preferentially in epithelial-derived cells with secretory functions. Furthermore, TIPE3 protein is highly expressed in most human carcinoma cell lines. These results suggest that TIPE3 may play important roles in carcinogenesis and cell secretion.

  1. Identical Expression Profiling of Human and Murine TIPE3 Protein Reveals Links to Its Functions

    PubMed Central

    Cui, Jian; Hao, Chunyan; Zhang, Wenqian; Shao, Jie; Zhang, Na; Zhang, Guizhong

    2015-01-01

    Tumor necrosis factor-alpha-induced protein-8 like-3 (TNFAIP8L3, TIPE3) is a newly discovered member of TNFAIP8 family and regarded as a lipid second messenger transfer protein that promotes cancer. Yet the nature of the cells and tissues that express TIPE3 protein has not been determined. In this study, we examined TIPE3 expression in various murine and human tissues by immunohistochemistry and quantitative PCR. We found that TIPE3 expression was almost identical in most organs from human and mice. TIPE3 is a cytoplasmic protein expressed preferentially in epithelial-derived cells with secretory functions. Furthermore, TIPE3 protein is highly expressed in most human carcinoma cell lines. These results suggest that TIPE3 may play important roles in carcinogenesis and cell secretion. PMID:25479791

  2. 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.

  3. Chromatographic isolation of the functionally active MutS protein covalently linked to deoxyribonucleic acid.

    PubMed

    Monakhova, Mayya; Ryazanova, Alexandra; Hentschel, Andreas; Viryasov, Mikhail; Oretskaya, Tatiana; Friedhoff, Peter; Kubareva, Elena

    2015-04-10

    DNA metabolism is based on formation of different DNA-protein complexes which can adopt various conformations. To characterize functioning of such complexes, one needs a solution-based technique which allows fixing a complex in a certain transient conformation. The crosslinking approach is a popular tool for such studies. However, it is under debate if the protein components retain their natural activities in the resulting crosslinked complexes. In the present work we demonstrate the possibility of obtaining pure DNA conjugate with functionally active protein using as example MutS protein from Escherichia coli mismatch repair system. A conjugate of a chemically modified mismatch-containing DNA duplex with MutS is fixed by thiol-disulfide exchange reaction. To perform a reliable test of the protein activity in the conjugate, such conjugate must be thoroughly separated from the uncrosslinked protein and DNA prior to the test. In the present work, we employ anion exchange chromatography for this purpose for the first time and demonstrate this technique to be optimal for the conjugate purification. The activity test is a FRET-based detection of DNA unbending. We show experimentally that MutS in the conjugate retains its ability to unbend DNA in response to ATP addition and find out for the first time that the DNA unbending rate increases with increasing ATP concentration. Since the crosslinked complexes contain active MutS protein, they can be used in further experiments to investigate MutS interactions with other proteins of the mismatch repair system.

  4. Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link

    PubMed Central

    Jang, Hyunbum; Arce, Fernando Teran; Mustata, Mirela; Ramachandran, Srinivasan; Capone, Ricardo; Nussinov, Ruth; Lal, Ratnesh

    2011-01-01

    Protegrin-1 (PG-1) is an 18 residues long, cysteine-rich β-sheet antimicrobial peptide (AMP). PG-1 induces strong cytotoxic activities on cell membrane and acts as a potent antibiotic agent. Earlier we reported that its cytotoxicity is mediated by its channel-forming ability. In this study, we have examined the amyloidogenic fibril formation properties of PG-1 in comparison with a well-defined amyloid, the amyloid-β (Aβ1–42) peptide. We have used atomic force microscopy (AFM) and thioflavin-T staining to investigate the kinetics of PG-1 fibrils growth and molecular dynamics simulations to elucidate the underlying mechanism. AFM images of PG-1 on a highly hydrophilic surface (mica) show fibrils with morphological similarities to Aβ1–42 fibrils. Real-time AFM imaging of fibril growth suggests that PG-1 fibril growth follows a relatively fast kinetics compared to the Aβ1–42 fibrils. The AFM results are in close agreement with results from thioflavin-T staining data. Furthermore, the results indicate that PG-1 forms fibrils in solution. Significantly, in contrast, we do not detect fibrillar structures of PG-1 on an anionic lipid bilayer 2-dioleoyl-sn-glycero-3-phospho-L-serine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine; only small PG-1 oligomers can be observed. Molecular dynamics simulations are able to identify the presence of these small oligomers on the membrane bilayer. Thus, our current results show that cytotoxic AMP PG-1 is amyloidogenic and capable of forming fibrils. Overall, comparing β-rich AMPs and amyloids such as Aβ, in addition to cytotoxicity and amyloidogenicity, they share a common structural motif, and are channel forming. These combined properties support a functional relationship between amyloidogenic peptides and β-sheet-rich cytolytic AMPs, suggesting that amyloids channels may have an antimicrobial function. PMID:21463591

  5. Broca's region: linking human brain functional connectivity data and non-human primate tracing anatomy studies.

    PubMed

    Kelly, Clare; Uddin, Lucina Q; Shehzad, Zarrar; Margulies, Daniel S; Castellanos, F Xavier; Milham, Michael P; Petrides, Michael

    2010-08-01

    Brodmann areas 6, 44 and 45 in the ventrolateral frontal cortex of the left hemisphere of the human brain constitute the anterior language production zone. The anatomical connectivity of these areas with parietal and temporal cortical regions was recently examined in an autoradiographic tract-tracing study in the macaque monkey. Studies suggest strong correspondence between human resting state functional connectivity (RSFC) based on functional magnetic resonance imaging data and experimentally demonstrated anatomical connections in non-human primates. Accordingly, we hypothesized that areas 6, 44 and 45 of the human brain would exhibit patterns of RSFC consistent with patterns of anatomical connectivity observed in the macaque. In a primary analysis, we examined the RSFC associated with regions-of-interest placed in ventrolateral frontal areas 6, 44 and 45, on the basis of local sulcal and gyral anatomy. We validated the results of the primary hypothesis-driven analysis with a data-driven partitioning of ventrolateral frontal cortex into regions exhibiting distinct RSFC patterns, using a spectral clustering algorithm. The RSFC of ventrolateral frontal areas 6, 44 and 45 was consistent with patterns of anatomical connectivity shown in the macaque. We observed a striking dissociation between RSFC for the ventral part of area 6 that is involved in orofacial motor control and RSFC associated with Broca's region (areas 44 and 45). These findings indicate rich and differential RSFC patterns for the ventrolateral frontal areas controlling language production, consistent with known anatomical connectivity in the macaque brain, and suggest conservation of connectivity during the evolution of the primate brain.

  6. The rat retrosplenial cortex as a link for frontal functions: A lesion analysis.

    PubMed

    Powell, Anna L; Nelson, Andrew J D; Hindley, Emma; Davies, Moira; Aggleton, John P; Vann, Seralynne D

    2017-09-29

    Cohorts of rats with excitotoxic retrosplenial cortex lesions were tested on four behavioural tasks sensitive to dysfunctions in prelimbic cortex, anterior cingulate cortex, or both. In this way the study tested whether retrosplenial cortex has nonspatial functions that reflect its anatomical interactions with these frontal cortical areas. In Experiment 1, retrosplenial cortex lesions had no apparent effect on a set-shifting digging task that taxed intradimensional and extradimensional attention, as well as reversal learning. Likewise, retrosplenial cortex lesions did not impair a strategy shift task in an automated chamber, which involved switching from visual-based to response-based discriminations and, again, included a reversal (Experiment 2). Indeed, there was evidence that the retrosplenial lesions aided the initial switch to response-based selection. No lesion deficit was found on an automated cost-benefit task that pitted size of reward against effort to achieve that reward (Experiment 3). Finally, while retrosplenial cortex lesions affected matching-to-place task in a T-maze, the profile of deficits differed from that associated with prelimbic cortex damage (Experiment 4). When the task was switched to a nonmatching design, retrosplenial cortex lesions had no apparent effect on performance. The results from the four experiments show that many frontal tasks do not require the retrosplenial cortex, highlighting the specificity of their functional interactions. The results show how retrosplenial cortex lesions spare those learning tasks in which there is no mismatch between the internal and external representations used to guide behavioural choice. In addition, these experiments further highlight the importance of the retrosplenial cortex in solving tasks with a spatial component. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

    PubMed Central

    Amend, Anthony S; Martiny, Adam C; Allison, Steven D; Berlemont, Renaud; Goulden, Michael L; Lu, Ying; Treseder, Kathleen K; Weihe, Claudia; Martiny, Jennifer B H

    2016-01-01

    The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertilization. The responses of leaf litter bacteria and fungi to these simulated changes were significantly phylogenetically conserved. Proportional changes in abundance were highly correlated among related organisms, such that relatives with approximately 5% ribosomal DNA genetic distance showed similar responses to the treatments. A microbe's change in relative abundance was significantly correlated between the treatments, suggesting a compromise between numerical abundance in undisturbed environments and resistance to change in general, independent of disturbance type. Lineages in which at least 90% of the microbes shared the same response were circumscribed at a modest phylogenetic depth (τD 0.014–0.021), but significantly larger than randomized simulations predict. In several clades, phylogenetic depth of trait consensus was higher. Fungal response to drought was more conserved than was response to nitrogen fertilization, whereas bacteria responded equally to both treatments. Finally, we show that a bacterium's response to the manipulations is correlated with its potential functional traits (measured here as the number of glycoside hydrolase genes encoding the capacity to degrade different types of carbohydrates). Together, these results suggest that a phylogenetic, trait-based framework may be useful for predicting shifts in microbial composition and functioning in the face of global change. PMID:26046258

  8. 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.

  9. Functional coupling analysis suggests link between the obesity gene FTO and the BDNF-NTRK2 signaling pathway

    PubMed Central

    2011-01-01

    Background The Fat mass and obesity gene (FTO) has been identified through genome wide association studies as an important genetic factor contributing to a higher body mass index (BMI). However, the molecular context in which this effect is mediated has yet to be determined. We investigated the potential molecular network for FTO by analyzing co-expression and protein-protein interaction databases, Coxpresdb and IntAct, as well as the functional coupling predicting multi-source database, FunCoup. Hypothalamic expression of FTO-linked genes defined with this bioinformatics approach was subsequently studied using quantitative real time-PCR in mouse feeding models known to affect FTO expression. Results We identified several candidate genes for functional coupling to FTO through database studies and selected nine for further study in animal models. We observed hypothalamic expression of Profilin 2 (Pfn2), cAMP-dependent protein kinase catalytic subunit beta (Prkacb), Brain derived neurotrophic factor (Bdnf), neurotrophic tyrosine kinase, receptor, type 2 (Ntrk2), Signal transducer and activator of transcription 3 (Stat3), and Btbd12 to be co-regulated in concert with Fto. Pfn2 and Prkacb have previously not been linked to feeding regulation. Conclusions Gene expression studies validate several candidates generated through database studies of possible FTO-interactors. We speculate about a wider functional role for FTO in the context of current and recent findings, such as in extracellular ligand-induced neuronal plasticity via NTRK2/BDNF, possibly via interaction with the transcription factor CCAAT/enhancer binding protein β (C/EBPβ). PMID:22087873

  10. A functional link between heme oxygenase-1 and tristetraprolin in the anti-inflammatory effects of nicotine

    PubMed Central

    Uddin, Md. Jamal; Joe, Yeonsoo; Zheng, Min; Blackshear, Perry J.; Ryter, Stefan W.; Park, Jeong Woo; Chung, Hun Taeg

    2016-01-01

    Nicotine stimulates the cholinergic anti-inflammatory pathway and prevents excessive inflammation by inhibiting the release of inflammatory cytokines from macrophages. We have previously reported that heme oxygenase-1 (HO-1) and tristetraprolin (TTP) are induced by nicotine and mediate the anti-inflammatory function of nicotine in macrophages. However, it was not clear whether two molecules are functionally linked. In this study, we sought to determine whether HO-1 associates with TTP to mediate the anti-inflammatory effects of nicotine. Inhibition of HO-1 activity or HO-1 expression attenuated the effects of nicotine on STAT3 activation, TTP induction, and TNF-α production in LPS-treated macrophages. Induction of HO-1 expression increased the level of TTP in the absence of nicotine. In a LPS-induced endotoxemia model, HO-1 deficiency blocked the effects of nicotine on the STAT3 phosphorylation, TTP induction and LPS-induced TNF-α production in the liver. Downregulation of STAT3 by siRNA attenuated the effect of nicotine on TTP expression and TNF-α production but did not affect the nicotine-mediated induction of HO-1. In TTP knockout mice, nicotine treatment enhanced HO-1 expression and STAT3 activation but failed to inhibit LPS-induced TNF-α production. Our results suggest that HO-1 and TTP are functionally linked in mediating anti-inflammatory effects of nicotine; HO-1 is necessary for the induction of TTP by nicotine. This novel nicotine-HO-1-TTP signaling pathway provides new possibilities for the treatment of inflammatory diseases. PMID:24095726

  11. Cholera Toxin B Subunit Linked to Glutamic Acid Decarboxylase Suppresses Dendritic Cell Maturation and Function

    PubMed Central

    Odumosu, Oludare; Nicholas, Dequina; Payne, Kimberly; Langridge, William

    2012-01-01

    Dendritic cells are the largest population of antigen presenting cells in the body. One of their main functions is to regulate the delicate balance between immunity and tolerance responsible for maintenance of immunological homeostasis. Disruption of this delicate balance often results in chronic inflammation responsible for initiation of organ specific autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and type I diabetes. The cholera toxin B subunit (CTB) is a weak mucosal adjuvant known for its ability to stimulate immunity to antigenic proteins. However, conjugation of CTB to many autoantigens can induce immunological tolerance resulting in suppression of autoimmunity. In this study, we examined whether linkage of CTB to a 5 kDa C-terminal protein fragment of the major diabetes autoantigen glutamic acid decarboxylase (GAD35), can block dendritic cell (DC) functions such as biosynthesis of co-stimulatory factor proteins CD86, CD83, CD80 and CD40 and secretion of inflammatory cytokines. The results of human umbilical cord blood monocyte-derived DC - GAD35 autoantigen incubation experiments showed that inoculation of immature DCs (iDCs), with CTB-GAD35 protein dramatically suppressed levels of CD86, CD83, CD80 and CD40 co-stimulatory factor protein biosynthesis in comparison with GAD35 alone inoculated iDCs. Surprisingly, incubation of iDCs in the presence of the CTB-autoantigen and the strong immunostimulatory molecules PMA and Ionomycin revealed that CTB-GAD35 was capable of arresting PMA + Ionomycin induced DC maturation. Consistant with this finding, CTB-GAD35 mediated suppression of DC maturation was accompanied by a dramatic decrease in the secretion of the pro-inflammatory cytokines IL-12/23p40 and IL-6 and a significant increase in secretion of the immunosuppressive cytokine IL-10. Taken together, our experimental data suggest that linkage of the weak adjuvant CTB to the dominant type 1 diabetes autoantigen GAD strongly inhibits DC

  12. Linking functional response and bioenergetics to estimate juvenile salmon growth in a reservoir food web.

    PubMed

    Haskell, Craig A; Beauchamp, David A; Bollens, Stephen M

    2017-01-01

    Juvenile salmon (Oncorhynchus spp.) use of reservoir food webs is understudied. We examined the feeding behavior of subyearling Chinook salmon (O. tshawytscha) and its relation to growth by estimating the functional response of juvenile salmon to changes in the density of Daphnia, an important component of reservoir food webs. We then estimated salmon growth across a broad range of water temperatures and daily rations of two primary prey, Daphnia and juvenile American shad (Alosa sapidissima) using a bioenergetics model. Laboratory feeding experiments yielded a Type-II functional response curve: C = 29.858 P *(4.271 + P)-1 indicating that salmon consumption (C) of Daphnia was not affected until Daphnia densities (P) were < 30 · L-1. Past field studies documented Daphnia densities in lower Columbia River reservoirs of < 3 · L-1 in July but as high as 40 · L-1 in August. Bioenergetics modeling indicated that subyearlings could not achieve positive growth above 22°C regardless of prey type or consumption rate. When feeding on Daphnia, subyearlings could not achieve positive growth above 20°C (water temperatures they commonly encounter in the lower Columbia River during summer). At 16-18°C, subyearlings had to consume about 27,000 Daphnia · day-1 to achieve positive growth. However, when feeding on juvenile American shad, subyearlings had to consume 20 shad · day-1 at 16-18°C, or at least 25 shad · day-1 at 20°C to achieve positive growth. Using empirical consumption rates and water temperatures from summer 2013, subyearlings exhibited negative growth during July (-0.23 to -0.29 g · d-1) and August (-0.05 to -0.07 g · d-1). By switching prey from Daphnia to juvenile shad which have a higher energy density, subyearlings can partially compensate for the effects of higher water temperatures they experience in the lower Columbia River during summer. However, achieving positive growth as piscivores requires subyearlings to feed at higher consumption rates than

  13. 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

  14. Daily Parental Knowledge of Youth Activities Is Linked to Youth Physical Symptoms and HPA functioning

    PubMed Central

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

    2015-01-01

    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 eight consecutive evenings. On four study days, cortisol samples were collected at 4 time points (waking, 30 min after waking, before dinner, bedtime). Multi-level 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 eight-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

  15. 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

    2013-12-02

    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.

  16. 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.

  17. Genetic analysis demonstrates a direct link between rho signaling and nonmuscle myosin function during Drosophila morphogenesis.

    PubMed Central

    Halsell, S R; Chu, B I; Kiehart, D P

    2000-01-01

    A dynamic actomyosin cytoskeleton drives many morphogenetic events. Conventional nonmuscle myosin-II (myosin) is a key chemomechanical motor that drives contraction of the actin cytoskeleton. We have explored the regulation of myosin activity by performing genetic screens to identify gene products that collaborate with myosin during Drosophila morphogenesis. Specifically, we screened for second-site noncomplementors of a mutation in the zipper gene that encodes the nonmuscle myosin-II heavy chain. We determined that a single missense mutation in the zipper(Ebr) allele gives rise to its sensitivity to second-site noncomplementation. We then identify the Rho signal transduction pathway as necessary for proper myosin function. First we show that a lethal P-element insertion interacts genetically with zipper. Subsequently we show that this second-site noncomplementing mutation disrupts the RhoGEF2 locus. Next, we show that two EMS-induced mutations, previously shown to interact genetically with zipper(Ebr), disrupt the RhoA locus. Further, we have identified their molecular lesions and determined that disruption of the carboxyl-terminal CaaX box gives rise to their mutant phenotype. Finally, we show that RhoA mutations themselves can be utilized in genetic screens. Biochemical and cell culture analyses suggest that Rho signal transduction regulates the activity of myosin. Our studies provide direct genetic proof of the biological relevance of regulation of myosin by Rho signal transduction in an intact metazoan. PMID:10880486

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

    PubMed

    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.

  19. 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.

  20. Linking imaging spectroscopy and trait data to better understand spatial and temporal variability in functional traits

    NASA Astrophysics Data System (ADS)

    Townsend, Philip; Kruger, Eric; Wang, Zhihui; Singh, Aditya

    2017-04-01

    Imaging spectroscopy exhibits great potential for mapping foliar functional traits that are impractical or expensive to regularly measure on the ground, and are essentially impossible to characterize comprehensively across space. Specifically, the high information content in spectroscopic data enables us to identify narrow spectral feature that are associated with vegetation primary and secondary biochemistry (nutrients, pigments, defensive compounds), leaf structure (e.g., leaf mass per area), canopy structure, and physiological capacity. Ultimately, knowledge of the variability in such traits is critical to understanding vegetation productivity, as well as responses to climatic variability, disturbances, pests and pathogens. The great challenge to the use of imaging spectroscopy to supplement trait databases is the development of trait retrieval approaches that are broadly applicable within and between ecosystem types. Here, we outline how we are using the US National Ecological Observatory Network (NEON) to prototype the scaling and comparison of trait distributions derived from field measurements and imagery. We find that algorithms to map traits from imagery are robust across ecosystem types, when controlling for physiognomy and vegetation percent cover, and that among all vegetation types, the chemometric algorithms utilize similar features for mapping of traits.

  1. Heme Biosynthetic Pathway is Functionally Linked to Adipogenesis via Mitochondrial Respiratory Activity.

    PubMed

    Moreno-Navarrete, José María; Rodríguez, Amaia; Ortega, Francisco; Becerril, Sara; Girones, Jordi; Sabater-Masdeu, Mònica; Latorre, Jéssica; Ricart, Wifredo; Frühbeck, Gema; Fernández-Real, José Manuel

    2017-10-01

    To investigate key enzymes of heme biosynthesis in human adipocytes and adipose tissue (AT). Heme biosynthesis-related gene expression (ALAS1, ALAD, HMBS) was investigated in whole AT from humans (n = 178 and n = 75) and rats according to obesity status and during adipogenesis of human preadipocytes. The effects of aminotriazole (an ALAD inhibitor) and of ALAD knockdown were also studied. Consistent heme biosynthesis-related gene expression was detected in both subcutaneous AT (SAT) and visceral AT (VAT) and was significantly increased in SAT. ALAS1, ALAD, and HMBS mRNAs were positively associated with adipogenic gene expression in human AT and significantly decreased in subjects with obesity. These results were replicated in an independent cohort. Both SAT and VAT heme levels were positively correlated with ALAS1, ALAD, and HMBS mRNAs. ALAD and HMBS were mainly expressed in adipocytes and increased during differentiation of human adipocytes in parallel to adipogenic genes. In rats, high-fat diet-induced weight gain resulted in decreased Alad and Hmbs mRNAs in a similar way to what was observed with Adipoq. Aminotriazole administration or ALAD knockdown attenuated adipogenesis in parallel with decreased glucose uptake and impaired mitochondrial respiratory function during human adipocyte differentiation. Current data suggest a possible role of heme biosynthesis in human adipogenesis. © 2017 The Obesity Society.

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

    PubMed

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

    2014-04-01

    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 efforts, 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 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.

  3. Links between tree species, symbiotic fungal diversity and ecosystem functioning in simplified tropical ecosystems.

    PubMed

    Lovelock, Catherine E; Ewel, John J

    2005-07-01

    We studied the relationships among plant and arbuscular mycorrhizal (AM) fungal diversity, and their effects on ecosystem function, in a series of replicate tropical forestry plots in the La Selva Biological Station, Costa Rica. Forestry plots were 12 yr old and were either monocultures of three tree species, or polycultures of the tree species with two additional understory species. Relationships among the AM fungal spore community, host species, plant community diversity and ecosystem phosphorus-use efficiency (PUE) and net primary productivity (NPP) were assessed. Analysis of the relative abundance of AM fungal spores found that host tree species had a significant effect on the AM fungal community, as did host plant community diversity (monocultures vs polycultures). The Shannon diversity index of the AM fungal spore community differed significantly among the three host tree species, but was not significantly different between monoculture and polyculture plots. Over all the plots, significant positive relationships were found between AM fungal diversity and ecosystem NPP, and between AM fungal community evenness and PUE. Relative abundance of two of the dominant AM fungal species also showed significant correlations with NPP and PUE. We conclude that the AM fungal community composition in tropical forests is sensitive to host species, and provide evidence supporting the hypothesis that the diversity of AM fungi in tropical forests and ecosystem NPP covaries.

  4. Kinetics study of invertase covalently linked to a new functional nanogel.

    PubMed

    Raj, Lok; Chauhan, Ghanshyam S; Azmi, Wamik; Ahn, J-H; Manuel, James

    2011-02-01

    Nanogels are promising materials as supports for enzyme immobilization. A new hydrogel comprising of methacrylic acid (MAAc) and N-vinyl pyrrolidone (N-VP) and ethyleneglycol dimethacrylate (EGDMA) was synthesized and converted to nanogel by an emulsification method. Nanogel was further functionalized by Curtius azide reaction for use as support for the covalent immobilization of invertase (Saccharomyces cerevisiae). As-prepared or invertase-immobilized nanogel was characterized by FTIR, XRD, TEM and nitrogen analysis. The characterization of both free and the immobilized-invertase were performed using a spectrophotometric method at 540 nm. The values of V(max), maximum reaction rate, (0.123 unit/mg), k(m), Michaelis constant (7.429 mol/L) and E(a), energy of activation (3.511 kj/mol) for the immobilized-invertase are comparable with those of the free invertase at optimum conditions (time 70 min, pH 6.0 and temperature 45°C). The covalent immobilization enhanced the pH and thermal stability of invertase. The immobilized biocatalyst was efficiently reused up to eight cycles.

  5. Accelerating Nanoscale Research with Neutron Total Scattering: Linking Structure and Function in Finite Materials

    NASA Astrophysics Data System (ADS)

    Page, Katharine

    2012-10-01

    h -abstract-pard In contrast to bulk materials, nanomaterials and nanoparticles, comprised of a few hundred to tens of thousands of atoms, require every atom's position to be located in order to understand their structure-property relationships. New behavior can arise with a constricted, expanded, or distorted lattice, variation in surface termination structure, ligand capping or stabilization, or with the increasingly diverse set of shapes and architectures appearing in nanoscience literature today: tubes, pyramids, stars, core-shell and matrix-confined particles, multilayer films, etc. Pair distribution function (PDF) analysis, based on spallation neutron or synchrotron x-ray total scattering data, has emerged as a very promising characterization method for nanomaterials in recent years. Total scattering methods provide information about every pair of atoms probed in a diffraction experiment and thus contain an unexploited wealth of information for finite systems. In this contribution we will present our work establishing the influence of particle size and shape on the nature and correlation of local atomic dipoles in finite ferroelectric systems. We also review current data-driven modeling capabilities and outline the need for evolution of robust computational tools to follow other complex nanoscale phenomena with scattering data. pard-/abstract-

  6. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

    PubMed

    Yahara, Koji; Méric, Guillaume; Taylor, Aidan J; de Vries, Stefan P W; Murray, Susan; Pascoe, Ben; Mageiros, Leonardos; Torralbo, Alicia; Vidal, Ana; Ridley, Anne; Komukai, Sho; Wimalarathna, Helen; Cody, Alison J; Colles, Frances M; McCarthy, Noel; Harris, David; Bray, James E; Jolley, Keith A; Maiden, Martin C J; Bentley, Stephen D; Parkhill, Julian; Bayliss, Christopher D; Grant, Andrew; Maskell, Duncan; Didelot, Xavier; Kelly, David J; Sheppard, Samuel K

    2017-01-01

    Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Linking phloem function to structure: analysis with a coupled xylem-phloem transport model.

    PubMed

    Hölttä, T; Mencuccini, M; Nikinmaa, E

    2009-07-21

    We carried out a theoretical analysis of phloem transport based on Münch hypothesis by developing a coupled xylem-phloem transport model. Results showed that the maximum sugar transport rate of the phloem was limited by solution viscosity and that transport requirements were strongly affected by prevailing xylem water potential. The minimum number of xylem and phloem conduits required to sustain transpiration and assimilation, respectively, were calculated. At its maximum sugar transport rate, the phloem functioned with a high turgor pressure difference between the sugar sources and sinks but the turgor pressure difference was reduced if additional parallel conduits were added or solute relays were introduced. Solute relays were shown to decrease the number of parallel sieve tubes needed for phloem transport, leading to a more uniform turgor pressure and allowing faster information transmission within the phloem. Because xylem water potential affected both xylem and phloem transport, the conductance of the two systems was found to be coupled such that large structural investments in the xylem reduced the need for investment in the phloem and vice versa.

  8. Architectural niche organization by LHX2 is linked to hair follicle stem cell function.

    PubMed

    Folgueras, Alicia R; Guo, Xingyi; Pasolli, H Amalia; Stokes, Nicole; Polak, Lisa; Zheng, Deyou; Fuchs, Elaine

    2013-09-05

    In adult skin, self-renewing, undifferentiated hair follicle stem cells (HF-SCs) reside within a specialized niche, where they spend prolonged times as a single layer of polarized, quiescent epithelial cells. When sufficient activating signals accumulate, HF-SCs become mobilized to fuel tissue regeneration and hair growth. Here, we show that architectural organization of the HF-SC niche by transcription factor LHX2 plays a critical role in HF-SC behavior. Using genome-wide chromatin and transcriptional profiling of HF-SCs in vivo, we show that LHX2 directly transactivates genes that orchestrate cytoskeletal dynamics and adhesion. Conditional ablation of LHX2 results in gross cellular disorganization and HF-SC polarization within the niche. LHX2 loss leads to a failure to maintain HF-SC quiescence and hair anchoring, as well as progressive transformation of the niche into a sebaceous gland. These findings suggest that niche organization underlies the requirement for LHX2 in hair follicle structure and function. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Fabrication of homogeneously cross-linked, functional alginate microcapsules validated by NMR-, CLSM- and AFM-imaging.

    PubMed

    Zimmermann, H; Hillgärtner, M; Manz, B; Feilen, P; Brunnenmeier, F; Leinfelder, U; Weber, M; Cramer, H; Schneider, S; Hendrich, C; Volke, F; Zimmermann, U

    2003-05-01

    Cross-linked alginate microcapsules of sufficient mechanical strength can immunoisolate cells for the long-term treatment of hormone and other deficiency diseases in human beings. However, gelation of alginate by external Ba(2+) (or other divalent cations) produces non-homogeneous cross-linking of the polymeric mannuronic (M) and guluronic (G) acid chains. The stability of such microcapsules is rather limited. Here, we show that homogeneous cross-linking can be achieved by injecting BaCl(2) crystals into alginate droplets before they come into contact with external BaCl(2). The high effectiveness of this crystal gun method is demonstrated by confocal laser scanning microscopy and by advanced nuclear magnetic resonance imaging. Both techniques gave clear-cut evidence that homogeneous cross-linkage throughout the microcapsule is only obtained with simultaneous internal and external gelation. Atomic force microscopy showed a very smooth surface topography for microcapsules made by the crystal gun method, provided that excess Ba(2+) ions were removed immediately after gelation. In vitro experiments showed greatly suppressed swelling for crystal gun microcapsules. Even alginate extracted from Lessonia nigrescens (highly biocompatible) yielded microcapsules with long-term mechanical stability not hitherto possible. Encapsulation of rat islets, human monoclonal antibodies secreting hybridoma cells and murine mesenchymal stem cells transfected with cDNA encoding for bone morphogenetic protein (BMP-4) revealed that injection of BaCl(2) crystals has no adverse side effects on cell viability and function. However, the release of low-molecular weight factors (such as insulin) may be delayed when using alginate concentrations in the usual range.

  10. Functional responses of human neonatal B lymphocytes to antigen receptor cross-linking and CpG DNA

    PubMed Central

    TASKER, L; MARSHALL-CLARKE, S

    2003-01-01

    Human neonates are immunologically immature and consequently are highly susceptible to infection. The cellular basis for the dysfunctional immune responses of neonates is not clear, but is likely to reflect the immaturity of both B and T cell populations. Here we have examined the ability of human cord blood B cells to respond to antigen receptor cross-linking and also to CpG containing oligodeoxynucleotides (ODN), and compared their responses with those of adult peripheral blood B cells. Antigen receptor cross-linking with soluble F(ab′)2 anti-IgM antibodies, induced HLA-DR and CD86 up-regulation and proliferation to a similar extent in adult and cord blood B cells. Both interleukin (IL)-2 and IL-4 co-stimulated anti-IgM-induced proliferation, but cord blood B cells were less sensitive than adult B cells to the co-stimulatory effects of IL-2. Antigen receptor cross-linking induced secretion of the chemokines macrophage inflammatory protein-1α (MIP-1α) and MIP-1β in adult and cord blood B cells, and secretion was enhanced by IL-2 or IL-4. CpG-ODN induced up-regulation of HLA-DR and CD86 expression and proliferation of adult and cord blood B cells, and anti-IgM and CPG-ODN synergized in the induction of proliferation. CpG-ODN also induced MIP-1α and MIP-1α secretion in adult and cord blood B cells. In addition to functional studies we examined the expression of CD62L (l-selectin), CCR7 and CXCR5. Our data show that surface expression of CD62L and CCR7 is lower on cord blood B cells than on adult B cells, suggesting that human cord blood B cells may exhibit homing defects. PMID:14632745

  11. Physical and functional links between anion exchanger-1 and sodium pump.

    PubMed

    Su, Ya; Al-Lamki, Rafia S; Blake-Palmer, Katherine G; Best, Alison; Golder, Zoe J; Zhou, Aiwu; Karet Frankl, Fiona E

    2015-02-01

    Anion exchanger-1 (AE1) mediates chloride-bicarbonate exchange across the plasma membranes of erythrocytes and, via a slightly shorter transcript, kidney epithelial cells. On an omnivorous human diet, kidney AE1 is mainly active basolaterally in α-intercalated cells of the collecting duct, where it is functionally coupled with apical proton pumps to maintain normal acid-base homeostasis. The C-terminal tail of AE1 has an important role in its polarized membrane residency. We have identified the β1 subunit of Na(+),K(+)-ATPase (sodium pump) as a binding partner for AE1 in the human kidney. Kidney AE1 and β1 colocalized in renal α-intercalated cells and coimmunoprecipitated (together with the catalytic α1 subunit of the sodium pump) from human kidney membrane fractions. ELISA and fluorescence titration assays confirmed that AE1 and β1 interact directly, with a Kd value of 0.81 μM. GST-AE1 pull-down assays using human kidney membrane proteins showed that the last 11 residues of AE1 are important for β1 binding. siRNA-induced knockdown of β1 in cell culture resulted in a significant reduction in kidney AE1 levels at the cell membrane, whereas overexpression of kidney AE1 increased cell surface sodium pump levels. Notably, membrane staining of β1 was reduced throughout collecting ducts of AE1-null mouse kidney, where increased fractional excretion of sodium has been reported. These data suggest a requirement of β1 for proper kidney AE1 membrane residency, and that activities of AE1 and the sodium pump are coregulated in kidney.

  12. Modeled hydrologic metrics show links between hydrology and the functional composition of stream assemblages.

    PubMed

    Patrick, Christopher J; Yuan, Lester L

    2017-07-01

    Flow alteration is widespread in streams, but current understanding of the effects of differences in flow characteristics on stream biological communities is incomplete. We tested hypotheses about the effect of variation in hydrology on stream communities by using generalized additive models to relate watershed information to the values of different flow metrics at gauged sites. Flow models accounted for 54-80% of the spatial variation in flow metric values among gauged sites. We then used these models to predict flow metrics in 842 ungauged stream sites in the mid-Atlantic United States that were sampled for fish, macroinvertebrates, and environmental covariates. Fish and macroinvertebrate assemblages were characterized in terms of a suite of metrics that quantified aspects of community composition, diversity, and functional traits that were expected to be associated with differences in flow characteristics. We related modeled flow metrics to biological metrics in a series of stressor-response models. Our analyses identified both drying and base flow instability as explaining 30-50% of the observed variability in fish and invertebrate community composition. Variations in community composition were related to variations in the prevalence of dispersal traits in invertebrates and trophic guilds in fish. The results demonstrate that we can use statistical models to predict hydrologic conditions at bioassessment sites, which, in turn, we can use to estimate relationships between flow conditions and biological characteristics. This analysis provides an approach to quantify the effects of spatial variation in flow metrics using readily available biomonitoring data. © 2017 by the Ecological Society of America.

  13. 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.

  14. Linking Gene Expression and Functional Network Data in Human Heart Failure

    PubMed Central

    Camargo, Anyela; Azuaje, Francisco

    2007-01-01

    Background Gene expression profiling and the analysis of protein-protein interaction (PPI) networks may support the identification of disease bio-markers and potential drug targets. Thus, a step forward in the development of systems approaches to medicine is the integrative analysis of these data sources in specific pathological conditions. We report such an integrative bioinformatics analysis in human heart failure (HF). A global PPI network in HF was assembled, which by itself represents a useful compendium of the current status of human HF-relevant interactions. This provided the basis for the analysis of interaction connectivity patterns in relation to a HF gene expression data set. Results Relationships between the significance of the differentiation of gene expression and connectivity degrees in the PPI network were established. In addition, relationships between gene co-expression and PPI network connectivity were analysed. Highly-connected proteins are not necessarily encoded by genes significantly differentially expressed. Genes that are not significantly differentially expressed may encode proteins that exhibit diverse network connectivity patterns. Furthermore, genes that were not defined as significantly differentially expressed may encode proteins with many interacting partners. Genes encoding network hubs may exhibit weak co-expression with the genes encoding their interacting protein partners. We also found that hubs and superhubs display a significant diversity of co-expression patterns in comparison to peripheral nodes. Gene Ontology (GO) analysis established that highly-connected proteins are likely to be engaged in higher level GO biological process terms, while low-connectivity proteins tend to be engaged in more specific disease-related processes. Conclusion This investigation supports the hypothesis that the integrative analysis of differential gene expression and PPI network analysis may facilitate a better understanding of functional roles

  15. Hyperosmolality-mediated peritoneal microvascular vasodilation is linked to aquaporin function.

    PubMed

    Zakaria, El Rasheid; Althani, Asma; Fawzi, Ashraf A; Fituri, Omar M

    2014-01-01

    Glucose-based peritoneal dialysis (PD) solutions dilate the parietal and visceral peritoneal microvasculature by endothelium-dependent mechanisms that primarily involve hyperosmolality. This PD-mediated dilation occurs by active intracellular glucose uptake and adenosine Al receptor activation, and by hyperosmolality-stimulated glibenclamide-sensitive potassium channels. Both pathways invoke NO as a second messenger for vasodilation. We hypothesized that during crystalloid-induced osmosis, the osmotic water flux through the transendothelial water-exclusive aquaporin 1 (AQP1) channels is the primary mechanism whereby the endothelium is being stimulated to instigate hyperosmolality-driven vasodilation. Four microvascular levels (diameters in the range 6 - 100 microm) were visualized by intravital videomicroscopy of the terminal ileum in anesthetized rats. Microvascular diameters and flow were measured after topical exposure to a 5% hypertonic mannitol or 2.5% glucose-based PD solution, at baseline and after brief tissue pre-treatment (with 0.1% glutaraldehyde for 10 seconds) or after combined tissue pre-treatment and pharmacologic blockade of AQP1 with HgCl2 (100 micromol/L). Vascular endothelial integrity was verified by the response to acetylcholine (10(-4) mol/L) and sodium nitroprusside (10(-4) mol/L). The hyperosmolar solutions both caused rapid and sustained vasodilation at all microvascular levels, which was not altered by tissue pre-treatment. Inhibition of AQP1 completely abolished the mannitol-induced vasodilation and markedly attenuated the PD fluid-mediated vasodilation. Neither glutaraldehyde pre-treatment nor HgCl2 affected tissue integrity or endothelial cell function. We conclude that the peritoneal microvascular vasodilation caused by hyperosmolar PD fluid is instigated by the osmotic water flux through AQP1. Clinical PD solutions have components other than hyperosmolality that can induce endothelium-dependent peritoneal microvascular vasodilation

  16. Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export

    PubMed Central

    Jani, Divyang; Lutz, Sheila; Hurt, Ed; Laskey, Ronald A.; Stewart, Murray; Wickramasinghe, Vihandha O.

    2012-01-01

    Export of messenger RNA (mRNA) from the nucleus to the cytoplasm is a critical step in the gene expression pathway of eukaryotic cells. Here, we report the functional and structural characterization of the mammalian TREX-2 complex and show how it links transcription/processing with nuclear mRNA export. Mammalian TREX-2 is based on a germinal-centre associated nuclear protein (GANP) scaffold to which ENY2, PCID2 and centrins bind and depletion of any of these components inhibits mRNA export. The crystal structure of the GANP:ENY2 complex shows that two ENY2 chains interact directly with GANP, but they have different orientations from those observed on yeast Sac3. GANP is required to recruit ENY2 to nuclear pore complexes (NPCs), but ENY2 is not necessary to recruit GANP, which requires both its CID and MCM3AP domains, together with nucleoporin Nup153. GANP and ENY2 associate with RNA polymerase II and inhibition of mRNA processing redistributes GANP from NPCs into nuclear foci indicating that mammalian TREX-2 is associated with transcription. Thus, we implicate TREX-2 as an integral component of the mammalian mRNA export machinery where it links transcription and nuclear export by facilitating the transfer of mature mRNPs from the nuclear interior to NPCs. PMID:22307388

  17. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

    PubMed Central

    Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

    2013-01-01

    The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

  18. Enchytraeids and microbes in Zn polluted soil: no link between organism-level stress responses and ecosystem functioning.

    PubMed

    Salminen, J; Anh, B T; Van Gestel, C A

    2001-12-01

    We studied the presence of zinc tolerance in enchytraeid worm (Cognettia sphagnetorum, Oligochaeta) from a metal-polluted forest soil in The Netherlands. In a dose response experiment, we compared Zn sensitivity, measured as body growth and reproduction, of these enchytraeids with that of animals taken from three unpolluted sites. Because C. sphagnetorum is a keystone species, regulating microbial processes in coniferous forest soil, we performed a microcosm experiment to study the interaction of enchytraeids from several sites with soil microbes. The idea was to study whether there is a link between metal stress response of individuals (tolerance level, life history alteration) and changes observed at higher organization levels of the biological system (trophic interaction and decomposition processes). We did not find evidence for increased metal tolerance of C. sphagnetorum. Worms from the polluted site actually had reduced body growth, indicating negative fitness effects caused by long-lasting metal stress. The density and biomass of the worm population from the polluted site was low in Zn contaminated soil. Presence of enchytraeids enhanced and Zn contamination reduced the activity of microbes in the soil. Enchytraeids from different sites with different life histories and population development, however, had the same effect on microbes. Hence, observed stress responses of individuals and populations could not be linked to density-dependent trophic interactions and ecosystem functioning in the soil-decomposer food chain.

  19. 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

  20. Linking ocean biogeochemical cycles and ecosystem structure and function: results of the complex SWAMCO-4 model

    NASA Astrophysics Data System (ADS)

    Pasquer, Bénédicte; Laruelle, Goulven; Becquevort, Sylvie; Schoemann, Véronique; Goosse, Hugues; Lancelot, Christiane

    2005-01-01

    We present results obtained with SWAMCO-4, a complex model of the marine planktonic system calculating C, N, P, Si, Fe cycling within the upper ocean, the export production and the exchange of CO 2 between the ocean and atmosphere. The model, constrained by physical, chemical and biological (grazing, lysis) controls, explicitly details the dynamics of four relevant phytoplankton functional groups with respect to C, N, P, Si, Fe cycling and climate change. Those are diatoms, pico/nano phytoplankton, coccolithophorids, and Phaeocystis spp. whose growth regulation by light, temperature and nutrients has been obtained based on a comprehensive analysis of literature reviews on these taxonomic groups. The performance of SWAMCO-4 is first evaluated in a 1D physical frame throughout its cross application in provinces with contrasted key species dominance, export production, CO 2 air-sea fluxes and where biogeochemical time-series data are available for model initialisation and comparison of results. These are: (i) the ice-free Southern Ocean Time Series station KERFIX (50°40S, 68°E) for the period 1993-1994 (diatom-dominated); (ii) the sea-ice associated Ross Sea domain (Station S; 76°S, 180°W) of the Antarctic Environment and Southern Ocean Process Study AESOPS in 1996-1997 ( Phaeocystis-dominated); and (iii) the North Atlantic Bloom Experiment NABE (60°N, 20°W) in 1991 (coccolithophorids). We then explore and compare the ocean response to increased atmospheric CO 2 by running SWAMCO-4 at the different locations over the last decade. Results show that at all tested latitudes the prescribed increase of atmospheric CO 2 enhances the carbon uptake by the ocean. However, the amplitude of the predicted atmospheric CO 2 sinks displays large regional and interannual variations due to the actual meteorological forcing that drives the local hydrodynamics. This is particularly true in the marginal ice zone of the Ross Sea (AESOPS) where the magnitude of the predicted annual

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

    PubMed

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

    2008-03-01

    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 age 15 and from adolescents and their romantic partners at age 18. Teens' relational aggression and romantic partners' victimization were predicted from levels of best friends' pressuring behaviors toward teens in an observed interaction as well as from best friends' ratings of how much pressure teens experienced from their peer group. Romantic partner relational aggression and teen victimization were predicted by pressure from teens' peer group only. Adolescents' romantic relational aggression and victimization were also associated with elevated levels of depressive symptoms and increased alcohol use. Results are discussed in terms of the connection of relational aggression in romantic relationships to the broader task of establishing autonomy with peers in psychosocial development.

  2. Caenorhabditis elegans POLQ-1 and HEL-308 function in two distinct DNA interstrand cross-link repair pathways.

    PubMed

    Muzzini, Diego M; Plevani, Paolo; Boulton, Simon J; Cassata, Giuseppe; Marini, Federica

    2008-06-01

    DNA interstrand cross-links (ICLs) are highly cytotoxic DNA lesions hindering DNA replication and transcription. Whereas in bacteria and yeast the molecular mechanisms involved in ICL repair are genetically well dissected, the scenario in multicellular organisms remains unclear. Here, we report that the two new mus308 genes, polq-1 and hel-308 are involved in ICL repair in Caenorhabditis elegans. After treatment with ICL agents, a decrease in survival and an increase in checkpoint-induced cell-cycle arrest and apoptosis of germ cells is observed in mutants of both genes. Although sensitive to ICL agents and to a minor extent to IR, cytological and epistatic analyses suggest that polq-1 and hel-308 are involved in different DNA repair pathways. While hel-308 functions in a Fanconi anemia-dependent pathway, polq-1 has a role in a novel distinct and brc-1 (CeBRCA1)-dependent ICL repair process in metazoans.

  3. Generation of Functional Neutrophils from a Mouse Model of X-Linked Chronic Granulomatous Disorder Using Induced Pluripotent Stem Cells

    PubMed Central

    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 gp91phox 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. PMID:21408614

  4. 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

  5. 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.

  6. Loss-of-function mutations in IGSF1 cause an X-linked syndrome of central hypothyroidism and testicular enlargement

    PubMed Central

    Sun, Yu; Bak, Beata; Schoenmakers, Nadia; van Trotsenburg, A.S. Paul; Oostdijk, Wilma; Voshol, Peter; Cambridge, Emma; White, Jacqueline K.; le Tissier, Paul; Gharavy, S. Neda Mousavy; Martinez-Barbera, Juan P.; Stokvis-Brantsma, Wilhelmina H.; Vulsma, Thomas; Kempers, Marlies J.; Persani, Luca; Campi, Irene; Bonomi, Marco; Beck-Peccoz, Paolo; Zhu, Hongdong; Davis, Timothy M.E.; Hokken-Koelega, Anita C.S.; Del Blanco, Daria Gorbenko; Rangasami, Jayanti J.; Ruivenkamp, Claudia A.L.; Laros, Jeroen F.J.; Kriek, Marjolein; Kant, Sarina G.; Bosch, Cathy A.J.; Biermasz, Nienke R.; Appelman-Dijkstra, Natasha M.; Corssmit, Eleonora P.; Hovens, Guido C.J.; Pereira, Alberto M.; den Dunnen, Johan T.; Wade, Michael G.; Breuning, Martijn H.; Hennekam, Raoul C.; Chatterjee, Krishna; Dattani, Mehul T.; Wit, Jan M.; Bernard, Daniel J.

    2012-01-01

    Congenital central hypothyroidism occurs either in isolation or in conjunction with other pituitary hormone deficits. Using exome and candidate gene sequencing, we identified eight distinct mutations and two deletions in IGSF1 in males from eleven unrelated families with central hypothyroidism, testicular enlargement, and variably low prolactin concentrations. IGSF1 is a membrane glycoprotein highly expressed in the anterior pituitary gland and the identified mutations impair its trafficking to the cell surface in heterologous cells. Igsf1-deficient male mice show diminished pituitary and serum thyroid-stimulating hormone (TSH) concentrations, reduced pituitary thyrotropin-releasing hormone (TRH) receptor expression, decreased triiodothyronine concentrations, and increased body mass. Collectively, our observations delineate a novel X-linked disorder in which loss-of-function mutations in IGSF1 cause central hypothyroidism, likely secondary to an associated impairment in pituitary TRH signaling. PMID:23143598

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

    PubMed Central

    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 age 15 and from adolescents and their romantic partners at age 18. Teens’ relational aggression and romantic partners’ victimization were predicted from levels of best friends’ pressuring behaviors toward teens in an observed interaction as well as from best friends’ ratings of how much pressure teens experienced from their peer group. Romantic partner relational aggression and teen victimization were predicted by pressure from teens’ peer group only. Adolescents’ romantic relational aggression and victimization were also associated with elevated levels of depressive symptoms and increased alcohol use. Results are discussed in terms of the connection of relational aggression in romantic relationships to the broader task of establishing autonomy with peers in psychosocial development. PMID:18523685

  8. 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.

  9. CD46: a complement regulator and pathogen receptor that mediates links between innate and acquired immune function.

    PubMed

    Russell, S

    2004-08-01

    In the last 10 years, the human cell-surface molecule, CD46, has evolved from 'just another complement regulator' to a receptor for a striking array of pathogens. CD46 not only protects cells from complement-mediated attack and facilitates infection by a large number of pathogens, but also exerts complex effects on cellular immune function. It has been proposed that CD46 links innate and adaptive immunity by affecting cellular immune function in response to complement binding, and the role of CD46 in the pathogenesis of many infectious pathogens is now the subject of intense investigation. So far, the flood of information that implicates CD46 in modifying a host response to measles, Neisseria, human herpes virus 6, and pathogens that activate complement has not yet been matched with a comprehensive understanding of the molecular mechanisms by which CD46 affects immune function. This review summarizes the evidence that points to a significant role for CD46 in a range of pathological processes and describes how CD46 might exert its effects by altering signal transduction and antigen presentation pathways.

  10. A dual role for integrin-linked kinase in platelets: regulating integrin function and α-granule secretion

    PubMed Central

    Sage, Tanya; Stevens, Joanne M.; Jordan, Peter A.; Jones, Sarah; Barrett, Natasha E.; St-Arnaud, Rene; Frampton, Jonathan; Dedhar, Shoukat; Gibbins, Jonathan M.

    2008-01-01

    Integrin-linked kinase (ILK) has been implicated in the regulation of a range of fundamental biological processes such as cell survival, growth, differentiation, and adhesion. In platelets ILK associates with β1- and β3-containing integrins, which are of paramount importance for the function of platelets. Upon stimulation of platelets this association with the integrins is increased and ILK kinase activity is up-regulated, suggesting that ILK may be important for the coordination of platelet responses. In this study a conditional knockout mouse model was developed to examine the role of ILK in platelets. The ILK-deficient mice showed an increased bleeding time and volume, and despite normal ultrastructure the function of ILK-deficient platelets was decreased significantly. This included reduced aggregation, fibrinogen binding, and thrombus formation under arterial flow conditions. Furthermore, although early collagen stimulated signaling such as PLCγ2 phosphorylation and calcium mobilization were unaffected in ILK-deficient platelets, a selective defect in α-granule, but not dense-granule, secretion was observed. These results indicate that as well as involvement in the control of integrin affinity, ILK is required for α-granule secretion and therefore may play a central role in the regulation of platelet function. PMID:18772455

  11. Altered fronto-striatal functions in the Gdi1-null mouse model of X-linked Intellectual Disability.

    PubMed

    Morè, Lorenzo; Künnecke, Basil; Yekhlef, Latefa; Bruns, Andreas; Marte, Antonella; Fedele, Ernesto; Bianchi, Veronica; Taverna, Stefano; Gatti, Silvia; D'Adamo, Patrizia

    2017-03-06

    RAB-GDP dissociation inhibitor 1 (GDI1) loss-of-function mutations are responsible for a form of non-specific X-linked Intellectual Disability (XLID) where the only clinical feature is cognitive impairment. GDI1 patients are impaired in specific aspects of executive functions and conditioned response, which are controlled by fronto-striatal circuitries. Previous molecular and behavioral characterization of the Gdi1-null mouse revealed alterations in the total number/distribution of hippocampal and cortical synaptic vesicles as well as hippocampal short-term synaptic plasticity, and memory deficits. In this study, we employed cognitive protocols with high translational validity to human condition that target the functionality of cortico-striatal circuitry such as attention and stimulus selection ability with progressive degree of complexity. We previously showed that Gdi1-null mice are impaired in some hippocampus-dependent forms of associative learning assessed by aversive procedures. Here, using appetitive-conditioning procedures we further investigated associative learning deficits sustained by the fronto-striatal system. We report that Gdi1-null mice are impaired in attention and associative learning processes, which are a key part of the cognitive impairment observed in XLID patients.

  12. 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.

  13. Mutational and functional analysis of N-linked glycosylation of envelope fusion protein F of Helicoverpa armigera nucleopolyhedrovirus.

    PubMed

    Shen, Shu; Wang, Manli; Li, Xin; Li, Shufen; van Oers, Monique M; Vlak, Just M; Braakman, Ineke; Hu, Zhihong; Deng, Fei; Wang, Hualin

    2016-04-01

    The envelope fusion (F) protein of baculoviruses is a heavily N-glycosylated protein that plays a significant role in the virus infection cycle. N-Linked glycosylation of virus envelope glycoprotein is important for virus envelope glycoprotein folding and its function in general. There are six predicted N-glycosylation sites in the F (HaF) protein of Helicoverpa armigera nucleopolyhedrovirus (HearNPV). The N-glycosylation site located in the F(2) subunit (N104) of HaF has been identified and functionally characterized previously (Long et al., 2007). In this study, the other five potential N-glycosylation sites located in the HaF1 subunit, namely, N293, N361, N526, N571 and N595, were analysed extensively to examine their N-glycosylation and relative importance to the function of HaF. The results showed that four of these five potential glycosylation sites in the F(1) subunit, N293, N361, N526 and N571, were N-glycosylated in F proteins of mature HearNPV budded viruses (BVs) but that N595 was not. In general, the conserved site N526 was critical to the functioning of HaF, as absence of N-glycosylation of N526 reduced the efficiency of HaF folding and trafficking, consequently decreased fusogenicity and modified the subcellular localization of HaF proteins, and thus impaired virus production and infectivity. The absence of N-glycosylation at other individual sites was found to have different effects on the fusogenicity and subcelluar distribution of HaF proteins in HzAM1 cells. In summary, N-glycosylation plays comprehensive roles in HaF function and virus infectivity, which is further discussed.

  14. 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

  15. X-linked retinitis pigmentosa: mutation spectrum of the RPGR and RP2 genes and correlation with visual function.

    PubMed

    Sharon, D; Bruns, G A; McGee, T L; Sandberg, M A; Berson, E L; Dryja, T P

    2000-08-01

    To assess the frequency of RPGR and RP2 mutations in a set of 85 patients with X-linked retinitis pigmentosa (XLRP) and to compare the visual function of patients with mutations in RPGR versus RP2. Eighty-five unrelated patients with XLRP were ascertained, mainly from North America. The single-strand conformation polymorphism (SSCP) and a direct sequencing technique were used to screen their DNA for mutations in the coding region and splice sites of RPGR and RP2. The Snellen visual acuities, visual field areas, and 0.5-Hz and 30-Hz electroretinograms (ERGs) were measured in male patients. The visual function parameters were compared using multiple regression analysis. A wide spectrum of mutations was found in both genes, including missense, nonsense, splice-site, and frameshift mutations. Twenty putative pathogenic mutations in RPGR, 15 of which were novel, were found in 22 patients (26%), whereas 6 mutations in RP2, 4 of which were novel, were found in 6 patients (7%). A high fraction of the mutations in both genes affected amino acid residues within or adjacent to presumed functional domains. Comparison of visual function between comparably aged patients with mutations in RPGR versus RP2 showed that, on average, patients with RPGR mutations have lower ERG amplitudes and smaller visual field areas. Mutations in RPGR and RP2 genes together account for approximately 33% of cases of XLRP in North America. Patients with RPGR mutations have less overall retinal function on average than those with RP2 mutations, on the basis of measurements of visual field areas and full-field ERG amplitudes.

  16. An Improved Ensemble of Random Vector Functional Link Networks Based on Particle Swarm Optimization with Double Optimization Strategy.

    PubMed

    Ling, Qing-Hua; Song, Yu-Qing; Han, Fei; Yang, Dan; Huang, De-Shuang

    2016-01-01

    For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system.

  17. 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.

  18. 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

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

    PubMed

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

    2011-01-18

    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.

  20. Individual Differences in Amygdala-Medial Prefrontal Anatomy Link Negative Affect, Impaired Social Functioning, and Polygenic Depression Risk

    PubMed Central

    Holmes, Avram J.; Lee, Phil H.; Hollinshead, Marisa O.; Bakst, Leah; Roffman, Joshua L.; Smoller, Jordan W.; Buckner, Randy L.

    2013-01-01

    Individual differences in affective and social processes may arise from variability in amygdala-medial prefrontal (mPFC) circuitry and related genetic heterogeneity. To explore this possibility in humans, we examined the structural correlates of trait negative affect in a sample of 1050 healthy young adults with no history of psychiatric illness. Analyses revealed that heightened negative affect was associated with increased amygdala volume and reduced thickness in a left mPFC region encompassing the subgenual and rostral anterior cingulate cortex. The most extreme individuals displayed an inverse correlation between amygdala volume and mPFC thickness, suggesting that imbalance between these structures is linked to negative affect in the general population. Subgroups of participants were further evaluated on social (n = 206) and emotional (n = 533) functions. Individuals with decreased mPFC thickness exhibited the poorest social cognition and were least able to correctly identify facial emotion. Given prior links between disrupted amygdala–mPFC circuitry and the presence of major depressive disorder (MDD), we explored whether the individual differences in anatomy observed here in healthy young adults were associated with polygenic risk for MDD (n = 438) using risk scores derived from a large genome-wide association analysis (n = 18,759). Analyses revealed associations between increasing polygenic burden for MDD and reduced cortical thickness in the left mPFC. These collective findings suggest that, within the healthy population, there is significant variability in amygdala–mPFC circuitry that is associated with poor functioning across affective and social domains. Individual differences in this circuitry may arise, in part, from common genetic variability that contributes to risk for MDD. PMID:23238724

  1. A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes.

    PubMed

    Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

    2011-04-01

    Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed.

  2. An Improved Ensemble of Random Vector Functional Link Networks Based on Particle Swarm Optimization with Double Optimization Strategy

    PubMed Central

    Ling, Qing-Hua; Song, Yu-Qing; Han, Fei; Yang, Dan; Huang, De-Shuang

    2016-01-01

    For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system. PMID:27835638

  3. Care Transitions and Adult Day Services Moderate the Longitudinal Links between Stress Biomarkers and Family Caregivers' Functional Health.

    PubMed

    Liu, Yin; Almeida, David M; Rovine, Michael J; Zarit, Steven H

    2017-05-19

    Stress biomarkers have been linked to health and well-being. There are, however, few studies on how dysregulation in the hypothalamic-pituitary-adrenal axis and sympathetic nervous system actually affects functional health of family caregivers of persons with dementia. Further, it is not clear whether and how factors affecting caregiving stressor exposures such as care transitions and adult day services (ADS) use may affect such association. First, to examine the association of daily stress biomarkers and functional health over time among family caregivers of persons with dementia. Second, to examine effects of care transitions and ADS use on the association between baseline stress biomarkers and functional health over time. At baseline, caregivers provided 5 saliva samples each day during an 8-day diary study, where all caregivers were having a varying number of ADS days per week. There were 2 longitudinal follow-ups at 6 and 12 months on ADS use, care transitions, and caregivers' functional health. The average daily total output across days was computed at baseline for salivary cortisol, the sulfated form of dehydroepiandrosterone (DHEA-s), and salivary alpha amylase (sAA), which were used as predictors of caregivers' longitudinal functional limitation trajectories. Care transitions and total number of ADS days per week at baseline were considered as moderators of the associations between stress biomarkers and health over time. The associations between functional limitation trajectories and daily total outputs of cortisol and sAA were modified by ADS use and care transitions. Among caregivers who experienced a transition, and who used less than average ADS days per week, lower daily cortisol total output and lower daily sAA total output were associated with increasing functional limitations. Caregivers who experienced a transition but used greater than average ADS days per week did not show such patterns of association. No significant effect was found for DHEA

  4. Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity

    PubMed Central

    Moustafa, Ibrahim M.; Shen, Hujun; Morton, Brandon; Colina, Coray M.; Cameron, Craig E.

    2011-01-01

    The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics (MD) simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30–74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. Dynamics of residues participating in the same biochemical property, for example RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional, structural elements suggest co-evolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template-nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and NTP channels, which might be relevant to NTP entry, PPi exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme. PMID:21575642

  5. Buckling analysis of defective cross-linked functionalized single- and double-walled carbon nanotubes with polyethylene chains using molecular dynamics simulations.

    PubMed

    Ajori, S; Ansari, R; Parsapour, H

    2016-12-01

    Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two different configurations with the consideration of vacancy defects, namely mapped and wrapped, are selected. According to the results, critical buckling force of cross-linked functionalized CNTs with PE chains increases as compared to pure CNTs, especially in the case of double-walled carbon nanotubes (DWCNTs). By contrast, it is demonstrated that critical strain of cross-linked functionalized CNTs decreases as compared to that of pristine CNTs. Also, it is observed that increasing the weight percentage leads to the higher increase and the decrease in critical buckling force and strain of cross-linked functionalized CNTs, respectively. Moreover, the presence of defect considerably reduces both critical buckling force and strain of cross-linked functionalized CNTs. Finally, it is shown that the critical buckling strain is more sensitive to the presence of defects as compared to critical buckling force.

  6. Increased Motor Activity During REM Sleep Is Linked with Dopamine Function in Idiopathic REM Sleep Behavior Disorder and Parkinson Disease

    PubMed Central

    Zoetmulder, Marielle; Nikolic, Miki; Biernat, Heidi; Korbo, Lise; Friberg, Lars; Jennum, Poul

    2016-01-01

    Study Objectives: Rapid eye movement (REM) sleep behavior disorder (RBD) is a parasomnia characterized by impaired motor inhibition during REM sleep, and dream-enacting behavior. RBD is especially associated with α-synucleinopathies, such as Parkinson disease (PD). Follow-up studies have shown that patients with idiopathic RBD (iRBD) have an increased risk of developing an α-synucleinopathy in later life. Although abundant studies have shown that degeneration of the nigrostriatal dopaminergic system is associated with daytime motor function in Parkinson disease, only few studies have investigated the relation between this system and electromyographic (EMG) activity during sleep. The objective of this study was to investigate the relationship between the nigrostriatal dopamine system and muscle activity during sleep in iRBD and PD. Methods: 10 iRBD patients, 10 PD patients with PD, 10 PD patients without RBD, and 10 healthy controls were included and assessed with (123)I-N-omega-fluoropropyl-2-beta-carboxymethoxy-3beta-(4-iodophenyl) nortropane ((123)I-FP-CIT) Single-photon emission computed tomography (SPECT) scanning (123I-FP-CIT SPECT), neurological examination, and polysomnography. Results: iRBD patients and PD patients with RBD had increased EMG-activity compared to healthy controls. 123I-FP-CIT uptake in the putamen-region was highest in controls, followed by iRBD patients, and lowest in PD patients. In iRBD patients, EMG-activity in the mentalis muscle was correlated to 123I-FP-CIT uptake in the putamen. In PD patients, EMG-activity was correlated to anti-Parkinson medication. Conclusions: Our results support the hypothesis that increased EMG-activity during REM sleep is at least partly linked to the nigrostriatal dopamine system in iRBD, and with dopamine function in PD. Citation: Zoetmulder M, Nikolic M, Biernat H, Korbo L, Friberg L, Jennum P. Increased motor activity during rem sleep is linked with dopamine function in idiopathic REM sleep behavior

  7. 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.

  8. The N-linked sugar chains of human immunoglobulin G: their unique pattern, and their functional roles.

    PubMed

    Kobata, Akira

    2008-03-01

    In contrast to other serum glycoproteins, the majority of the N-linked sugar chains of human serum IgG are not sialylated. In addition, extremely high micro-heterogeneity occurs in the serum IgG sugar chains. This micro-heterogeneity is mainly produced by the presence or absence of the two galactoses, the bisecting GlcNAc, and the fucose residue. Interesting evidence is that the molar ratio of each sugar chain of the serum IgG samples is quite constant in healthy individuals. By adding the information of the characteristic feature of the sugar patterns of myeloma IgG samples and glycosylated Bence Jones proteins, which are the products of monoclonal B-cells, it was proposed that B-cells in the human blood are a mixture of clones equipped with different sets and ratios of glycosyltransferases. It was also proposed that each glycoform of IgG might have a different function. This hypothesis was realized by the comparative studies of the function of IgG samples before and after removal of galactose residues, fucose residue, or sialic acid residues.

  9. Engineered disulfide bonds restore chaperone-like function of DJ-1 mutants linked to familial Parkinson's disease.

    PubMed

    Logan, Todd; Clark, Lindsay; Ray, Soumya S

    2010-07-13

    Loss-of-function mutations such as L166P, A104T, and M26I in the DJ-1 gene (PARK7) have been linked to autosomal-recessive early onset Parkinson's disease (PD). Cellular and structural studies of the familial mutants suggest that these mutations may destabilize the dimeric structure. To look for common dynamical signatures among the DJ-1 mutants, short MD simulations of up to 1000 ps were conducted to identify the weakest region of the protein (residues 38-70). In an attempt to stabilize the protein, we mutated residue Val 51 to cysteine (V51C) to make a symmetry-related disulfide bridge with the preexisting Cys 53 on the opposite subunit. We found that the introduction of this disulfide linkage stabilized the mutants A104T and M26I against thermal denaturation, improved their ability to scavenge reactive oxygen species (ROS), and restored a chaperone-like function of blocking alpha-synuclein aggregation. The L166P mutant was far too unstable to be rescued by introduction of the V51C mutation. The results presented here point to the possible development of pharmacological chaperones, which may eventually lead to PD therapeutics.

  10. Efficient, dual-stimuli responsive cytosolic gene delivery using a RGD modified disulfide-linked polyethylenimine functionalized gold nanorod.

    PubMed

    Wang, Feihu; Shen, Yuanyuan; Zhang, Wenjun; Li, Min; Wang, Yun; Zhou, Dejian; Guo, Shengrong

    2014-12-28

    Controlled-release systems capable of responding to external stimuli and/or unique internal environments have received great interests in site-specific gene and/or drug delivery. In this work, a functionalized gene nanocarrier for dual-stimuli triggered cytosolic gene delivery is developed and showing high gene delivery efficacy with low cytotoxicity. The nanocarrier is prepared by conjugating gold nanorod (GNR) with multiple disulfide cross-linked short PEIs to harness the advantageous properties of GNR based near infrared (NIR) laser induced photothermal heating and intracellular stimuli-triggered degradability of disulfide cross-linked short PEIs (DSPEI). The DSPEI is further grafted with a poly(ethylene glycol) (PEG) section to afford high carrier stability in cell cultures and a terminal RGD peptide for specific targeting of cancer cells. The nanocarrier is found to effectively condense plasmid DNA to form a highly stable GNR-DSPEI-PEG-RGD/DNA complex with tumor cell-targeting ability that can be efficiently uptaken by cancer cells. Moreover, the loaded genes can be effectively released from the complex triggered by the high intracellular glutathione content and/or by photothermal effect of NIR irradiation at 808 nm. Interestingly, the GNRs-based complex can easily escape from intracellular endo-/lyso-somal compartments and release the gene load into the cytosol upon exposure to NIR irradiation, resulting in significantly improved gene transfection efficiency. Our new gene carrier exhibits high gene transfection efficiency, comparable to or even better than that of high MW PEIs, but with a much lower cytotoxicity. Additionally, neither the GNR-based carrier nor the laser treatment shows any significant evidence of cytotoxicity. This work demonstrates a promising strategy for intracellular stimuli triggered, photothermal controllable gene delivery system, which can be further applied to many other nanomedicine fields.

  11. Pleiotropic functions of embryonic sonic hedgehog expression link jaw and taste bud amplification with eye loss during cavefish evolution.

    PubMed

    Yamamoto, Yoshiyuki; Byerly, Mardi S; Jackman, William R; Jeffery, William R

    2009-06-01

    This study addresses the role of sonic hedgehog (shh) in increasing oral-pharyngeal constructive traits (jaws and taste buds) at the expense of eyes in the blind cavefish Astyanax mexicanus. In cavefish embryos, eye primordia degenerate under the influence of hyperactive Shh signaling. In concert, cavefish show amplified jaw size and taste bud numbers as part of a change in feeding behavior. To determine whether pleiotropic effects of hyperactive Shh signaling link these regressive and constructive traits, shh expression was compared during late development of the surface-dwelling (surface fish) and cave-dwelling (cavefish) forms of Astyanax. After an initial expansion along the midline of early embryos, shh was elevated in the oral-pharyngeal region in cavefish and later was confined to taste buds. The results of shh inhibition and overexpression experiments indicate that Shh signaling has an important role in oral and taste bud development. Conditional overexpression of an injected shh transgene at specific times in development showed that taste bud amplification and eye degeneration are sensitive to shh overexpression during the same early developmental period, although taste buds are not formed until much later. Genetic crosses between cavefish and surface fish revealed an inverse relationship between eye size and jaw size/taste bud number, supporting a link between oral-pharyngeal constructive traits and eye degeneration. The results suggest that hyperactive Shh signaling increases oral and taste bud amplification in cavefish at the expense of eyes. Therefore, selection for constructive oral-pharyngeal traits may be responsible for eye loss during cavefish evolution via pleiotropic function of the Shh signaling pathway.

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