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Sample records for understanding molecular coevolution

  1. Reducing the false positive rate in the non-parametric analysis of molecular coevolution

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    O'Dea Shirley

    2008-04-01

    analysis of the physico-chemical properties of amino acid sites in the context of the protein structure reveals striking dependencies among amino acid sites. Results indicate a covariation trend in the hydrophobicities and molecular weight characteristics of amino acid sites when analysing a non-redundant set of 8000 protein structures. Using this biological information as filter in coevolutionary analyses minimises the false positive rate of these methods. Application of these filters to three different proteins with known functional domains supports the importance of using biological filters to detect coevolution. Conclusion Coevolutionary analyses using non-parametric methods have proved difficult and highly prone to provide spurious results depending on the properties of MSAs and on the strength of coevolution between amino acid sites. The application of statistical filters to the number of pairs detected as coevolving reduces significantly the number of artifactual results. Analysis of the physico-chemical properties of amino acid sites in the protein structure context reveals their structure-dependent covariation. The application of this known biological information to the analysis of covariation greatly enhances the functional coevolutionary signal and removes historical covariation. Simultaneous use of statistical and biological data is instrumental in the detection of functional amino acid sites dependencies and compensatory changes at the protein level.

  2. Identifying the molecular basis of host-parasite coevolution: merging models and mechanisms.

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    Dybdahl, Mark F; Jenkins, Christina E; Nuismer, Scott L

    2014-07-01

    Mathematical models of the coevolutionary process have uncovered consequences of host-parasite interactions that go well beyond the traditional realm of the Red Queen, potentially explaining several important evolutionary transitions. However, these models also demonstrate that the specific consequences of coevolution are sensitive to the structure of the infection matrix, which is embedded in models to describe the likelihood of infection in encounters between specific host and parasite genotypes. Traditional cross-infection approaches to estimating infection matrices might be unreliable because evolutionary dynamics and experimental sampling lead to missing genotypes. Consequently, our goal is to identify the likely structure of infection matrices by synthesizing molecular mechanisms of host immune defense and parasite counterdefense with coevolutionary models. This synthesis reveals that the molecular mechanisms of immune reactions, although complex and diverse, conform to two basic models commonly used within coevolutionary theory: matching infection and targeted recognition. Our synthesis also overturns conventional wisdom, revealing that the general models are not taxonomically restricted but are applicable to plants, invertebrates, and vertebrates. Finally, our synthesis identifies several important areas for future research that should improve the explanatory power of coevolutionary models. The most important among these include empirical studies to identify the molecular hotspots of genotypic specificity and theoretical studies examining the consequences of matrices that more accurately represent multistep infection processes and quantitative defenses.

  3. Fifty years of co-evolution and beyond: integrating co-evolution from molecules to species.

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    Carmona, Diego; Fitzpatrick, Connor R; Johnson, Marc T J

    2015-11-01

    Fifty years after Ehrlich and Raven's seminal paper, the idea of co-evolution continues to grow as a key concept in our understanding of organic evolution. This concept has not only provided a compelling synthesis between evolutionary biology and community ecology, but has also inspired research that extends beyond its original scope. In this article, we identify unresolved questions about the co-evolutionary process and advocate for the integration of co-evolutionary research from molecular to interspecific interactions. We address two basic questions: (i) What is co-evolution and how common is it? (ii) What is the unit of co-evolution? Both questions aim to explore the heart of the co-evolutionary process. Despite the claim that co-evolution is ubiquitous, we argue that there is in fact little evidence to support the view that reciprocal natural selection and coadaptation are common in nature. We also challenge the traditional view that co-evolution only occurs between traits of interacting species. Co-evolution has the potential to explain evolutionary processes and patterns that result from intra- and intermolecular biochemical interactions within cells, intergenomic interactions (e.g. nuclear-cytoplasmic) within species, as well as intergenomic interactions mediated by phenotypic traits between species. Research that bridges across these levels of organization will help to advance our understanding of the importance of the co-evolutionary processes in shaping the diversity of life on Earth. © 2015 John Wiley & Sons Ltd.

  4. Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations.

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    Holding, Matthew L; Drabeck, Danielle H; Jansa, Sharon A; Gibbs, H Lisle

    2016-11-01

    SynopsisVenom and venom resistance are molecular phenotypes widely considered to have diversified through coevolution between predators and prey. However, while evolutionary and functional studies on venom have been extensive, little is known about the molecular basis, variation, and complexity of venom resistance. We review known mechanisms of venom resistance and relate these mechanisms to their predicted impact on coevolutionary dynamics with venomous enemies. We then describe two conceptual approaches which can be used to examine venom/resistance systems. At the intraspecific level, tests of local adaptation in venom and resistance phenotypes can identify the functional mechanisms governing the outcomes of coevolution. At deeper evolutionary timescales, the combination of phylogenetically informed analyses of protein evolution coupled with studies of protein function promise to elucidate the mode and tempo of evolutionary change on potentially coevolving genes. We highlight case studies that use each approach to extend our knowledge of these systems as well as address larger questions about coevolutionary dynamics. We argue that resistance and venom are phenotypic traits which hold exceptional promise for investigating the mechanisms, dynamics, and outcomes of coevolution at the molecular level. Furthermore, extending the understanding of single gene-for-gene interactions to the whole resistance and venom phenotypes may provide a model system for examining the molecular and evolutionary dynamics of complex multi-gene interactions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  5. Co-evolution of somatic variation in primary and metastatic colorectal cancer may expand biopsy indications in the molecular era.

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    Richard Kim

    Full Text Available Metastasis is thought to be a clonal event whereby a single cell initiates the development of a new tumor at a distant site. However the degree to which primary and metastatic tumors differ on a molecular level remains unclear. To further evaluate these concepts, we used next generation sequencing (NGS to assess the molecular composition of paired primary and metastatic colorectal cancer tissue specimens.468 colorectal tumor samples from a large personalized medicine initiative were assessed by targeted gene sequencing of 1,321 individual genes. Eighteen patients produced genomic profiles for 17 paired primary:metastatic (and 2 metastatic:metastatic specimens.An average of 33.3 mutations/tumor were concordant (shared between matched samples, including common well-known genes (APC, KRAS, TP53. An average of 2.3 mutations/tumor were discordant (unshared among paired sites. KRAS mutational status was always concordant. The overall concordance rate for mutations was 93.5%; however, nearly all (18/19 (94.7% paired tumors showed at least one mutational discordance. Mutations were seen in: TTN, the largest gene (5 discordant pairs, ADAMTS20, APC, MACF1, RASA1, TP53, and WNT2 (2 discordant pairs, SMAD2, SMAD3, SMAD4, FBXW7, and 66 others (1 discordant pair.Whereas primary and metastatic tumors displayed little variance overall, co-evolution produced incremental mutations in both. These results suggest that while biopsy of the primary tumor alone is likely sufficient in the chemotherapy-naïve patient, additional biopsies of primary or metastatic disease may be necessary to precisely tailor therapy following chemotherapy resistance or insensitivity in order to adequately account for tumor evolution.

  6. Understanding molecular structure from molecular mechanics.

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    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  7. Understanding molecular simulation: from algorithms to applications

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    Frenkel, D.; Smit, B.

    2002-01-01

    Second and revised edition Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique

  8. Protein co-evolution: how do we combine bioinformatics and experimental approaches?

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    Sandler, Inga; Abu-Qarn, Mehtap; Aharoni, Amir

    2013-02-02

    Molecular co-evolution is manifested by compensatory changes in proteins designed to enable adaptation to their natural environment. In recent years, bioinformatics approaches allowed for the detection of co-evolution at the level of the whole protein or of specific residues. Such efforts enabled prediction of protein-protein interactions, functional assignments of proteins and the identification of interacting residues, thereby providing information on protein structure. Still, despite such advances, relatively little is known regarding the functional implications of sequence divergence resulting from protein co-evolution. While bioinformatics approaches usually analyze thousands of proteins to obtain a broad view of protein co-evolution, experimental evaluation of protein co-evolution serves to study only individual proteins. In this review, we describe recent advances in bioinformatics and experimental efforts aimed at examining protein co-evolution. Accordingly, we discuss possible modes of crosstalk between the bioinformatics and experimental approaches to facilitate the identification of co-evolutionary signals in proteins and to understand their implications for the structure and function of proteins.

  9. Understanding molecular simulation from algorithms to applications

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    Frenkel, Daan

    2001-01-01

    Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the ""recipes"" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practic

  10. The potential of a population genomics approach to analyse geographic mosaics of plant–insect coevolution

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    Vermeer, K.M.C.A.; Dicke, M.; Jong, de P.W.

    2011-01-01

    A central issue in the evolutionary ecology of species interactions is coevolution, which involves the reciprocal selection between individuals of interacting species. Understanding the importance of coevolution in shaping species interactions requires the consideration of spatial variation in their

  11. Hydrologic Synthesis Across the Critical Zone Observatory Network: A Step Towards Understanding the Coevolution of Critical Zone Function and Structure

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    Wlostowski, A. N.; Harman, C. J.; Molotch, N. P.

    2017-12-01

    generation). Storage-discharge relationships vary widely across the Network, and may be associated with inter-site differences in sub-surface architecture. Moving forward, we seek to reconcile top-down analysis results against the bottom-up understanding of critical zone structure and hydrologic function at each CZO site.

  12. Detection of significant protein coevolution.

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    Ochoa, David; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2015-07-01

    The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. In this work, we developed a method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. Understanding the molecular mechanisms of reprogramming

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    Krause, Marie N. [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); University Hospital of Würzburg, Department of Pediatrics, 2 Josef-Schneiderstrasse, 97080 Würzburg (Germany); Sancho-Martinez, Ignacio [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); Centre for Stem Cells and Regenerative Medicine, King' s College London, 28th Floor, Tower Wing, Guy' s Hospital, Great Maze Pond, London (United Kingdom); Izpisua Belmonte, Juan Carlos, E-mail: belmonte@salk.edu [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States)

    2016-05-06

    Despite the profound and rapid advancements in reprogramming technologies since the generation of the first induced pluripotent stem cells (iPSCs) in 2006[1], the molecular basics of the process and its implications are still not fully understood. Recent work has suggested that a subset of TFs, so called “Pioneer TFs”, play an important role during the stochastic phase of iPSC reprogramming [2–6]. Pioneer TFs activities differ from conventional transcription factors in their mechanism of action. They bind directly to condensed chromatin and elicit a series of chromatin remodeling events that lead to opening of the chromatin. Chromatin decondensation by pioneer factors progressively occurs during cell division and in turn exposes specific gene promoters in the DNA to which TFs can now directly bind to promoters that are readily accessible[2, 6]. Here, we will summarize recent advancements on our understanding of the molecular mechanisms underlying reprogramming to iPSC as well as the implications that pioneer Transcription Factor activities might play during different lineage conversion processes. - Highlights: • Pioneer transcription factor activity underlies the initial steps of iPSC generation. • Reprogramming can occur by cis- and/or trans- reprogramming events. • Cis-reprogramming implies remodeling of the chromatin for enabling TF accessibility. • Trans-reprogramming encompasses direct binding of Tfs to their target gene promoters.

  14. Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution

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    Martina Jelocnik

    2016-02-01

    Full Text Available Background. Highly stable, evolutionarily conserved, small, non-integrative plasmids are commonly found in members of the Chlamydiaceae and, in some species, these plasmids have been strongly linked to virulence. To date, evidence for such a plasmid in Chlamydia pecorum has been ambiguous. In a recent comparative genomic study of porcine, ovine, bovine, and koala C. pecorum isolates, we identified plasmids (pCpec in a pig and three koala strains, respectively. Screening of further porcine, ovine, bovine, and koala C. pecorum isolates for pCpec showed that pCpec is common, but not ubiquitous in C. pecorum from all of the infected hosts. Methods. We used a combination of (i bioinformatic mining of previously sequenced C. pecorum genome data sets and (ii pCpec PCR-amplicon sequencing to characterise a further 17 novel pCpecs in C. pecorum isolates obtained from livestock, including pigs, sheep, and cattle, as well as those from koala. Results and Discussion. This analysis revealed that pCpec is conserved with all eight coding domain sequences (CDSs present in isolates from each of the hosts studied. Sequence alignments revealed that the 21 pCpecs show 99% nucleotide sequence identity, with 83 single nucleotide polymorphisms (SNPs shown to differentiate all of the plasmids analysed in this study. SNPs were found to be mostly synonymous and were distributed evenly across all eight pCpec CDSs as well as in the intergenic regions. Although conserved, analyses of the 21 pCpec sequences resolved plasmids into 12 distinct genotypes, with five shared between pCpecs from different isolates, and the remaining seven genotypes being unique to a single pCpec. Phylogenetic analysis revealed congruency and co-evolution of pCpecs with their cognate chromosome, further supporting polyphyletic origin of the koala C. pecorum. This study provides further understanding of the complex epidemiology of this pathogen in livestock and koala hosts and paves the way for

  15. Molecular understanding of curcumin in diabetic nephropathy.

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    Soetikno, Vivian; Suzuki, Kenji; Veeraveedu, Punniyakoti T; Arumugam, Somasundaram; Lakshmanan, Arun P; Sone, Hirohito; Watanabe, Kenichi

    2013-08-01

    Diabetic nephropathy is characterized by a plethora of signaling abnormalities. Recent trials have suggested that intensive glucose-lowering treatment leads to hypoglycemic events, which can be dangerous. Curcumin is the active ingredient of turmeric, which has been widely used in many countries for centuries to treat numerous diseases. The preventive and therapeutic properties of curcumin are associated with its antioxidant and anti-inflammatory properties. Here, we highlight the renoprotective role of curcumin in diabetes mellitus (DM) with an emphasis on the molecular basis of this effect. We also briefly discuss the numerous approaches that have been undertaken to improve the pharmacokinetics of curcumin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Modeling Coevolution between Language and Memory Capacity during Language Origin.

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    Gong, Tao; Shuai, Lan

    2015-01-01

    Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language.

  17. What Can Phages Tell Us about Host-Pathogen Coevolution?

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    John J. Dennehy

    2012-01-01

    Full Text Available The outcomes of host-parasite interactions depend on the coevolutionary forces acting upon them, but because every host-parasite relation is enmeshed in a web of biotic and abiotic interactions across a heterogeneous landscape, host-parasite coevolution has proven difficult to study. Simple laboratory phage-bacteria microcosms can ameliorate this difficulty by allowing controlled, well-replicated experiments with a limited number of interactors. Genetic, population, and life history data obtained from these studies permit a closer examination of the fundamental correlates of host-parasite coevolution. In this paper, I describe the results of phage-bacteria coevolutionary studies and their implications for the study of host-parasite coevolution. Recent experimental studies have confirmed phage-host coevolutionary dynamics in the laboratory and have shown that coevolution can increase parasite virulence, specialization, adaptation, and diversity. Genetically, coevolution frequently proceeds in a manner best described by the Gene for Gene model, typified by arms race dynamics, but certain contexts can result in Red Queen dynamics according to the Matching Alleles model. Although some features appear to apply only to phage-bacteria systems, other results are broadly generalizable and apply to all instances of antagonistic coevolution. With laboratory host-parasite coevolutionary studies, we can better understand the perplexing array of interactions that characterize organismal diversity in the wild.

  18. Molecular Technique to Understand Deep Microbial Diversity

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    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  19. Evolving deltas: Conceptualising coevolution with engineered interventions

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    Welch, Amy; Nicholls, Robert; Lazar, Attila

    2017-04-01

    Mid to low latitude deltas have been populated for thousands of years due to their fertile soil and coastal location. This has led to an alteration in the land cover of deltas to primary agriculture and dense rural settlements and more recently, major cities and megacities have developed on or adjacent to many deltas. Deltas may be prosperous in terms of their outputs and services; however, they are also susceptible to many hazards due to their location and low-lying nature. Hazards include storm surges, fluvial flooding and erosion of both coastal and riverine areas, as well as subsidence, relative sea-level rise and pollution. This can have severe impacts on the delta, its population and its services. Therefore engineered interventions have been used for some time to protect the population and the valuable land from the consequences of hazards. Coevolution can be described as a feedback loop between nature and humans: each has an effect on how the other behaves and hence this inter-dependence interaction continues. Therefore the natural evolution of the delta interacts with engineered interventions, such as promoting accelerated subsidence over time, necessitating further adaptation. The deltaic landscape and associated livelihoods are thus the result of this co-evolution process between natural delta processes and engineered interventions. This presentation will identify and discuss various drivers and consequences of large scale engineered interventions, comparing and contrasting the management approaches taken in five populated deltas (Ganges-Brahmaputra-Meghna, Yangtze, Rhine-Meuse-Scheldt, Mekong and Nile). The type of engineered intervention and management approaches had a direct effect on the coevolution of deltas, with each of the deltas being at different stages in terms of extent of coevolution. A qualitative timeline of the typical steps of coevolution between the human system and the delta system of the studied deltas was produced. The major

  20. Practical aspects of protein co-evolution.

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    Ochoa, David; Pazos, Florencio

    2014-01-01

    Co-evolution is a fundamental aspect of Evolutionary Theory. At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago. Due to the complexity of the problem and the amount of genomic data required for these approaches to achieve good performances, it took a relatively long time from the appearance of the first ideas and concepts to the quotidian application of these approaches and their incorporation to the standard toolboxes of bioinformaticians and molecular biologists. Today, these methodologies are mature (both in terms of performance and usability/implementation), and the genomic information that feeds them large enough to allow their general application. This review tries to summarize the current landscape of co-evolution-based methodologies, with a strong emphasis on describing interesting cases where their application to important biological systems, alone or in combination with other computational and experimental approaches, allowed getting new insight into these.

  1. Indirect effects drive coevolution in mutualistic networks.

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    Guimarães, Paulo R; Pires, Mathias M; Jordano, Pedro; Bascompte, Jordi; Thompson, John N

    2017-10-26

    Ecological interactions have been acknowledged to play a key role in shaping biodiversity. Yet a major challenge for evolutionary biology is to understand the role of ecological interactions in shaping trait evolution when progressing from pairs of interacting species to multispecies interaction networks. Here we introduce an approach that integrates coevolutionary dynamics and network structure. Our results show that non-interacting species can be as important as directly interacting species in shaping coevolution within mutualistic assemblages. The contribution of indirect effects differs among types of mutualism. Indirect effects are more likely to predominate in nested, species-rich networks formed by multiple-partner mutualisms, such as pollination or seed dispersal by animals, than in small and modular networks formed by intimate mutualisms, such as those between host plants and their protective ants. Coevolutionary pathways of indirect effects favour ongoing trait evolution by promoting slow but continuous reorganization of the adaptive landscape of mutualistic partners under changing environments. Our results show that coevolution can be a major process shaping species traits throughout ecological networks. These findings expand our understanding of how evolution driven by interactions occurs through the interplay of selection pressures moving along multiple direct and indirect pathways.

  2. Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

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    Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

    2017-11-22

    Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

  3. Antagonistic experimental coevolution with a parasite increases host recombination frequency

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    Kerstes Niels AG

    2012-02-01

    Full Text Available Abstract Background One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation.

  4. Malignant Catarrhal Fever: Understanding Molecular Diagnostics in Context of Epidemiology

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    Hong Li

    2011-10-01

    Full Text Available Malignant catarrhal fever (MCF is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species, which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant challenges in laboratory diagnostics. The recent development of specific assays for viral DNA and antibodies has expanded and improved the inventory of laboratory tests and opened new opportunities for use of MCF diagnostics. Issues related to understanding and implementing appropriate assays for specific diagnostic needs must be addressed in order to take advantage of molecular diagnostics in the laboratory.

  5. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

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    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  6. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence

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    Ciamak Ghazaei

    2018-01-01

    Full Text Available Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution. Recent advances in molecular profiling of pathogenic species of the genus Leptospira have improved our understanding of the evolutionary factors that determine virulence and mechanisms that the bacteria employ to survive. However, a major impediment to the formulation of intervention strategies has been the limited understanding of the disease determinants. Consequently, the association of the biological mechanisms to the pathogenesis of Leptospira, as well as the functions of numerous essential virulence factors still remain implicit. This review examines recent advances in genetic screening technologies, the underlying microbiological processes, the virulence factors and associated molecular mechanisms driving pathogenesis of Leptospira species.

  7. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence

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    Ghazaei, Ciamak

    2018-01-01

    Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution. Recent advances in molecular profiling of pathogenic species of the genus Leptospira have improved our understanding of the evolutionary factors that determine virulence and mechanisms that the bacteria employ to survive. However, a major impediment to the formulation of intervention strategies has been the limited understanding of the disease determinants. Consequently, the association of the biological mechanisms to the pathogenesis of Leptospira, as well as the functions of numerous essential virulence factors still remain implicit. This review examines recent advances in genetic screening technologies, the underlying microbiological processes, the virulence factors and associated molecular mechanisms driving pathogenesis of Leptospira species. PMID:29445617

  8. Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli.

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    Akiko Kashiwagi

    2011-08-01

    Full Text Available According to the Red Queen hypothesis or arms race dynamics, coevolution drives continuous adaptation and counter-adaptation. Experimental models under simplified environments consisting of bacteria and bacteriophages have been used to analyze the ongoing process of coevolution, but the analysis of both parasites and their hosts in ongoing adaptation and counter-adaptation remained to be performed at the levels of population dynamics and molecular evolution to understand how the phenotypes and genotypes of coevolving parasite-host pairs change through the arms race. Copropagation experiments with Escherichia coli and the lytic RNA bacteriophage Qβ in a spatially unstructured environment revealed coexistence for 54 days (equivalent to 163-165 replication generations of Qβ and fitness analysis indicated that they were in an arms race. E. coli first adapted by developing partial resistance to infection and later increasing specific growth rate. The phage counter-adapted by improving release efficiency with a change in host specificity and decrease in virulence. Whole-genome analysis indicated that the phage accumulated 7.5 mutations, mainly in the A2 gene, 3.4-fold faster than in Qβ propagated alone. E. coli showed fixation of two mutations (in traQ and csdA faster than in sole E. coli experimental evolution. These observations suggest that the virus and its host can coexist in an evolutionary arms race, despite a difference in genome mutability (i.e., mutations per genome per replication of approximately one to three orders of magnitude.

  9. Increasing productivity accelerates host-parasite coevolution.

    Science.gov (United States)

    Lopez-Pascua, L d C; Buckling, A

    2008-05-01

    Host-parasite coevolution is believed to influence a range of evolutionary and ecological processes, including population dynamics, evolution of diversity, sexual reproduction and parasite virulence. The impact of coevolution on these processes will depend on its rate, which is likely to be affected by the energy flowing through an ecosystem, or productivity. We addressed how productivity affected rates of coevolution during a coevolutionary arms race between experimental populations of bacteria and their parasitic viruses (phages). As hypothesized, the rate of coevolution between bacterial resistance and phage infectivity increased with increased productivity. This relationship can in part be explained by reduced competitiveness of resistant bacteria in low compared with high productivity environments, leading to weaker selection for resistance in the former. The data further suggest that variation in productivity can generate variation in selection for resistance across landscapes, a result that is crucial to the geographic mosaic theory of coevolution.

  10. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  11. Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict.

    Science.gov (United States)

    Brennan, Patricia L R; Prum, Richard O

    2015-07-01

    Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male-male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism

    Science.gov (United States)

    Douam, Florian; Mancip, Jimmy; Mailly, Laurent; Montserret, Roland; Ding, Qiang; Verhoeyen, Els; Baumert, Thomas F.; Ploss, Alexander; Carbone, Alessandra

    2018-01-01

    Amino-acid coevolution can be referred to mutational compensatory patterns preserving the function of a protein. Viral envelope glycoproteins, which mediate entry of enveloped viruses into their host cells, are shaped by coevolution signals that confer to viruses the plasticity to evade neutralizing antibodies without altering viral entry mechanisms. The functions and structures of the two envelope glycoproteins of the Hepatitis C Virus (HCV), E1 and E2, are poorly described. Especially, how these two proteins mediate the HCV fusion process between the viral and the cell membrane remains elusive. Here, as a proof of concept, we aimed to take advantage of an original coevolution method recently developed to shed light on the HCV fusion mechanism. When first applied to the well-characterized Dengue Virus (DENV) envelope glycoproteins, coevolution analysis was able to predict important structural features and rearrangements of these viral protein complexes. When applied to HCV E1E2, computational coevolution analysis predicted that E1 and E2 refold interdependently during fusion through rearrangements of the E2 Back Layer (BL). Consistently, a soluble BL-derived polypeptide inhibited HCV infection of hepatoma cell lines, primary human hepatocytes and humanized liver mice. We showed that this polypeptide specifically inhibited HCV fusogenic rearrangements, hence supporting the critical role of this domain during HCV fusion. By combining coevolution analysis and in vitro assays, we also uncovered functionally-significant coevolving signals between E1 and E2 BL/Stem regions that govern HCV fusion, demonstrating the accuracy of our coevolution predictions. Altogether, our work shed light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the

  13. Actinides and environmental interfaces: striving for molecular-level understanding

    International Nuclear Information System (INIS)

    Heino Nitsche

    2005-01-01

    Actinides can undergo a variety of complex chemical reactions in the environment. In addition to the formation of solid precipitates, colloids and dissolved solution species common to aqueous systems, actinide ions can interact with the surrounding geo and biomedia to change oxidation states or sorb on surfaces and colloids. The rate of migration is determined by aqueous solubility, and interactions with solid surfaces such as minerals, soils, natural organic matter, and soil microorganisms Sorption of aqueous actinide species on biological and geological matrices can be quantitatively described by a surface complexation or site-binding model. The disadvantage of this model is the difficulty in the experimental determination of the model parameters and surface reaction constants. Usually, a set of surface reactions and species are proposed based on knowledge of the solution speciation of the solute, and the reaction constants are usually derived by fitting computer-calculated absorption curves to experimental data. Because this process typically involves a large number of potentially adjustable parameters, it is likely to lead to non-unique parameter fitting and does not always result in a consistent set of parameters for the same systems. A fundamental molecular-level understanding of sorption processes of actinides on environmental surfaces is required to better understand and predict their transport behavior in nature. Several different surface spectroscopic techniques have been applied to the characterization of the adsorbed species and surface reactions and a direct determination of the sorbed species and surface reactions has become possible. The non-linear optical techniques of second harmonic and sum frequency generation (SHG and SFG) are ideally suited to study surfaces and interfaces of mineral oxides, biosurfactants and biopolymers, organic adlayers adsorbed on solid/mineral surfaces and soil organic matter, including humic and fulvic acids. Resonant

  14. Molecular Understanding of Organic Solar Cells: The Challenges

    KAUST Repository

    Brédas, Jean-Luc

    2009-11-17

    (Figure presented) Our objective in this Account is 3-fold. First, we provide an overview of the optical and electronic processes that take place in a solid-state organic solar cell, which we define as a cell in which the semiconducting materials between the electrodes are organic, be them polymers, oligomers, or small molecules; this discussion is also meant to set the conceptual framework in which many of the contributions to this Special Issue on Photovoltaics can We viewed. We successively turn our attention to (i) optical absorption and exciton formation, (ii) exciton migration to the donor - acceptor interface, (iii) exciton dissociation into charge carriers, resulting in the appearance of holes in the donor and electrons in the acceptor, (iv) charge-carrier mobility, and (v) charge collection at the electrodes. For each of these processes, we also describe the theoretical challenges that need to be overcome to gain a comprehensive understanding at the molecular level. Finally, we highlight recent theoretical advances, in particular regarding the determination of the energetics and dynamics at organic - organic interfaces, and underline that the right balance needs to be found for the optimization of material parameters that often result in opposite effects on the photovoltaic performance. © 2009 American Chemical Society.

  15. Understanding ion association states and molecular dynamics using infrared spectroscopy

    Science.gov (United States)

    Masser, Hanqing

    A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO

  16. Coevolution and the diversification of life.

    Science.gov (United States)

    Hembry, David H; Yoder, Jeremy B; Goodman, Kari Roesch

    2014-10-01

    Coevolution, reciprocal adaptation between two or more taxa, is commonly invoked as a primary mechanism responsible for generating much of Earth's biodiversity. This conceptually appealing hypothesis is incredibly broad in evolutionary scope, encompassing diverse patterns and processes operating over timescales ranging from microbial generations to geological eras. However, we have surprisingly little evidence that large-scale associations between coevolution and diversity reflect a causal relationship at smaller timescales, in which coevolutionary selection is directly responsible for the formation of new species. In this synthesis, we critically evaluate evidence for the often-invoked hypothesis that coevolution is an important process promoting biological diversification. We conclude that the lack of widespread evidence for coevolutionary diversification may be best explained by the fact that coevolution's importance in diversification varies depending on the type of interaction and the scale of the diversification under consideration.

  17. Coevolution: A synergy in biology and ecology

    Directory of Open Access Journals (Sweden)

    WenJun Zhang

    2015-06-01

    Full Text Available Synergy refers to that in an open and complex system consisting of a large number of subsystems, far from equilibrium, its subsystems interact in a nonlinear way to produce synergistic effects and thus make the system generate a self-organization structure in space/time with certain functions. Biologists and ecologists, tend to use coevolution/coadaptation to represent the terminology "synergy". Coevolution and research methodology were briefly discussed in present paper.

  18. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  19. Coevolution of gene expression among interacting proteins

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, Hunter B.; Hirsh, Aaron E.; Wall, Dennis P.; Eisen,Michael B.

    2004-03-01

    Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

  20. Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

    Science.gov (United States)

    Corbi, Jonathan; Dutheil, Julien Y; Damerval, Catherine; Tenaillon, Maud I; Manicacci, Domenica

    2012-03-01

    ADP-glucose pyrophosphorylase (AGPase) is a key enzyme of starch biosynthesis. In the green plant lineage, it is composed of two large (LSU) and two small (SSU) sub-units encoded by paralogous genes, as a consequence of several rounds of duplication. First, our aim was to detect specific patterns of molecular evolution following duplication events and the divergence between monocotyledons and dicotyledons. Secondly, we investigated coevolution between amino acids both within and between sub-units. A phylogeny of each AGPase sub-unit was built using all gymnosperm and angiosperm sequences available in databases. Accelerated evolution along specific branches was tested using the ratio of the non-synonymous to the synonymous substitution rate. Coevolution between amino acids was investigated taking into account compensatory changes between co-substitutions. We showed that SSU paralogues evolved under high functional constraints during angiosperm radiation, with a significant level of coevolution between amino acids that participate in SSU major functions. In contrast, in the LSU paralogues, we identified residues under positive selection (1) following the first LSU duplication that gave rise to two paralogues mainly expressed in angiosperm source and sink tissues, respectively; and (2) following the emergence of grass-specific paralogues expressed in the endosperm. Finally, we found coevolution between residues that belong to the interaction domains of both sub-units. Our results support the view that coevolution among amino acid residues, especially those lying in the interaction domain of each sub-unit, played an important role in AGPase evolution. First, within SSU, coevolution allowed compensating mutations in a highly constrained context. Secondly, the LSU paralogues probably acquired tissue-specific expression and regulatory properties via the coevolution between sub-unit interacting domains. Finally, the pattern we observed during LSU evolution is consistent

  1. Landscape co-evolution and river discharge.

    Science.gov (United States)

    van der Velde, Ype; Temme, Arnaud

    2015-04-01

    Fresh water is crucial for society and ecosystems. However, our ability to secure fresh water resources under climatic and anthropogenic change is impaired by the complexity of interactions between human society, ecosystems, soils, and topography. These interactions cause landscape properties to co-evolve, continuously changing the flow paths of water through the landscape. These co-evolution driven flow path changes and their effect on river runoff are, to-date, poorly understood. In this presentation we introduce a spatially distributed landscape evolution model that incorporates growing vegetation and its effect on evapotranspiration, interception, infiltration, soil permeability, groundwater-surface water exchange and erosion. This landscape scale (10km2) model is calibrated to evolve towards well known empirical organising principles such as the Budyko curve and Hacks law under different climate conditions. To understand how positive and negative feedbacks within the model structure form complex landscape patterns of forests and peat bogs that resemble observed landscapes under humid and boreal climates, we analysed the effects of individual processes on the spatial distribution of vegetation and river peak and mean flows. Our results show that especially river peak flows and droughts decrease with increasing evolution of the landscape, which is a result that has direct implications for flood management.

  2. Understanding molecular interactions between scavenger receptor A and its natural product inhibitors through molecular modeling studies.

    Science.gov (United States)

    Pagare, Piyusha P; Zaidi, Saheem A; Zhang, Xiaomei; Li, Xia; Yu, Xiaofei; Wang, Xiang-Yang; Zhang, Yan

    2017-10-01

    Scavenger receptor A (SRA), as an immune regulator, has been shown to play important roles in lipid metabolism, cardiovascular diseases, and pathogen recognition. Several natural product inhibitors of SRA have been studied for their potential application in modulating SRA functions. To understand the binding mode of these inhibitors on SRA, we conducted systematic molecular modeling studies in order to identify putative binding domain(s) that may be responsible for their recognition to the receptor as well as their inhibitory activity. Treatment of SRA with one of the natural product inhibitors, rhein, led to significant dissociation of SRA oligomers to its trimer and dimer forms, which further supported our hypothesis on their putative mechanism of action. Such information is believed to shed light on design of more potent inhibitors for the receptor in order to develop potential therapeutics through immune system modulation. Published by Elsevier Inc.

  3. Recent developments in the molecular genetic understanding of breast cancer

    NARCIS (Netherlands)

    Devilee, P.; Schuuring, E.; van de Vijver, M. J.; Cornelisse, C. J.

    1994-01-01

    The molecular genetic characterization of breast cancer has implicated or identified the involvement of at least 10 distinct gene alterations in the genesis or progression of this disease. The genes involved fall into three distinct classes, possibly reflecting their particular function in the

  4. Public Space and the Coevolution of Digital and Digitized Media

    Directory of Open Access Journals (Sweden)

    Niels Ole Finneman

    2006-09-01

    Full Text Available In the first section it is argued that digital media are characterized by a variable functional architecture. In the second section, it is argued that theories af replacement and convergence ought to be replaced by a theory of coevolution in order to understand how the internet and mo- bile media are integrated in different societies. The third section discus- ses whether the influence of the old media in this coevolutionary pro- cess also implies that differences in the existing media systems will lead to different developments in the internet.

  5. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    Science.gov (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  6. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    ) in water and organic solvents. The effects of solvent on structural and dynamical enzyme properties are studied, and special attention is given to how enzyme properties in organic solvents are affected by the hydration level, which is shown to be related to the water activity. In experimental studies...... of enzyme kinetics in non-aqueous media, it has been a fruitful approach to fix the enzyme hydration level by controlling the water activity of the medium. In this work, a protocol is therefore developed for determining the water activity in non-aqueous protein simulations. The method relies on determining......This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...

  7. Understanding the Molecular Genetics of Basal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Cristina Pellegrini

    2017-11-01

    Full Text Available Basal cell carcinoma (BCC is the most common human cancer and represents a growing public health care problem. Several tumor suppressor genes and proto-oncogenes have been implicated in BCC pathogenesis, including the key components of the Hedgehog pathway, PTCH1 and SMO, the TP53 tumor suppressor, and members of the RAS proto-oncogene family. Aberrant activation of the Hedgehog pathway represents the molecular driver in basal cell carcinoma pathogenesis, with the majority of BCCs carrying somatic point mutations, mainly ultraviolet (UV-induced, and/or copy-loss of heterozygosis in the PTCH1 gene. Recent advances in sequencing technology allowed genome-scale approaches to mutation discovery, identifying new genes and pathways potentially involved in BCC carcinogenesis. Mutational and functional analysis suggested PTPN14 and LATS1, both effectors of the Hippo–YAP pathway, and MYCN as new BCC-associated genes. In addition, emerging reports identified frequent non-coding mutations within the regulatory promoter sequences of the TERT and DPH3-OXNAD1 genes. Thus, it is clear that a more complex genetic network of cancer-associated genes than previously hypothesized is involved in BCC carcinogenesis, with a potential impact on the development of new molecular targeted therapies. This article reviews established knowledge and new hypotheses regarding the molecular genetics of BCC pathogenesis.

  8. Understanding the Molecular Genetics of Basal Cell Carcinoma

    Science.gov (United States)

    Maturo, Maria Giovanna; Ciciarelli, Valeria; Gutiérrez García-Rodrigo, Carlota; Fargnoli, Maria Concetta

    2017-01-01

    Basal cell carcinoma (BCC) is the most common human cancer and represents a growing public health care problem. Several tumor suppressor genes and proto-oncogenes have been implicated in BCC pathogenesis, including the key components of the Hedgehog pathway, PTCH1 and SMO, the TP53 tumor suppressor, and members of the RAS proto-oncogene family. Aberrant activation of the Hedgehog pathway represents the molecular driver in basal cell carcinoma pathogenesis, with the majority of BCCs carrying somatic point mutations, mainly ultraviolet (UV)-induced, and/or copy-loss of heterozygosis in the PTCH1 gene. Recent advances in sequencing technology allowed genome-scale approaches to mutation discovery, identifying new genes and pathways potentially involved in BCC carcinogenesis. Mutational and functional analysis suggested PTPN14 and LATS1, both effectors of the Hippo–YAP pathway, and MYCN as new BCC-associated genes. In addition, emerging reports identified frequent non-coding mutations within the regulatory promoter sequences of the TERT and DPH3-OXNAD1 genes. Thus, it is clear that a more complex genetic network of cancer-associated genes than previously hypothesized is involved in BCC carcinogenesis, with a potential impact on the development of new molecular targeted therapies. This article reviews established knowledge and new hypotheses regarding the molecular genetics of BCC pathogenesis. PMID:29165358

  9. Molecular tools in understanding the evolution of Vibrio cholerae

    Science.gov (United States)

    Rahaman, Md. Habibur; Islam, Tarequl; Colwell, Rita R.; Alam, Munirul

    2015-01-01

    Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies. PMID:26500613

  10. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    International Nuclear Information System (INIS)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-01-01

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

  11. Nasopharyngeal carcinoma: understanding its molecular biology at a fine scale.

    Science.gov (United States)

    Paul, Prosenjit; Deka, Himangshu; Malakar, Arup K; Halder, Binata; Chakraborty, Supriyo

    2018-01-01

    Among all cancers, the incidence of nasopharyngeal carcinoma (NPC) is quite high in the endemic regions. NPC is a head and neck cancer with poor survival rate, and is rare throughout most of the world but common in certain geographic areas, like southern Asia and some regions of North East India (Nagaland, Manipur, and Mizoram). A clear understanding of its etiology is still lacking, but NPC is widely suspected to be the result of both genetic susceptibility and exposure to environmental factors or Epstein-Barr virus infection. Diagnosis in the early stages needs a high index of clinical acumen, and, although most cross-sectional imaging investigations show the tumor with precision, confirmation is dependent on histology. This article reviews all related research reports on NPC histopathological classifications worldwide that have been published within the past 20 years. Genome-wide association studies suggested that there might be common disease mechanisms between that disease and NPC. Personalized management rules, quality assessment of life in patients, and an understanding of the essential mechanisms of recurrence could be directed toward research into recurrent NPC. Hence, this literature would offer otolaryngologists a deeper insight into the etiological and management aspects of NPC.

  12. Understanding the Molecular Aspects of Tetrahydrocannabinol and Cannabidiol as Antioxidants

    Directory of Open Access Journals (Sweden)

    Káthia M. Honório

    2013-10-01

    Full Text Available An antioxidant mechanism of tetrahydrocannabinol (THC and cannabidiol (CBD were compared with a simplified model of α-tocopherol, butylhydroxytoluene and hydroxytoluene in order to understand the antioxidant nature of THC and CBD molecules using DFT. The following electronic properties were evaluated: frontier orbitals nature, ionization potential, O-H bond dissociation energy (BDEOH, stabilization energy, and spin density distribution. An important factor that shows an influence in the antioxidant property of THC is the electron abstraction at the phenol position. Our data indicate that the decrease of the HOMO values and the highest ionization potential values are related to phenol, ether, and alkyl moieties. On the other hand, BDEOH in molecules with the cyclohexenyl group at ortho position of phenol are formed from lower energies than the molecules with an ether group at the meta position. In the light of our results, the properties calculated here predict that THC has a sightly higher antioxidant potential than CBD.

  13. Using STOQS to Understand Molecular Biology and Oceanographic Data

    Science.gov (United States)

    McCann, M. P.; Ryan, J. P.; Messié, M.; Harvey, J.; Cline, D.; Michisaki, R.

    2014-12-01

    Advances in technology enable us to collect massive amounts of diverse data. With the ability to collect more data, the problem of comparative analysis becomes increasing difficult. The Monterey Bay Aquarium Research Institute (MBARI) designed the Spatial Temporal Oceanographic Query System (STOQS) to create new capabilities for scientists to gain insight from data collected by oceanographic platforms. STOQS uses a geospatial database and a web-based user interface (UI) to allow scientists to explore large collections of data. The UI is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter and platform space. A user may zoom into a feature of interest and select it, initiating a filter operation updating the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and check boxes can be selected to generate a number of different types of visualizations. These include color-filled temporal section plots, parameter-parameter plots, and both 2D and 3D spatial visualizations. The ISO/IEC 19775-1, Extensible 3D (X3D) standard provides the technology for presenting 3D data in a web browser. STOQS has been in use at MBARI for four years and is helping us manage and visualize data from month-long multi-platform observational campaigns. These campaigns produce tens of millions of diverse measurements. These volumes are too great to really understand - even with an effective data exploration UI. Effective management of these diverse data in STOQS is achieved through a two-step harmonization process: 1) conversion of all data to OGC CF-NetCDF Discrete Sampling Geometry feature types and 2) loading all data into the STOQS data model. Having all of the data easily accessible via this data model made development of the UI possible. This same method of access is also being used for development of visualization and analysis programs for tasks that cannot be executed within the UI

  14. Laboratory Activities to Support Student Understanding of the Molecular Mechanisms of Mutation & Natural Selection

    Science.gov (United States)

    Hubler, Tina; Adams, Patti; Scammell, Jonathan

    2015-01-01

    The molecular basis of evolution is an important and challenging concept for students to understand. In a previous article, we provided some of the scientific background necessary to teach this topic. This article features a series of laboratory activities demonstrating that molecular events can alter the genomes of organisms. These activities are…

  15. The coevolution of long-term pair bonds and cooperation.

    Science.gov (United States)

    Song, Z; Feldman, M W

    2013-05-01

    The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  16. Molecular Approaches to Understanding C & N Dynamics in MArine Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Arturo Massol; James Tiedje; Jizhong Zhou; Allan Devol

    2007-05-16

    Continental margin sediments constitute only about 10% of the total sediment surface area in the world’s oceans, nevertheless they are the dominant sites of nitrogen (N) cycling. Recent studies suggest that the oceanic nitrogen budget is unbalanced, primarily due to a higher nitrogen removal rate in contrast to the fixation rate, and it has been suggested that denitrification activity contributes significantly to this imbalance. Although denitrification in marine environments has been studied intensively at the process level, little is known about the species abundance, composition, distribution, and functional differences of the denitrifying population. Understanding the diversity of microbial populations in marine environments, their responses to various environmental factors such as NO3-, and how this impact the rate of denitrification is critical to predict global N dynamics. Environmental Microbiology has the prompt to study the influence of each microbial population on a biogeochemical process within a given ecosystem. Culture-dependent and –independent techniques using nucleic acid probes can access the identity and activity of cultured and uncultured microorganisms. Nucleic acid probes can target distintict genes which set phylogenetic relationships, such as rDNA 16S, DNA gyrase (gyrB) and RNA polymerase sigma 70 factor (rpoD). In the other hand, the genetic capabilities and their expression could be tracked using probes that target several functional genes, such as nirS, nirK, nosZ, and nifH, which are genes involved in denitrification. Selective detection of cells actively expressing functional genes within a community using In Situ Reverse Transcription-PCR (ISRT-PCR) could become a powerful culture-independent technique in microbial ecology. Here we describe an approach to study the expression of nirS genes in denitrifying bacteria. Pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans, as well as co-cultures with non

  17. Physical mode of bacteria and virus coevolution

    Science.gov (United States)

    Han, Pu; Niestemski, Liang; Deem, Michael

    2013-03-01

    Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.

  18. Collaborative Problem-solution Co-evolution in Creative Design

    DEFF Research Database (Denmark)

    Wiltschnig, Stefan; Christensen, Bo; J. Ball, Linden

    2013-01-01

    . The analysis revealed that co-evolution episodes occurred regularly and embodied various directional transitions between problem and solution spaces. Moreover, the team leader often initiated this co-evolution. Co-evolution episodes linked with other creative activities such as analogising and mental......Creative design concepts are often viewed as developing iteratively, with the design problem and solutions ‘co-evolving’ in a mutually adaptive manner. We report a study examining whether the co-evolution concept captures the creativity arising in collaborative, team-based design practice...... simulation and there was a clear association between co-evolution and expressions of epistemic uncertainty, suggesting that designers were dealing with considerable complexity and ambiguity. Our findings support the view that co-evolution is the ‘engine’ of creativity in collaborative design....

  19. A coevolution analysis for identifying protein-protein interactions by Fourier transform

    Science.gov (United States)

    Yin, Changchuan; Yau, Stephen S. -T.

    2017-01-01

    Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI). PMID:28430779

  20. A coevolution analysis for identifying protein-protein interactions by Fourier transform.

    Directory of Open Access Journals (Sweden)

    Changchuan Yin

    Full Text Available Protein-protein interactions (PPIs play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA; however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40. The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI.

  1. Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    Science.gov (United States)

    2016-06-06

    grant for Education , Research and Engineering: The number of undergraduates funded by your agreement who graduated during this period and intend to work...40Ca magneto-optical trap ( MOT ) co- located with a linear quadrupole radio- frequency ion trap (LQT) system. The 40Ca MOT laser...the linear quadrupole trap, while ultracold atoms are collected in a MOT . The ultracold atoms quickly cool the atomic/molecular ion’s

  2. Co-Evolution: Law and Institutions in International Ethics Research

    NARCIS (Netherlands)

    Millar-Schijf, Carla C.J.M.; Cheng, Philip Y.K.; Choi, Chong-Ju

    2009-01-01

    Despite the importance of the co-evolution approach in various branches of research, such as strategy, organisation theory, complexity, population ecology, technology and innovation (Lewin et al., 1999; March, 1991), co-evolution has been relatively neglected in international business and ethics

  3. Advanced understanding on electronic structure of molecular semiconductors and their interfaces

    Science.gov (United States)

    Akaike, Kouki

    2018-03-01

    Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

  4. The impact of molecular data on our understanding of bee phylogeny and evolution.

    Science.gov (United States)

    Danforth, Bryan N; Cardinal, Sophie; Praz, Christophe; Almeida, Eduardo A B; Michez, Denis

    2013-01-01

    Our understanding of bee phylogeny has improved over the past fifteen years as a result of new data, primarily nucleotide sequence data, and new methods, primarily model-based methods of phylogeny reconstruction. Phylogenetic studies based on single or, more commonly, multilocus data sets have helped resolve the placement of bees within the superfamily Apoidea; the relationships among the seven families of bees; and the relationships among bee subfamilies, tribes, genera, and species. In addition, molecular phylogenies have played an important role in inferring evolutionary patterns and processes in bees. Phylogenies have provided the comparative framework for understanding the evolution of host-plant associations and pollen specialization, the evolution of social behavior, and the evolution of parasitism. In this paper, we present an overview of significant discoveries in bee phylogeny based primarily on the application of molecular data. We review the phylogenetic hypotheses family-by-family and then describe how the new phylogenetic insights have altered our understanding of bee biology.

  5. Cows Desiring to Be Milked? Milking Robots and the Co-Evolution of Ethics and Technology on Dutch Dairy Farms

    NARCIS (Netherlands)

    Driessen, C.P.G.; Heutinck, L.F.M.

    2015-01-01

    Ethical concerns regarding agricultural practices can be found to co-evolve with technological developments. This paper aims to create an understanding of ethics that is helpful in debating technological innovation by studying such a co-evolution process in detail: the development and adoption of

  6. The challenges of understanding glycolipid functions: An open outlook based on molecular simulations

    DEFF Research Database (Denmark)

    Manna, M.; Rog, T.; Vattulainen, I.

    2014-01-01

    and molecular simulations can be used to shed light on the role of glycolipids in membrane structure and dynamics, receptor function, and other phenomena related to emergence of diseases such as Parkinson's. The cases we discuss highlight the challenge to understand how glycolipids function in cell membranes......Glycolipids are the most complex lipid type in cell membranes, characterized by a great diversity of different structures and functions. The underlying atomistic/molecular interactions and mechanisms associated with these functions are not well understood. Here we discuss how atomistic...

  7. Co-evolution of Industry Strategies and Government Policies: The Case of the Brazilian Automotive Industry

    Directory of Open Access Journals (Sweden)

    Roberto Gonzalez Duarte

    2017-07-01

    Full Text Available This study examines the evolution of the automotive industry in Brazil and its key drivers. We argue that the rules of the game – industry policies – are an outcome of exchanges between the host government and industry. These arise from changes in economic and political environments and interdependence between industry and the country’s economy. To this end, we draw upon literature on institutions and co-evolution to understand the industry footprint over a 50-year period, as well as its relationship with changes in government policies. This study generates new insights on institutional and co-evolution political perspectives by showing that the rules of the game are not only the making of the government, but are also the result of interdependencies between industry and government.

  8. Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

    Science.gov (United States)

    Endah Saraswati, Teguh; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

    2017-01-01

    Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH3). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory.

  9. Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

    International Nuclear Information System (INIS)

    Saraswati, Teguh Endah; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

    2017-01-01

    Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH_3). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory. (paper)

  10. "Intelligent" design of molecular materials: Understanding the concepts of design in supramolecular synthesis of network solids

    Science.gov (United States)

    Moulton, Brian D.

    This work endeavors to delineate modern paradigms for crystal engineering, i.e. the design and supramolecular synthesis of functional molecular materials. Paradigms predicated on an understanding of the geometry of polygons and polyhedra are developed. The primary focus is on structural determination by single crystal X-ray crystallography, structural interpretation using a suite of graphical visualization and molecular modeling software, and on the importance of proper graphical representation in the presentation and explanation of crystal structures. A detailed analysis of a selected series of crystal structures is presented. The reduction of these molecular networks to schematic representations that illustrate their fundamental connectivity facilitates the understanding of otherwise complex supramolecular solids. Circuit symbols and Schlafli notation are used to describe the network topologies, which enables networks of different composition and metrics to be easily compared. This reveals that molecular orientations in the crystals and networks are commensurate with networks that can be derived from spherical close packed lattices. The development of a logical design strategy for a new class of materials based on our understanding of the chemical composition and topology of these networks is described. The synthesis and crystal structure of a series of new materials generated by exploitation of this design strategy is presented, in addition to a detailed analysis of the topology of these materials and their relationship to a 'parent' structure. In summary, this dissertation demonstrates that molecular polygons can self-assemble at their vertexes to produce molecular architectures and crystal structures that are consistent with long established geometric dogma. The design strategy represents a potentially broad ranging approach to the design of nanoporous structures from a wide range of chemical components that are based on molecular shape rather than chemical

  11.  Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula

    DEFF Research Database (Denmark)

    De Mita, Stephane; Santoni, Sylvain; Hochu, Isabelle

    2006-01-01

     Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity...... domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular coevolution between microorganisms' signaling molecules and legumes' receptors....

  12. Therapeutics in Osteoarthritis Based on an Understanding of Its Molecular Pathogenesis

    Directory of Open Access Journals (Sweden)

    Ju-Ryoung Kim

    2018-02-01

    Full Text Available Osteoarthritis (OA is the most prevalent joint disease in older people and is characterized by the progressive destruction of articular cartilage, synovial inflammation, changes in subchondral bone and peri-articular muscle, and pain. Because our understanding of the aetiopathogenesis of OA remains incomplete, we haven’t discovered a cure for OA yet. This review appraises novel therapeutics based on recent progress in our understanding of the molecular pathogenesis of OA, including pro-inflammatory and pro-catabolic mediators and the relevant signalling mechanisms. The changes in subchondral bone and peri-articular muscle accompanying cartilage damage are also reviewed.

  13. DP 71 AND BETA DYSTROGLYCAN INTERACTION: A MOLECULAR MODELING APPROACH TO UNDERSTAND DUCHENNE MUSCULAR DYSTROPHY

    Directory of Open Access Journals (Sweden)

    Simanti Bhattacharya,

    2013-12-01

    Full Text Available Dp 71 is the most prevalent and widely expressed non muscle isoform of dystrophin (Dp and its mutations are associated with Duchenne muscular dystrophy, a severe form of muscular disorder. Dp 71 deviates from the canonical Dp by means of its truncated N terminal which also has abolished certain amino acids that comprise WW domain in the canonical form. This WW domain is very crucial for Dp’s interaction with partner proteins to establish a bridge between extra cellular matrices and cellular cytoskeleton. In our current study we have employed molecular modeling technique to understand the structural architecture of the N terminal region of Dp 71 and its deviation from the canonical form. We have further extended our studies to analyze the interaction probabilities between Dp 71 and β-DG applying molecular docking. Our studies for the first time have revealed that in spite of the underlying differences in terms of amino acids and structural organization, Dp 71 can interact with β-DG with its N terminal region which shares the similar molecular surface with the canonical form of Dp. These findings have opened up a platform to investigate the molecular interactions, spatio temporal orientations of the amino acids of Dp 71 and β-DG to understand the onset of DMD in much more greater detail

  14. MISTIC: mutual information server to infer coevolution

    DEFF Research Database (Denmark)

    Simonetti, Franco L.; Teppa, Elin; Chernomoretz, Ariel

    2013-01-01

    MISTIC (mutual information server to infer coevolution) is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families. The server outputs a graphical visualization...... containing all results can be downloaded. The server is available at http://mistic.leloir.org.ar. In summary, MISTIC allows for a comprehensive, compact, visually rich view of the information contained within an MSA in a manner unique to any other publicly available web server. In particular, the use...... of several information-related quantities using a circos representation. This provides an integrated view of the MSA in terms of (i) the mutual information (MI) between residue pairs, (ii) sequence conservation and (iii) the residue cumulative and proximity MI scores. Further, an interactive interface...

  15. Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

    Science.gov (United States)

    Cowled, Brendan D.; Ward, Michael P.; Laffan, Shawn W.; Galea, Francesca; Garner, M. Graeme; MacDonald, Anna J.; Marsh, Ian; Muellner, Petra; Negus, Katherine; Quasim, Sumaiya; Woolnough, Andrew P.; Sarre, Stephen D.

    2012-01-01

    Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa) population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design) versus transmission (molecular case series study design) and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37–45%). The median Salmonella DICE coefficient (or Salmonella genetic similarity) was 52% (interquartile range [IQR]: 42–62%). Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density) determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is driven by

  16. Integrating survey and molecular approaches to better understand wildlife disease ecology.

    Directory of Open Access Journals (Sweden)

    Brendan D Cowled

    Full Text Available Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design versus transmission (molecular case series study design and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37-45%. The median Salmonella DICE coefficient (or Salmonella genetic similarity was 52% (interquartile range [IQR]: 42-62%. Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is

  17. Reno-endocrinal disorders: A basic understanding of the molecular genetics

    Directory of Open Access Journals (Sweden)

    Sukhminder Jit Singh Bajwa

    2012-01-01

    Full Text Available The successful management of endocrine diseases is greatly helped by the complete understanding of the underlying pathology. The knowledge about the molecular genetics contributes immensely in the appropriate identification of the causative factors of the diseases and their subsequent management. The fields of nephrology and endocrinology are also interrelated to a large extent. Besides performing the secretory functions, the renal tissue also acts as target organ for many hormones such as antidiuretic hormone (ADH, atrial natriuretic peptides (ANP, and aldosterone. Understanding the molecular genetics of these hormones is important because the therapeutic interventions in many of these conditions is related to shared renal and endocrine functions, including the anemia of renal disease, chronic kidney disease, mineral bone disorders, and hypertension related to chronic kidney disease. Their understanding and in-depth knowledge is very essential in designing and formulating the therapeutic plans and innovating new management strategies. However, we still have to go a long way in order to completely understand the various confounding causative relationships between the pathology and disease of these reno-endocrinal manifestations.

  18. Coevolution in the Galapagos: An Example for the Biology Classroom.

    Science.gov (United States)

    Biggs, Alton L.

    1990-01-01

    Several examples of coevolution which can be used in biology classes are presented. Discussed are evolutionary processes in general, giant cacti, and reptile and cacti association. The effects of human interference are briefly described. (CW)

  19. Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco.

    Science.gov (United States)

    Wang, Mingcong; Kapralov, Maxim V; Anisimova, Maria

    2011-09-23

    One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories. We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time. Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

  20. Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

    Directory of Open Access Journals (Sweden)

    Kapralov Maxim V

    2011-09-01

    Full Text Available Abstract Background One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories. Results We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time. Conclusion Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

  1. NEW CO-EVOLUTION STRATEGIES OF THIRD MILLENNIUM; METHODOLOGICAL ASPECT

    Directory of Open Access Journals (Sweden)

    E. K. Bulygo

    2006-01-01

    Full Text Available The paper is devoted to an application of the co-evolution methodology to the social space. Principles of instability and non-linearity that are typical for contemporary natural science are used as a theoretical background of a new social methodology. Authors try to prove that the co-evolution strategy has a long pre-history in the ancient oriental philosophy and manifests itself in forms of modem culture

  2. Co-evolution of electric and telecommunications networks

    Energy Technology Data Exchange (ETDEWEB)

    Rivkin, S.R.

    1998-05-01

    There are potentially significant societal benefits in co-evolution between electricity and telecommunications in the areas of common infrastructure, accelerated deployment of distributed energy, tighter integration of information flow for energy management and distribution, and improved customer care. With due regard for natural processes that are more potent than any regulation and more real than any ideology, the gains from co-evolution would far outweigh the attenuated and speculative savings from restructuring of electricity that is too simplistic.

  3. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  4. Choroid plexus papillomas: advances in molecular biology and understanding of tumorigenesis.

    Science.gov (United States)

    Safaee, Michael; Oh, Michael C; Bloch, Orin; Sun, Matthew Z; Kaur, Gurvinder; Auguste, Kurtis I; Tihan, Tarik; Parsa, Andrew T

    2013-03-01

    Choroid plexus papillomas are rare, benign tumors originating from the choroid plexus. Although generally found within the ventricular system, they can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. We sought to review recent advances in our understanding of the molecular biology and oncogenic pathways associated with this disease. A comprehensive PubMed literature review was conducted to identify manuscripts discussing the clinical, molecular, and genetic features of choroid plexus papillomas. Articles concerning diagnosis, treatment, and long-term patient outcomes were also reviewed. The introduction of atypical choroid plexus papilloma as a distinct entity has increased the need for accurate histopathologic diagnosis. Advances in immunohistochemical staining have improved our ability to differentiate choroid plexus papillomas from other intracranial tumors or metastatic lesions using combinations of key markers and mitotic indices. Recent findings have implicated Notch3 signaling, the transcription factor TWIST1, platelet-derived growth factor receptor, and the tumor necrosis factor-related apoptosis-inducing ligand pathway in choroid plexus papilloma tumorigenesis. A combination of commonly occurring chromosomal duplications and deletions has also been identified. Surgical resection remains the standard of care, although chemotherapy and radiotherapy may be considered for recurrent or metastatic lesions. While generally considered benign, these tumors possess a complex biology that sheds insight into other choroid plexus tumors, particularly malignant choroid plexus carcinomas. Improving our understanding of the molecular biology, genetics, and oncogenic pathways associated with this tumor will allow for the development of targeted therapies and improved outcomes for patients with this disease.

  5. A Molecular-Scale Understanding of Cohesion and Fracture in P3HT:Fullerene Blends

    KAUST Repository

    Tummala, Naga Rajesh

    2015-04-21

    Quantifying cohesion and understanding fracture phenomena in thin-film electronic devices are necessary for improved materials design and processing criteria. For organic photovoltaics (OPVs), the cohesion of the photoactive layer portends its mechanical flexibility, reliability, and lifetime. Here, the molecular mechanism for the initiation of cohesive failure in bulk heterojunction (BHJ) OPV active layers derived from the semiconducting polymer poly-(3-hexylthiophene) [P3HT] and two mono-substituted fullerenes is examined experimentally and through molecular-dynamics simulations. The results detail how, under identical conditions, cohesion significantly changes due to minor variations in the fullerene adduct functionality, an important materials consideration that needs to be taken into account across fields where soluble fullerene derivatives are used.

  6. Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory?

    Science.gov (United States)

    Marshall, Paul; Bredy, Timothy W.

    2016-07-01

    A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. So far, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here, we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.

  7. F-Type Bacteriocins of Listeria monocytogenes: a New Class of Phage Tail-Like Structures Reveals Broad Parallel Coevolution between Tailed Bacteriophages and High-Molecular-Weight Bacteriocins.

    Science.gov (United States)

    Lee, Grace; Chakraborty, Urmi; Gebhart, Dana; Govoni, Gregory R; Zhou, Z Hong; Scholl, Dean

    2016-10-15

    Listeria monocytogenes is a significant foodborne human pathogen that can cause severe disease in certain high-risk individuals. L. monocytogenes is known to produce high-molecular-weight, phage tail-like bacteriocins, or "monocins," upon induction of the SOS system. In this work, we purified and characterized monocins and found them to be a new class of F-type bacteriocins. The L. monocytogenes monocin genetic locus was cloned and expressed in Bacillus subtilis, producing specifically targeted bactericidal particles. The receptor binding protein, which determines target cell specificity, was identified and engineered to change the bactericidal spectrum. Unlike the F-type pyocins of Pseudomonas aeruginosa, which are related to lambda-like phage tails, monocins are more closely related to TP901-1-like phage tails, structures not previously known to function as bacteriocins. Monocins therefore represent a new class of phage tail-like bacteriocins. It appears that multiple classes of phage tails and their related bacteriocins have coevolved separately in parallel. Phage tail-like bacteriocins (PTLBs) are structures widespread among the members of the bacterial kingdom that are evolutionarily related to the DNA delivery organelles of phages (tails). We identified and characterized "monocins" of Listeria monocytogenes and showed that they are related to the tail structures of TP901-1-like phages, structures not previously known to function as bacteriocins. Our results show that multiple types of envelope-penetrating machines have coevolved in parallel to function either for DNA delivery (phages) or as membrane-disrupting bacteriocins. While it has commonly been assumed that these structures were coopted from phages, we cannot rule out the opposite possibility, that ancient phages coopted complex bacteriocins from the cell, which then underwent adaptations to become efficient at translocating DNA. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. Gene-culture coevolution in whales and dolphins.

    Science.gov (United States)

    Whitehead, Hal

    2017-07-24

    Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.

  9. Gene–culture coevolution in whales and dolphins

    Science.gov (United States)

    Whitehead, Hal

    2017-01-01

    Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother–calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother–offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene–culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology. PMID:28739936

  10. ROS signalling in a destabilised world: A molecular understanding of climate change.

    Science.gov (United States)

    Carmody, Melanie; Waszczak, Cezary; Idänheimo, Niina; Saarinen, Timo; Kangasjärvi, Jaakko

    2016-09-20

    Climate change results in increased intensity and frequency of extreme abiotic and biotic stress events. In plants, reactive oxygen species (ROS) accumulate in proportion to the level of stress and are major signalling and regulatory metabolites coordinating growth, defence, acclimation and cell death. Our knowledge of ROS homeostasis, sensing, and signalling is therefore key to understanding the impacts of climate change at the molecular level. Current research is uncovering new insights into temporal-spatial, cell-to-cell and systemic ROS signalling pathways, particularly how these affect plant growth, defence, and more recently acclimation mechanisms behind stress priming and long term stress memory. Understanding the stabilising and destabilising factors of ROS homeostasis and signalling in plants exposed to extreme and fluctuating stress will concomitantly reveal how to address future climate change challenges in global food security and biodiversity management. Copyright © 2016 Elsevier GmbH. All rights reserved.

  11. College Chemistry Students' Understanding of Potential Energy in the Context of Atomic-Molecular Interactions

    Science.gov (United States)

    Becker, Nicole M.; Cooper, Melanie M.

    2014-01-01

    Understanding the energy changes that occur as atoms and molecules interact forms the foundation for understanding the macroscopic energy changes that accompany chemical processes. In order to identify ways to scaffold students' understanding of the connections between atomic-molecular and macroscopic energy perspectives, we conducted a…

  12. MISTIC: Mutual information server to infer coevolution.

    Science.gov (United States)

    Simonetti, Franco L; Teppa, Elin; Chernomoretz, Ariel; Nielsen, Morten; Marino Buslje, Cristina

    2013-07-01

    MISTIC (mutual information server to infer coevolution) is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families. The server outputs a graphical visualization of several information-related quantities using a circos representation. This provides an integrated view of the MSA in terms of (i) the mutual information (MI) between residue pairs, (ii) sequence conservation and (iii) the residue cumulative and proximity MI scores. Further, an interactive interface to explore and characterize the MI network is provided. Several tools are offered for selecting subsets of nodes from the network for visualization. Node coloring can be set to match different attributes, such as conservation, cumulative MI, proximity MI and secondary structure. Finally, a zip file containing all results can be downloaded. The server is available at http://mistic.leloir.org.ar. In summary, MISTIC allows for a comprehensive, compact, visually rich view of the information contained within an MSA in a manner unique to any other publicly available web server. In particular, the use of circos representation of MI networks and the visualization of the cumulative MI and proximity MI concepts is novel.

  13. Field-omics—understanding large-scale molecular data from field crops

    Science.gov (United States)

    Alexandersson, Erik; Jacobson, Dan; Vivier, Melané A.; Weckwerth, Wolfram; Andreasson, Erik

    2014-01-01

    The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: “Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with ‘-omics’ data.” PMID:24999347

  14. Features of Knowledge Building in Biology: Understanding Undergraduate Students’ Ideas about Molecular Mechanisms

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. PMID:26931398

  15. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design.

    Science.gov (United States)

    Albanaz, Amanda T S; Rodrigues, Carlos H M; Pires, Douglas E V; Ascher, David B

    2017-06-01

    Mutations introduce diversity into genomes, leading to selective changes and driving evolution. These changes have contributed to the emergence of many of the current major health concerns of the 21st century, from the development of genetic diseases and cancers to the rise and spread of drug resistance. The experimental systematic testing of all mutations in a system of interest is impractical and not cost-effective, which has created interest in the development of computational tools to understand the molecular consequences of mutations to aid and guide rational experimentation. Areas covered: Here, the authors discuss the recent development of computational methods to understand the effects of coding mutations to protein function and interactions, particularly in the context of the 3D structure of the protein. Expert opinion: While significant progress has been made in terms of innovative tools to understand and quantify the different range of effects in which a mutation or a set of mutations can give rise to a phenotype, a great gap still exists when integrating these predictions and drawing causality conclusions linking variants. This often requires a detailed understanding of the system being perturbed. However, as part of the drug development process it can be used preemptively in a similar fashion to pharmacokinetics predictions, to guide development of therapeutics to help guide the design and analysis of clinical trials, patient treatment and public health policy strategies.

  16. Mass Spectrometry-Based Approaches to Understand the Molecular Basis of Memory

    Science.gov (United States)

    Pontes, Arthur H.; de Sousa, Marcelo V.

    2016-01-01

    The central nervous system is responsible for an array of cognitive functions such as memory, learning, language, and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enabled the identification and quantification of thousands of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis. PMID:27790611

  17. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar Singh

    2018-04-01

    Full Text Available Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host–pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

  18. Understanding the reaction of nuclear graphite with molecular oxygen: Kinetics, transport, and structural evolution

    Science.gov (United States)

    Kane, Joshua J.; Contescu, Cristian I.; Smith, Rebecca E.; Strydom, Gerhard; Windes, William E.

    2017-09-01

    For the next generation of nuclear reactors, HTGRs specifically, an unlikely air ingress warrants inclusion in the license applications of many international regulators. Much research on oxidation rates of various graphite grades under a number of conditions has been undertaken to address such an event. However, consequences to the reactor result from the microstructural changes to the graphite rather than directly from oxidation. The microstructure is inherent to a graphite's properties and ultimately degradation to the graphite's performance must be determined to establish the safety of reactor design. To understand the oxidation induced microstructural change and its corresponding impact on performance, a thorough understanding of the reaction system is needed. This article provides a thorough review of the graphite-molecular oxygen reaction in terms of kinetics, mass and energy transport, and structural evolution: all three play a significant role in the observed rate of graphite oxidation. These provide the foundations of a microstructurally informed model for the graphite-molecular oxygen reaction system, a model kinetically independent of graphite grade, and capable of describing both the observed and local oxidation rates under a wide range of conditions applicable to air-ingress.

  19. A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution

    Science.gov (United States)

    Hartl, Daniel L.

    2016-01-01

    Much of the public lacks a proper understanding of Darwinian evolution, a problem that can be addressed with new learning and teaching approaches to be implemented both inside the classroom and in less formal settings. Few analogies have been as successful in communicating the basics of molecular evolution as John Maynard Smith’s protein space analogy (1970), in which he compared protein evolution to the transition between the terms WORD and GENE, changing one letter at a time to yield a different, meaningful word (in his example, the preferred path was WORD → WORE → GORE → GONE → GENE). Using freely available computer science tools (Google Books Ngram Viewer), we offer an update to Maynard Smith’s analogy and explain how it might be developed into an exploratory and pedagogical device for understanding the basics of molecular evolution and, more specifically, the adaptive landscape concept. We explain how the device works through several examples and provide resources that might facilitate its use in multiple settings, ranging from public engagement activities to formal instruction in evolution, population genetics, and computational biology. PMID:27736867

  20. Mass Spectrometry-based Approaches to Understand the Molecular Basis of Memory

    Directory of Open Access Journals (Sweden)

    Arthur Henriques Pontes

    2016-10-01

    Full Text Available The central nervous system is responsible for an array of cognitive functions such as memory, learning, language and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS have enable the identification and quantification of thousand of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.

  1. Mass Spectrometry-based Approaches to Understand the Molecular Basis of Memory

    Science.gov (United States)

    Pontes, Arthur; de Sousa, Marcelo

    2016-10-01

    The central nervous system is responsible for an array of cognitive functions such as memory, learning, language and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enable the identification and quantification of thousand of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.

  2. The molecular biology of prostate cancer: current understanding and clinical implications.

    Science.gov (United States)

    Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

    2017-12-27

    With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the

  3. Co-evolution of atmospheres, life, and climate.

    Science.gov (United States)

    Grenfell, J Lee; Rauer, Heike; Selsis, Franck; Kaltenegger, Lisa; Beichman, Charles; Danchi, William; Eiroa, Carlos; Fridlund, Malcolm; Henning, Thomas; Herbst, Tom; Lammer, Helmut; Léger, Alain; Liseau, René; Lunine, Jonathan; Paresce, Francesco; Penny, Alan; Quirrenbach, Andreas; Röttgering, Huub; Schneider, Jean; Stam, Daphne; Tinetti, Giovanna; White, Glenn J

    2010-01-01

    After Earth's origin, our host star, the Sun, was shining 20-25% less brightly than today. Without greenhouse-like conditions to warm the atmosphere, our early planet would have been an ice ball, and life may never have evolved. But life did evolve, which indicates that greenhouse gases must have been present on early Earth to warm the planet. Evidence from the geological record indicates an abundance of the greenhouse gas CO(2). CH(4) was probably present as well; and, in this regard, methanogenic bacteria, which belong to a diverse group of anaerobic prokaryotes that ferment CO(2) plus H(2) to CH(4), may have contributed to modification of the early atmosphere. Molecular oxygen was not present, as is indicated by the study of rocks from that era, which contain iron carbonate rather than iron oxide. Multicellular organisms originated as cells within colonies that became increasingly specialized. The development of photosynthesis allowed the Sun's energy to be harvested directly by life-forms. The resultant oxygen accumulated in the atmosphere and formed the ozone layer in the upper atmosphere. Aided by the absorption of harmful UV radiation in the ozone layer, life colonized Earth's surface. Our own planet is a very good example of how life-forms modified the atmosphere over the planets' lifetime. We show that these facts have to be taken into account when we discover and characterize atmospheres of Earth-like exoplanets. If life has originated and evolved on a planet, then it should be expected that a strong co-evolution occurred between life and the atmosphere, the result of which is the planet's climate.

  4. Co-evolution of insect proteases and plant protease inhibitors.

    Science.gov (United States)

    Jongsma, Maarten A; Beekwilder, Jules

    2011-08-01

    Plants are at the basis of the food chain, but there is no such thing as a "free lunch" for herbivores. To promote reproductive success, plants evolved multi-layered defensive tactics to avoid or discourage herbivory. To the detriment of plants, herbivores, in turn, evolved intricate strategies to find, eat, and successfully digest essential plant parts to raise their own offspring. In this battle the digestive tract is the arena determining final victory or defeat as measured by growth or starvation of the herbivore. Earlier, specific molecular opponents were identified as proteases and inhibitors: digestive proteases of herbivores evolved structural motifs to occlude plant protease inhibitors, or alternatively, the insects evolved proteases capable of specifically degrading the host plant inhibitors. In response plant inhibitors evolved hyper-variable and novel protein folds to remain active against potential herbivores. At the level of protease regulation in herbivorous insects, it was shown that inhibition-insensitive digestive proteases are up-regulated when sensitive proteases are inhibited. The way this regulation operates in mammals is known as negative feedback by gut-luminal factors, so-called 'monitor peptides' that are sensitive to the concentration of active enzymes. We propose that regulation of gut enzymes by endogenous luminal factors has been an open invitation to plants to "hijack" this regulation by evolving receptor antagonists, although yet these plant factors have not been identified. In future research the question of the co-evolution of insect proteases and plant inhibitors should, therefore, be better approached from a systems level keeping in mind that evolution is fundamentally opportunistic and that the plant's fitness is primarily improved by lowering the availability of essential amino acids to an herbivore by any available mechanism.

  5. Coevolution of axon guidance molecule Slit and its receptor Robo.

    Directory of Open Access Journals (Sweden)

    Qi Yu

    Full Text Available Coevolution is important for the maintenance of the interaction between a ligand and its receptor during evolution. The interaction between axon guidance molecule Slit and its receptor Robo is critical for the axon repulsion in neural tissues, which is evolutionarily conserved from planarians to humans. However, the mechanism of coevolution between Slit and Robo remains unclear. In this study, we found that coordinated amino acid changes took place at interacting sites of Slit and Robo by comparing the amino acids at these sites among different organisms. In addition, the high level correlation between evolutionary rate of Slit and Robo was identified in vertebrates. Furthermore, the sites under positive selection of slit and robo were detected in the same lineage such as mosquito and teleost. Overall, our results provide evidence for the coevolution between Slit and Robo.

  6. Molecular Understanding of Fullerene - Electron Donor Interactions in Organic Solar Cells

    KAUST Repository

    Ryno, Sean

    2016-09-13

    Organic solar cells hold promise of providing low-cost, renewable power generation, with current devices providing up to 13% power conversion efficiency. The rational design of more performant systems requires an in-depth understanding of the interactions between the electron donating and electron accepting materials within the active layers of these devices. Here, we explore works that give insight into the intermolecular interactions between electron donors and electron acceptors, and the impact of molecular orientations and environment on these interactions. We highlight, from a theoretical standpoint, the effects of intermolecular interactions on the stability of charge carriers at the donor/acceptor interface and in the bulk and how these interactions influence the nature of the charge transfer states as wells as the charge separation and charge transport processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Understanding DNA Under Oxidative Stress and Sensitization: The Role of Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Antonio eMonari

    2015-07-01

    Full Text Available DNA is constantly exposed to damaging threats coming from oxidative stress, i.e. from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, that dynamical effects are to be taken into account, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized.In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanism and also to the rational design of new chemo-therapeutic agents.

  8. Understanding the molecular mechanism of pulse current charging for stable lithium-metal batteries.

    Science.gov (United States)

    Li, Qi; Tan, Shen; Li, Linlin; Lu, Yingying; He, Yi

    2017-07-01

    High energy and safe electrochemical storage are critical components in multiple emerging fields of technologies. Rechargeable lithium-metal batteries are considered to be promising alternatives for current lithium-ion batteries, leading to as much as a 10-fold improvement in anode storage capacity (from 372 to 3860 mAh g -1 ). One of the major challenges for commercializing lithium-metal batteries is the reliability and safety issue, which is often associated with uneven lithium electrodeposition (lithium dendrites) during the charging stage of the battery cycling process. We report that stable lithium-metal batteries can be achieved by simply charging cells with square-wave pulse current. We investigated the effects of charging period and frequency as well as the mechanisms that govern this process at the molecular level. Molecular simulations were performed to study the diffusion and the solvation structure of lithium cations (Li + ) in bulk electrolyte. The model predicts that loose association between cations and anions can enhance the transport of Li + and eventually stabilize the lithium electrodeposition. We also performed galvanostatic measurements to evaluate the cycling behavior and cell lifetime under pulsed electric field and found that the cell lifetime can be more than doubled using certain pulse current waveforms. Both experimental and simulation results demonstrate that the effectiveness of pulse current charging on dendrite suppression can be optimized by choosing proper time- and frequency-dependent pulses. This work provides a molecular basis for understanding the mechanisms of pulse current charging to mitigating lithium dendrites and designing pulse current waveforms for stable lithium-metal batteries.

  9. Paving the way to understand humoral autoantibody epilepsy on the molecular level

    Directory of Open Access Journals (Sweden)

    Guiscard eSeebohm

    2015-07-01

    Full Text Available Correct function of neuronal networks is enabled by a delicate interplay among neurons communicating with each other. One of the keys is the communication at chemical synapses where neurotransmitters like glutamate, GABA and glycine enable signal transfer over the synaptic cleft. Thereby, the neurotransmitters are released from the presynapse and bind as ligands to specific receptors at the postsynaptic side to allow for modulation of the postsynaptic membrane potentials. The postsynaptic electrical signal, which is highly modulated by voltage gated ion channels, spreads over the dendritic tree and is thus integrated to allow for generation of action potentials at the axon hillock. This concert of receptors and voltage gated ion channels depends on correct function of all its components. Misfunction of receptors and/or voltage-gated potassium channels (VGKC leads to diverse adverse effects in patients. Such malfunctions can be the result of inherited genetic alterations or pharmacological side effects by drugs. Recently, auto-antibodies targeting receptor or channel complexes like NMDAR, AMPAR, GABA-receptors, glycine-receptors, LGI1 or CASPR2 (previously termed VGKC-complex antibodies have been discovered. The presence of specific auto-antibodies against these targets associates with severe forms of antibody-mediated encephalitis. Understanding the molecular details of auto-antibody actions on receptor and VGKC complexes is highly desirable and may open the path to develop specific therapies to treat humoral autoimmune encephalitis. Here, we summarize the current knowledge and discuss technical approaches to fill the gap of knowledge. These techniques include electrophysiology, biochemical approaches for epitope mapping and in silico modeling to simulate molecular interactions between autoantibody and its molecular target.

  10. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms.

    Science.gov (United States)

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. © 2016 K. Southard et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  11. Understanding the molecular mechanisms of human microtia via a pig model of HOXA1 syndrome

    Directory of Open Access Journals (Sweden)

    Ruimin Qiao

    2015-06-01

    Full Text Available Microtia is a congenital malformation of the outer ears. Although both genetic and environmental components have been implicated in microtia, the genetic causes of this innate disorder are poorly understood. Pigs have naturally occurring diseases comparable to those in humans, providing exceptional opportunity to dissect the molecular mechanism of human inherited diseases. Here we first demonstrated that a truncating mutation in HOXA1 causes a monogenic disorder of microtia in pigs. We further performed RNA sequencing (RNA-Seq analysis on affected and healthy pig embryos (day 14.25. We identified a list of 337 differentially expressed genes (DEGs between the normal and mutant samples, shedding light on the transcriptional network involving HOXA1. The DEGs are enriched in biological processes related to cardiovascular system and embryonic development, and neurological, renal and urological diseases. Aberrant expressions of many DEGs have been implicated in human innate deformities corresponding to microtia-associated syndromes. After applying three prioritizing algorithms, we highlighted appealing candidate genes for human microtia from the 337 DEGs. We searched for coding variants of functional significance within six candidate genes in 147 microtia-affected individuals. Of note, we identified one EVC2 non-synonymous mutation (p.Asp1174Asn as a potential disease-implicating variant for a human microtia-associated syndrome. The findings advance our understanding of the molecular mechanisms underlying human microtia, and provide an interesting example of the characterization of human disease-predisposing variants using pig models.

  12. What Is Our Current Understanding of PrPSc-Associated Neurotoxicity and Its Molecular Underpinnings?

    Science.gov (United States)

    Hughes, Daniel; Halliday, Mark

    2017-12-01

    The prion diseases are a collection of fatal, transmissible neurodegenerative diseases that cause rapid onset dementia and ultimately death. Uniquely, the infectious agent is a misfolded form of the endogenous cellular prion protein, termed PrP Sc . Despite the identity of the molecular agent remaining the same, PrP Sc can cause a range of diseases with hereditary, spontaneous or iatrogenic aetiologies. However, the link between PrP Sc and toxicity is complex, with subclinical cases of prion disease discovered, and prion neurodegeneration without obvious PrP Sc deposition. The toxic mechanisms by which PrP Sc causes the extensive neuropathology are still poorly understood, although recent advances are beginning to unravel the molecular underpinnings, including oxidative stress, disruption of proteostasis and induction of the unfolded protein response. This review will discuss the diseases caused by PrP Sc toxicity, the nature of the toxicity of PrP Sc , and our current understanding of the downstream toxic signaling events triggered by the presence of PrP Sc .

  13. Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bhatia, Harsh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gyulassy, Attila [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ong, Mitchell [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Draeger, Erik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pask, John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-09-27

    The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.

  14. Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening.

    Science.gov (United States)

    Palma, José M; Corpas, Francisco J; del Río, Luís A

    2011-08-12

    Fruit ripening is a developmental complex process which occurs in higher plants and involves a number of stages displayed from immature to mature fruits that depend on the plant species and the environmental conditions. Nowadays, the importance of fruit ripening comes mainly from the link between this physiological process in plants and the economic repercussions as a result of one of the human activities, the agricultural industry. In most cases, fruit ripening is accompanied by colour changes due to different pigment content and increases in sugar levels, among others. Major physiological modifications that affect colour, texture, flavour, and aroma are under the control of both external (light and temperature) and internal (developmental gene regulation and hormonal control) factors. Due to the huge amount of metabolic changes that take place during ripening in fruits from higher plants, the accomplishment of new throughput methods which can provide a global evaluation of this process would be desirable. Differential proteomics of immature and mature fruits would be a useful tool to gain information on the molecular changes which occur during ripening, but also the investigation of fruits at different ripening stages will provide a dynamic picture of the whole transformation of fruits. This subject is furthermore of great interest as many fruits are essential for human nutrition. Thus far different maturation profiles have been reported specific for each crop species. In this work, a thorough review of the proteomic database from fruit development and maturation of important crop species will be updated to understand the molecular physiology of fruits at ripening stages. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of

  16. Co-evolution of firms, industries and networks in space

    NARCIS (Netherlands)

    Wal, A.L.J. ter; Boschma, R.A.

    2011-01-01

    Co-evolution of firms, industries and networks in space, Regional Studies. The cluster literature suffers from a number of shortcomings: (1) it often neglects that cluster firms are heterogeneous in terms of capabilities; (2) it tends to overemphasize the importance of geographical proximity and

  17. Coevolution of variability models and related software artifacts

    DEFF Research Database (Denmark)

    Passos, Leonardo; Teixeira, Leopoldo; Dinztner, Nicolas

    2015-01-01

    models coevolve with other artifact types, we study a large and complex real-world variant-rich software system: the Linux kernel. Specifically, we extract variability-coevolution patterns capturing changes in the variability model of the Linux kernel with subsequent changes in Makefiles and C source...

  18. Exploration, Exploitation and Co-evolution in Innovation Networks

    NARCIS (Netherlands)

    V.A. Gilsing (Victor)

    2003-01-01

    textabstractThis PhD-thesis describes the co-evolution of sectoral characteristics, networks of firms and the embedded learning regime from the perspective of a sectoral innovation system (SIS). More specifically, this research aims to shed light on how the institutional environment of a SIS

  19. Contrasting effects of intralocus sexual conflict on sexually antagonistic coevolution

    NARCIS (Netherlands)

    Pennell, Tanya M; de Haas, Freek J H; Morrow, Edward H; van Doorn, G Sander

    2016-01-01

    Evolutionary conflict between the sexes can induce arms races in which males evolve traits that are detrimental to the fitness of their female partners, and vice versa. This interlocus sexual conflict (IRSC) has been proposed as a cause of perpetual intersexual antagonistic coevolution with

  20. Co-evolution of social networks and continuous actor attributes

    NARCIS (Netherlands)

    Niezink, Nynke M.D.; Snijders, Tom A.B.

    2017-01-01

    Social networks and the attributes of the actors in these networks are not static; they may develop interdependently over time. The stochastic actor-oriented model allows for statistical inference on the mechanisms driving this co-evolution process. In earlier versions of this model, dynamic actor

  1. Toward a molecular understanding of psychostimulant actions using genetically engineered dopamine receptor knockout mice as model systems.

    Science.gov (United States)

    Zhang, J; Xu, M

    2001-01-01

    A major focus in studying the progression and prevention of addictive diseases has been to understand the molecular and cellular mechanisms underlying drug addiction. The brain dopaminergic system plays a central role in reward and motivation and is thought to be the main neural substrate for the actions of abusive drugs. We have used the gene targeting technology to generate dopamine D1 and D3 receptor knockout mice and used these mice as model systems to gain a molecular understanding of acute effects of psychostimulants cocaine and amphetamine. The use of a combined approach involving behavioral, electrophysiological as well as molecular studies has allowed us to define initially the roles of dopamine D1 and D3 receptors in the acute effects of psychostimulants and will enable us to understand mechanisms underlying their chronic actions in the future.

  2. New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.; Dohnalkova, Alice C.

    2017-06-01

    Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. The aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.

  3. Towards understanding the molecular basis of ion channel modulation by lipids: Mechanistic models and current paradigms.

    Science.gov (United States)

    Poveda, José A; Marcela Giudici, A; Lourdes Renart, M; Morales, Andrés; González-Ros, José M

    2017-09-01

    Research on ion channel modulation has become a hot topic because of the key roles these membrane proteins play in both prokaryotic and eukaryotic organisms. In this respect, lipid modulation adds to the overall modulatory mechanisms as a potential via to find new pharmacological targets for drug design based on interfering with lipid/channel interactions. However, our knowledge in this field is scarce and often circumscribed to the sites where lipids bind and/or its final functional consequences. To fully understand this process it is necessary to improve our knowledge on its molecular basis, from the binding sites to the signalling pathways that derive in structural and functional effects on the ion channel. In this review, we have compiled information about such mechanisms and established a classification into four different modes of action. Afterwards, we have revised in more detail the lipid modulation of Cys-loop receptors and of the potassium channel KcsA, which were chosen as model channels modulated by specific lipids. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity.

    Science.gov (United States)

    Hembry, David H; Althoff, David M

    2016-10-01

    Brood pollination mutualisms-interactions in which specialized insects are both the pollinators (as adults) and seed predators (as larvae) of their host plants-have been influential study systems for coevolutionary biology. These mutualisms include those between figs and fig wasps, yuccas and yucca moths, leafflowers and leafflower moths, globeflowers and globeflower flies, Silene plants and Hadena and Perizoma moths, saxifrages and Greya moths, and senita cacti and senita moths. The high reciprocal diversity and species-specificity of some of these mutualisms have been cited as evidence that coevolution between plants and pollinators drives their mutual diversification. However, the mechanisms by which these mutualisms diversify have received less attention. In this paper, we review key hypotheses about how these mutualisms diversify and what role coevolution between plants and pollinators may play in this process. We find that most species-rich brood pollination mutualisms show significant phylogenetic congruence at high taxonomic scales, but there is limited evidence for the processes of both cospeciation and duplication, and there are no unambiguous examples known of strict-sense contemporaneous cospeciation. Allopatric speciation appears important across multiple systems, particularly in the insects. Host-shifts appear to be common, and widespread host-shifts by pollinators may displace other pollinator lineages. There is relatively little evidence for a "coevolution through cospeciation" model or that coevolution promotes speciation in these systems. Although we have made great progress in understanding the mechanisms by which brood pollination mutualisms diversify, many opportunities remain to use these intriguing symbioses to understand the role of biotic interactions in generating biological diversity. © 2016 Botanical Society of America.

  5. Asymmetry in host and parasitoid diffuse coevolution: when the red queen has to keep a finger in more than one pie

    Directory of Open Access Journals (Sweden)

    Guillemaud Thomas

    2005-03-01

    Full Text Available Abstract Background Coevolution between pairs of antagonistic species is generally considered an endless "arms race" between attack and defense traits to counteract the adaptive responses of the other species. Presentation of the hypothesis When more than two species are involved, diffuse coevolution of hosts and parasitoids could be asymmetric because consumers can choose their prey whereas preys do not choose their predator. This asymmetry may lead to differences in the rate of evolution of the antagonistic species in response to selection. The more long-standing the coevolution of a given pair of antagonistic populations, the higher should be the fitness advantage for the consumer. Therefore, the main prediction of the hypothesis is that the consumer trophic level is more likely to win the coevolution race. Testing the hypothesis We propose testing the asymmetry hypothesis by focusing on the tritrophic system plant/aphid/aphid parasitoid. The analysis of the genetic variability in the virulence of several parasitoid populations and in the defenses of several aphid species or several clones of the same aphid species could be compared. Moreover, the analysis of the neutral population genetic structure of the parasitoid as a function of the aphid host, the plant host and geographic isolation may complement the detection of differences between host and parasitoid trophic specialization. Implications of the hypothesis Genetic structures induced by the arms race between antagonistic species may be disturbed by asymmetry in coevolution, producing neither rare genotype advantages nor coevolutionary hotspots. Thus this hypothesis profoundly changes our understanding of coevolution and may have important implications in terms of pest management.

  6. Co-Evolutions of Ecosystems, Societies, and Economy in Dryland Asia

    Science.gov (United States)

    Chen, Jiquan; Ouyang, Zutao; John, Ranjeet; Dong, Gang; Fan, Peilei

    2015-04-01

    This presentation aims at the interactive changes of the natural system (NS) and the human system (HS) as well as the feedbacks in time and space for dryland Asia where multiple administrative units from several countries experience similar climates, ecosystems, cultures, and traditions but different governments, land uses, economic development, and demographic changes (e.g., ethnical composition). We compiled and examined the changes in major measures for ecosystems (e.g., PAR, LAI, GPP, ET), economy (GDP, export/import, EGS), and human demography (e.g., population, health, education) between 1981 through 2011 (30+ variables) for six Central Asian countries (Afghanistan, Turkmenistan, Tajikistan, Uzbekistan, Kazakhstan, Kyrgyzstan) and two East Asian countries (Mongolia and China). Particular attention was made to understand the co-evolutions of the ratios between the elements of HS and NS, such as: GDP: GPP, PET: FWW, R: PDSI, EGS: GPP, etc., so that feedbacks and interactions can be empirically studied. Spatial and temporal changes of each measure, as well as their ratios, were quantified to highlight the relative contributions of human activities (e.g., policy) and biophysical changes (e.g., climate). We found some tight connections between the HS and NS variables, but the co-evolutions have to be understood in the context of governments, policy, and other major institutional shifts.

  7. Analysis of Strategic Change from the Perspective of Coevolution: a study in an organization of the brazilian electricity sector

    Directory of Open Access Journals (Sweden)

    Cláudia Fabiana Gohr

    2013-08-01

    Full Text Available Strategic change has been a subject in evidence in organizational studies. In recent years, the concept of strategy has evolved from a purely static to a more dynamic point of view, renewing the research agenda on this subject. Thus, this article aims to analyze the strategic change that occurred in a state-owned Brazilian Electric Sector (SEB, using for that, the theory of coevolution as a conceptual framework. Most research about processes of change focuses on private organizations. Therefore, the analysis of strategic change in a state-owned company reveals peculiarities that are not usually addressed in the literature. Furthermore, the theory of coevolution, unlike other theories of analysis, adopts an integrated view on the issue of adaptation of organizations in relation to their environment, thus broadening the understanding of the phenomenon of strategic change. The research was characterized as a case study descriptive and longitudinal. Data were collected through semi-structured interviews, direct observation and document analysis. The results showed that the change in the company occurred in a coevolutionary process involving the competitive dynamics of the sector and institutional system in which organizations and industries interact with each other. The theory of coevolution demonstrated its potential to show results that would normally be withheld if it was adopted a narrower perspective of analysis.

  8. The Impact of Designing and Evaluating Molecular Animations on How Well Middle School Students Understand the Particulate Nature of Matter

    Science.gov (United States)

    Chang, Hsin-Yi; Quintana, Chris; Krajcik, Joseph S.

    2010-01-01

    In this study, we investigated whether the understanding of the particulate nature of matter by students was improved by allowing them to design and evaluate molecular animations of chemical phenomena. We developed Chemation, a learner-centered animation tool, to allow seventh-grade students to construct flipbook-like simple animations to show…

  9. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments.

    Science.gov (United States)

    Kudoh, Hiroshi

    2016-04-01

    Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  10. Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

    CERN Document Server

    Farantos, Stavros C

    2014-01-01

    This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

  11. Chaotic Red Queen coevolution in three-species food chains

    OpenAIRE

    Dercole, F.; Ferriere, R.; Rinaldi, S.

    2010-01-01

    Coevolution between two antagonistic species follows the so-called ‘Red Queen dynamics’ when reciprocal selection results in an endless series of adaptation by one species and counteradaptation by the other. Red Queen dynamics are ‘genetically driven’ when selective sweeps involving new beneficial mutations result in perpetual oscillations of the coevolving traits on the slow evolutionary time scale. Mathematical models have shown that a prey and a predator can coevolve along a genetically dr...

  12. Coevolution of Cryptosporidium tyzzeri and the house mouse (Mus musculus)

    Czech Academy of Sciences Publication Activity Database

    Kváč, Martin; McEvoy, J.; Loudová, M.; Stenger, B.; Sak, Bohumil; Květoňová, Dana; Ditrich, Oleg; Rašková, Veronika; Moriarty, E.; Rost, M.; Macholán, Miloš; Piálek, Jaroslav

    2013-01-01

    Roč. 43, č. 10 (2013), s. 805-817 ISSN 0020-7519 R&D Projects: GA ČR GA206/08/0640; GA MŠk(CZ) LH11061 Institutional support: RVO:60077344 ; RVO:67985904 ; RVO:68081766 Keywords : Cryptosporidium tyzzeri * house mouse * hybrid zone * coevolution Subject RIV: EG - Zoology; GJ - Animal Vermins ; Diseases, Veterinary Medicine (BC-A) Impact factor: 3.404, year: 2013

  13. Coevolution drives the emergence of complex traits and promotes evolvability.

    Directory of Open Access Journals (Sweden)

    Luis Zaman

    2014-12-01

    Full Text Available The evolution of complex organismal traits is obvious as a historical fact, but the underlying causes--including the role of natural selection--are contested. Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time. Others contend that selection, including coevolutionary arms races, can systematically push organisms toward more complex traits. Methodological challenges have largely precluded experimental tests of these hypotheses. Using the Avida platform for digital evolution, we show that coevolution of hosts and parasites greatly increases organismal complexity relative to that otherwise achieved. As parasites evolve to counter the rise of resistant hosts, parasite populations retain a genetic record of past coevolutionary states. As a consequence, hosts differentially escape by performing progressively more complex functions. We show that coevolution's unique feedback between host and parasite frequencies is a key process in the evolution of complexity. Strikingly, the hosts evolve genomes that are also more phenotypically evolvable, similar to the phenomenon of contingency loci observed in bacterial pathogens. Because coevolution is ubiquitous in nature, our results support a general model whereby antagonistic interactions and natural selection together favor both increased complexity and evolvability.

  14. Coevolution drives the emergence of complex traits and promotes evolvability.

    Science.gov (United States)

    Zaman, Luis; Meyer, Justin R; Devangam, Suhas; Bryson, David M; Lenski, Richard E; Ofria, Charles

    2014-12-01

    The evolution of complex organismal traits is obvious as a historical fact, but the underlying causes--including the role of natural selection--are contested. Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time. Others contend that selection, including coevolutionary arms races, can systematically push organisms toward more complex traits. Methodological challenges have largely precluded experimental tests of these hypotheses. Using the Avida platform for digital evolution, we show that coevolution of hosts and parasites greatly increases organismal complexity relative to that otherwise achieved. As parasites evolve to counter the rise of resistant hosts, parasite populations retain a genetic record of past coevolutionary states. As a consequence, hosts differentially escape by performing progressively more complex functions. We show that coevolution's unique feedback between host and parasite frequencies is a key process in the evolution of complexity. Strikingly, the hosts evolve genomes that are also more phenotypically evolvable, similar to the phenomenon of contingency loci observed in bacterial pathogens. Because coevolution is ubiquitous in nature, our results support a general model whereby antagonistic interactions and natural selection together favor both increased complexity and evolvability.

  15. Coevolution of CRISPR bacteria and phage in 2 dimensions

    Science.gov (United States)

    Han, Pu; Deem, Michael

    2014-03-01

    CRISPR (cluster regularly interspaced short palindromic repeats) is a newly discovered adaptive, heritable immune system of prokaryotes. It can prevent infection of prokaryotes by phage. Most bacteria and almost all archae have CRISPR. The CRISPR system incorporates short nucleotide sequences from viruses. These incorporated sequences provide a historical record of the host and predator coevolution. We simulate the coevolution of bacteria and phage in 2 dimensions. Each phage has multiple proto-spacers that the bacteria can incorporate. Each bacterium can store multiple spacers in its CRISPR. Phages can escape recognition by the CRISPR system via point mutation or recombination. We will discuss the different evolutionary consequences of point mutation or recombination on the coevolution of bacteria and phage. We will also discuss an intriguing ``dynamic phase transition'' in the number of phage as a function of time and mutation rate. We will show that due to the arm race between phages and bacteria, the frequency of spacers and proto-spacers in a population can oscillate quite rapidly.

  16. Running with the Red Queen: host-parasite coevolution selects for biparental sex.

    Science.gov (United States)

    Morran, Levi T; Schmidt, Olivia G; Gelarden, Ian A; Parrish, Raymond C; Lively, Curtis M

    2011-07-08

    Most organisms reproduce through outcrossing, even though it comes with substantial costs. The Red Queen hypothesis proposes that selection from coevolving pathogens facilitates the persistence of outcrossing despite these costs. We used experimental coevolution to test the Red Queen hypothesis and found that coevolution with a bacterial pathogen (Serratia marcescens) resulted in significantly more outcrossing in mixed mating experimental populations of the nematode Caenorhabditis elegans. Furthermore, we found that coevolution with the pathogen rapidly drove obligately selfing populations to extinction, whereas outcrossing populations persisted through reciprocal coevolution. Thus, consistent with the Red Queen hypothesis, coevolving pathogens can select for biparental sex.

  17. After 100 years, is coevolution relevant?

    Science.gov (United States)

    Geral I. McDonald

    2011-01-01

    On the 100th anniversary of the introduction of Cronartium ribicola into western North America, it is fitting to assess the philosophical foundation of plant pathology and forest ecology. We should ask whether this foundation provides sufficient understanding of blister rust, other diseases of North American forests, and general forest ecology to insure the application...

  18. Forty Years of Ebolavirus Molecular Biology: Understanding a Novel Disease Agent Through the Development and Application of New Technologies.

    Science.gov (United States)

    Groseth, Allison; Hoenen, Thomas

    2017-01-01

    Molecular biology is a broad discipline that seeks to understand biological phenomena at a molecular level, and achieves this through the study of DNA, RNA, proteins, and/or other macromolecules (e.g., those involved in the modification of these substrates). Consequently, it relies on the availability of a wide variety of methods that deal with the collection, preservation, inactivation, separation, manipulation, imaging, and analysis of these molecules. As such the state of the art in the field of ebolavirus molecular biology research (and that of all other viruses) is largely intertwined with, if not driven by, advancements in the technical methodologies available for these kinds of studies. Here we review of the current state of our knowledge regarding ebolavirus biology and emphasize the associated methods that made these discoveries possible.

  19. Understanding unusual thermal transport behavior in soft materials under mechanical strain - A molecular dynamics study

    Science.gov (United States)

    Murad, Sohail; Puri, Ishwar K.

    2015-04-01

    Experiments have shown a dependence of the thermal conductivity of soft polymer materials on shear stress, which is common to several applications, such as film processing, fiber spinning, blow molding, and vacuum forming. Experiments reveal that the conductivity initially decreases with shear, but then increases as additional shear rate is applied. Based on molecular principles, we hypothesize that when molecules are initially placed under tension and extended, they disentangle, which reduces the number of points of interaction and diminishes the heat flux. Further molecular stretching increases this flux because the molecules are now better axially aligned. Molecular dynamics simulations confirm this competition and reproduce the inflection in the flux-strain relationship, which has not been previously explained.

  20. Using Molecular-Assisted Alpha Taxonomy to Better Understand Red Algal Biodiversity in Bermuda

    Directory of Open Access Journals (Sweden)

    Elisabeth N. Cianciola

    2010-06-01

    Full Text Available Molecular-assisted alpha taxonomy has recently become an effective practice in reassessing biodiversity and floristics for a variety of different organisms. This paper presents a series of examples that have been drawn from biodiversity work being carried out on the marine red algae of Bermuda. Molecular sequencing of DNA from Bermuda samples has already begun to greatly alter the makeup of the flora as it was known just decades ago, and will help set a new database for future comparison as climate change affects species composition in the islands.

  1. Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2015-11-01

    Full Text Available Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO as a flocculant to remove methylene blue (MB from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

  2. Checkpoint recovery in cells: how a molecular understanding can help in the fight against cancer

    Czech Academy of Sciences Publication Activity Database

    Medema, R.H.; Macůrek, Libor

    2011-01-01

    Roč. 3, - (2011), e10 ISSN 1757-594X R&D Projects: GA ČR GAP301/10/1525; GA ČR GPP305/10/P420 Institutional research plan: CEZ:AV0Z50520514 Keywords : checkpoint * DNA damage * cancer Subject RIV: EB - Genetics ; Molecular Biology

  3. Understanding hydration of Zn(2+) in hydrothermal fluids with ab initio molecular dynamics

    NARCIS (Netherlands)

    Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.

    2011-01-01

    With ab initio molecular dynamics simulations, the free-energy profiles of hydrated Zn2+ are calculated for both gaseous and aqueous systems from ambient to supercritical conditions, and from the derived free-energy information, the speciation of hydrated Zn2+ has been revealed. It is shown that the

  4. MADS interactomics : towards understanding the molecular mechanisms of plant MADS-domain transcription factor function

    NARCIS (Netherlands)

    Smaczniak, C.D.

    2013-01-01

    Protein-protein and protein-DNA interactions are essential for the molecular action of transcription factors. By combinatorial binding to target gene promoters, transcription factors are able to up- or down-regulate the expression of these genes. MADS-domain proteins comprise a large family of

  5. Coevolution of Supermassive Black Holes and Galaxies across cosmic times

    Science.gov (United States)

    Aversa, Rossella

    2015-10-01

    Understanding how supermassive black holes (SMBHs) and galaxies coevolve within their host dark matter (DM) halos is a fundamental issue in astrophysics. This thesis is aimed to shed light on this topic. As a first step, we employ the recent wide samples of far-infrared (FIR) selected galaxies followed-up in X-rays, and of X-ray/optically selected active galactic nuclei (AGNs) followed-up in the FIR band, along with the classic data on AGN and stellar luminosity functions at redshift z & 1.5, to probe different stages in the coevolution of SMBHs and their host galaxies. The results of this analysis indicate the following scenario: (i) the star formation in the host galaxy proceeds within a heavily dust-enshrouded medium, at an almost constant rate, over a timescale . 0.5 - 1 Gyr, and then abruptly declines due to quasar feedback; (ii) part of the interstellar medium loses angular momentum, reaches the circum-nuclear regions, at a rate proportional to the star formation, and is temporarily stored into a massive reservoir/proto-torus, wherefrom it can be promptly accreted; (iii) the black hole (BH) grows by accretion in a self-regulated regime with radiative power that can slightly exceed the Eddington limit (L/LEdd . 4), particularly at the highest redshifts; (iv) the ensuing energy feedback from massive BHs, at its maximum, exceeds the stellar one and removes the interstellar gas, thus stopping the star formation and the fueling of the reservoir; (v) afterwards, if the gas stored in the reservoir is enough, a phase of supply-limited accretion follows, whose rate exponentially declines with a timescale of ∼3 e-folding times. We also discuss how the detailed properties and the specific evolution of the reservoir can be investigated via coordinated, high-resolution observations of starforming, strongly lensed galaxies in the (sub-)mm band with ALMA, and in the X-ray band with Chandra and the next generation of X-ray instruments. According to the scenario described

  6. Extremal dynamics and punctuated co-evolution

    Science.gov (United States)

    Sneppen, Kim

    1995-02-01

    Extremal dynamics opens up a new way for understanding the coherence that is observed in some large non-equilibrium systems. Extremal dynamics is characterized by quasistatic motion where only one part of the large system is active at a given instant: the part where a local variable assumes a global extremum value. Extremal dynamics may apply when the parts of the system nearly always are caught in metastable states. Examples from physics may include earthquakes, fluid invasion in porous media and possibly also dynamical roughening of interfaces. We discuss a simple model of extremal dynamics and its application to biological macroevolution. The model can be formulated as an ecology of adapting interacting species. The environment of any given species is affected by other species; hence it may change with time. For low mutation rate the model ecology expands at a self-organized critical state where periods of statis alternate with avalanches of evolutionary changes.

  7. Biological invasions and host-parasite coevolution: different coevolutionary trajectories along separate parasite invasion fronts

    NARCIS (Netherlands)

    Feis, M.E.; Goedknegt, M.A.; Thieltges, D.W.; Buschbaum, C.; Wegner, K.M.

    2016-01-01

    Host–parasite coevolution has rarely been observed in natural systems. Its study often relies on microparasitic infections introducing a potential bias in the estimation of the evolutionary change of host and parasite traits. Using biological invasions as a tool to study host–parasite coevolution in

  8. Complex Behavior in Simple Models of Biological Coevolution

    Science.gov (United States)

    Rikvold, Per Arne

    We explore the complex dynamical behavior of simple predator-prey models of biological coevolution that account for interspecific and intraspecific competition for resources, as well as adaptive foraging behavior. In long kinetic Monte Carlo simulations of these models we find quite robust 1/f-like noise in species diversity and population sizes, as well as power-law distributions for the lifetimes of individual species and the durations of quiet periods of relative evolutionary stasis. In one model, based on the Holling Type II functional response, adaptive foraging produces a metastable low-diversity phase and a stable high-diversity phase.

  9. Acid Hydrolysis and Molecular Density of Phytoglycogen and Liver Glycogen Helps Understand the Bonding in Glycogen α (Composite) Particles

    Science.gov (United States)

    Powell, Prudence O.; Sullivan, Mitchell A.; Sheehy, Joshua J.; Schulz, Benjamin L.; Warren, Frederick J.; Gilbert, Robert G.

    2015-01-01

    Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired. PMID:25799321

  10. Acid hydrolysis and molecular density of phytoglycogen and liver glycogen helps understand the bonding in glycogen α (composite particles.

    Directory of Open Access Journals (Sweden)

    Prudence O Powell

    Full Text Available Phytoglycogen (from certain mutant plants and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired.

  11. Toward understanding the influence of intermolecular interactions and molecular orientation on the chemical enhancement of SERS.

    Science.gov (United States)

    Cabalo, Jerry; Guicheteau, Jason A; Christesen, Steven

    2013-09-19

    Implementation of SERS as an analytical technique is limited because the factors that govern the enhancement of individual vibrational modes are not well understood. Although the chemical effect only accounts for up to two orders of magnitude enhancement, it can still have a significant impact on the consistency of chemical spectral signatures. We report on a combined theoretical and experimental study on the benzenethiol on silver and 4-mercaptophenol on silver systems. The primary and unique finding was that for the benzenethiol on silver system the inclusion of interaction between multiple benzenethiol analyte molecules was essential to account for the relative enhancements observed experimentally. An examination of the molecular orbitals showed sharing of electron density across the entire model of multiple benzenethiol molecules mediated by the metal atoms. The addition of multiple 4-mercaptophenol molecules to the theoretical model had little effect on the predicted spectra, and we attribute this to the fact that a much larger model is necessary to replicate the networks of hydrogen bonds. Molecular orientation was also found to affect the predicted spectra, and it was found that an upright position improved agreement between theoretical and experimental spectra. An analysis of the vibrational frequency shifts between the normal Raman spectrum of the neat compound and the SERS spectrum also suggests that both benzenethiol and 4-mercaptophenol are in an upright position.

  12. Developing teachers' understanding of molecular biology: Building a foundation for students.

    Science.gov (United States)

    Boulay, Rachel; Parisky, Alex; Campbell, Chris

    2010-01-01

    Molecular biology often uses participation in active research laboratories as a form of educational training. However, this approach to learning severely restricts access. As a way of addressing this need, the University of Hawaii launched a project to expand this model to include newly developed online training materials in addition to a hands-on laboratory experience. This paper further explores the process of material development and assessment plans. A pilot case study of a group of advanced biology teachers who embark on learning molecular biology over a four-month period through online training materials and working side-by-side with medical researchers in a laboratory is described. Teachers were positive in reporting about the many areas they gained instruction in although some feedback suggested that the initial online materials over-emphasised abstract concepts and laboratory techniques and did not adequately connect to the active research problems or local context of most interest to teachers and students. The experiences of the teachers are shared in an effort to gain insight on how teachers perceive their participation in the study.

  13. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    Science.gov (United States)

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  14. Recent advances in understanding the molecular mechanism of chloroplast photorelocation movement.

    Science.gov (United States)

    Kong, Sam-Geun; Wada, Masamitsu

    2014-04-01

    Plants are photosynthetic organisms that have evolved unique systems to adapt fluctuating environmental light conditions. In addition to well-known movement responses such as phototropism, stomatal opening, and nastic leaf movements, chloroplast photorelocation movement is one of the essential cellular responses to optimize photosynthetic ability and avoid photodamage. For these adaptations, chloroplasts accumulate at the areas of cells illuminated with low light (called accumulation response), while they scatter from the area illuminated with strong light (called avoidance response). Plant-specific photoreceptors (phototropin, phytochrome, and/or neochrome) mediate these dynamic directional movements in response to incident light position and intensity. Several factors involved in the mechanisms underlying the processes from light perception to actin-based movements have also been identified through molecular genetic approach. This review aims to discuss recent findings in the field relating to how chloroplasts move at molecular levels. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Understanding the molecular behavior of organotin compounds to design their effective use as agrochemicals: exploration via quantum chemistry and experiments.

    Science.gov (United States)

    Ramalho, Teodorico C; Rocha, Marcus V J; da Cunha, Elaine F F; Oliveira, Luiz C A; Carvalho, Kele T C

    2010-10-01

    The high frequency of contamination by herbicides suggests the need for more active and selective agrochemicals. Organotin compounds are the active component of some herbicides, such as Du-Ter and Brestan, which is also a potent inhibitor of the F1Fo ATP Synthase. That is a key enzyme, because the ATP production is one of the major chemical reactions in living organisms. Thus ATP Synthase is regarded as a prime target for organotin compounds. In this line, molecular modeling studies and DFT calculations were performed in order to understand the molecular behavior of those compounds in solution. In addition, we investigated the reaction mechanism by ESI-MS analyses of the diphenyltin dichloride. Our findings indicate that an unstable key-intermediate generated in situ might take place in the reaction with ATP Synthase.

  16. Toward understanding the anticorrosive mechanism of some thiourea derivatives for carbon steel corrosion: A combined DFT and molecular dynamics investigation.

    Science.gov (United States)

    Guo, Lei; Kaya, Savaş; Obot, Ime Bassey; Zheng, Xingwen; Qiang, Yujie

    2017-11-15

    The mutually corroborated density functional theory (DFT) and molecular dynamics (MD) simulation methodology were employed to evaluate the inhibition performance of three thiourea derivatives (Inh1, Inh2, and Inh3) on carbon steel corrosion. Experimental results have shown that the corrosion rate follows the order: Inh3>Inh2>Inh1. Quantum chemical descriptors such as the frontier orbital energies (E HOMO and E LUMO ), the energy gap between E LUMO and E HOMO (ΔE), dipole moment (μ), and Fukui index have been calculated and discussed. Some significant factors such as solvent, temperature, and coverage have been considered when investigating the adsorption of aforementioned thiourea derivatives on Fe(110) surface. Our results provide important atomic/molecular insights into the anticorrosive mechanism of inhibitor molecules, which could help in understanding the organic-metal interface and designing more appropriate organic corrosion inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Basal Cell Carcinoma: From the Molecular Understanding of the Pathogenesis to Targeted Therapy of Progressive Disease

    Directory of Open Access Journals (Sweden)

    Daniela Göppner

    2011-01-01

    Full Text Available Due to intensified research over the past decade, the Hedgehog (HH pathway has been identified as a pivotal defect implicated in roughly 25% of all cancers. As one of the most frequent cancer worldwide, the development of Basal cell carcinoma (BCC due to activation of the HH pathway has been convincingly demonstrated. Thus the discovery of this central tumor-promoting signalling pathway has not only revolutionized the understanding of BCC carcinogenesis but has also enabled the development of a completely novel therapeutic approach. Targeting just a few of several potential mutations, HH inhibitors such as GDC-0449 achieved already the first promising results in metastatic or locally advanced BCC. This paper summarizes the current understanding of BCC carcinogenesis and describes the current “mechanism-based” therapeutic strategies.

  18. Understanding heavy-oil molecular functionality and relations to fluid properties

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, S.I. [Schlumberger, DBR Technology Center, Edmonton AB (Canada)

    2011-07-01

    In the heavy oil industry, knowing oil properties is important to optimizing recovery, transport and refinery. Nitrogen, sulfur and oxygen compounds (NSOs) have an important impact on these properties but this is often overlooked. The purpose of this paper is to analyze the impact of functional groups in connection with heavy oil and asphaltenes. Experiments were carried out with asphaltenes altered by chemical surgery that removed specific functional interactions. Titration calorimetry and fluorescence spectroscopy were then done. Results highlighted the fact that functional groups are of key importance in the determination of heavy oil properties and that acidity can be considered the most important interaction. This paper demonstrated that the determination of specific interactions could be more important in assessing heavy oil properties than understanding their hydrocarbon structure; further work is needed to fully understand the role of sulfur and nitrogen species.

  19. Towards A Predictive First Principles Understanding Of Molecular Adsorption On Graphene

    Science.gov (United States)

    2016-10-05

    lubrication, friction, catalysis , coatings, and sensors to name but a few. In terms of understanding the properties of surfaces and the processes that occur...almost endless list of practical applications and everyday phenomena, such as corrosion, lubrication, friction, catalysis , coatings, crystal formation...methods perform to challenging 2D structures presenting dangling hydrogen bonds. A paper showing these results is submitted for publication [3]. 6

  20. Toward a simple molecular understanding of sum frequency generation at air-water interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Noah-Vanhoucke, Joyce; Smith, Jared D.; Geissler, Phillip L.

    2009-01-13

    Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D{sub 2}O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency-dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response.

  1. Molecular understanding of sulphuric acid-amine particle nucleation in the atmosphere.

    Science.gov (United States)

    Almeida, João; Schobesberger, Siegfried; Kürten, Andreas; Ortega, Ismael K; Kupiainen-Määttä, Oona; Praplan, Arnaud P; Adamov, Alexey; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; David, André; Dommen, Josef; Donahue, Neil M; Downard, Andrew; Dunne, Eimear; Duplissy, Jonathan; Ehrhart, Sebastian; Flagan, Richard C; Franchin, Alessandro; Guida, Roberto; Hakala, Jani; Hansel, Armin; Heinritzi, Martin; Henschel, Henning; Jokinen, Tuija; Junninen, Heikki; Kajos, Maija; Kangasluoma, Juha; Keskinen, Helmi; Kupc, Agnieszka; Kurtén, Theo; Kvashin, Alexander N; Laaksonen, Ari; Lehtipalo, Katrianne; Leiminger, Markus; Leppä, Johannes; Loukonen, Ville; Makhmutov, Vladimir; Mathot, Serge; McGrath, Matthew J; Nieminen, Tuomo; Olenius, Tinja; Onnela, Antti; Petäjä, Tuukka; Riccobono, Francesco; Riipinen, Ilona; Rissanen, Matti; Rondo, Linda; Ruuskanen, Taina; Santos, Filipe D; Sarnela, Nina; Schallhart, Simon; Schnitzhofer, Ralf; Seinfeld, John H; Simon, Mario; Sipilä, Mikko; Stozhkov, Yuri; Stratmann, Frank; Tomé, Antonio; Tröstl, Jasmin; Tsagkogeorgas, Georgios; Vaattovaara, Petri; Viisanen, Yrjo; Virtanen, Annele; Vrtala, Aron; Wagner, Paul E; Weingartner, Ernest; Wex, Heike; Williamson, Christina; Wimmer, Daniela; Ye, Penglin; Yli-Juuti, Taina; Carslaw, Kenneth S; Kulmala, Markku; Curtius, Joachim; Baltensperger, Urs; Worsnop, Douglas R; Vehkamäki, Hanna; Kirkby, Jasper

    2013-10-17

    Nucleation of aerosol particles from trace atmospheric vapours is thought to provide up to half of global cloud condensation nuclei. Aerosols can cause a net cooling of climate by scattering sunlight and by leading to smaller but more numerous cloud droplets, which makes clouds brighter and extends their lifetimes. Atmospheric aerosols derived from human activities are thought to have compensated for a large fraction of the warming caused by greenhouse gases. However, despite its importance for climate, atmospheric nucleation is poorly understood. Recently, it has been shown that sulphuric acid and ammonia cannot explain particle formation rates observed in the lower atmosphere. It is thought that amines may enhance nucleation, but until now there has been no direct evidence for amine ternary nucleation under atmospheric conditions. Here we use the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN and find that dimethylamine above three parts per trillion by volume can enhance particle formation rates more than 1,000-fold compared with ammonia, sufficient to account for the particle formation rates observed in the atmosphere. Molecular analysis of the clusters reveals that the faster nucleation is explained by a base-stabilization mechanism involving acid-amine pairs, which strongly decrease evaporation. The ion-induced contribution is generally small, reflecting the high stability of sulphuric acid-dimethylamine clusters and indicating that galactic cosmic rays exert only a small influence on their formation, except at low overall formation rates. Our experimental measurements are well reproduced by a dynamical model based on quantum chemical calculations of binding energies of molecular clusters, without any fitted parameters. These results show that, in regions of the atmosphere near amine sources, both amines and sulphur dioxide should be considered when assessing the impact of anthropogenic activities on particle formation.

  2. Toward an understanding of the molecular mechanisms of barnacle larval settlement: A comparative transcriptomic approach

    KAUST Repository

    Chen, Zhang-Fan

    2011-07-29

    Background: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Methodology and Principal Findings: Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Conclusions: Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species. © 2011 Chen et al.

  3. Rogue sperm indicate sexually antagonistic coevolution in nematodes.

    Directory of Open Access Journals (Sweden)

    Ronald E Ellis

    2014-07-01

    Full Text Available Intense reproductive competition often continues long after animals finish mating. In many species, sperm from one male compete with those from others to find and fertilize oocytes. Since this competition occurs inside the female reproductive tract, she often influences the outcome through physical or chemical factors, leading to cryptic female choice. Finally, traits that help males compete with each other are sometimes harmful to females, and female countermeasures may thwart the interests of males, which can lead to an arms race between the sexes known as sexually antagonistic coevolution. New studies from Caenorhabditis nematodes suggest that males compete with each other by producing sperm that migrate aggressively and that these sperm may be more likely to win access to oocytes. However, one byproduct of this competition appears to be an increased probability that these sperm will go astray, invading the ovary, prematurely activating oocytes, and sometimes crossing basement membranes and leaving the gonad altogether. These harmful effects are sometimes observed in crosses between animals of the same species but are most easily detected in interspecies crosses, leading to dramatically lowered fitness, presumably because the competitiveness of the sperm and the associated female countermeasures are not precisely matched. This mismatch is most obvious in crosses involving individuals from androdioecious species (which have both hermaphrodites and males, as predicted by the lower levels of sperm competition these species experience. These results suggest a striking example of sexually antagonistic coevolution and dramatically expand the value of nematodes as a laboratory system for studying postcopulatory interactions.

  4. Multispecies Coevolution Particle Swarm Optimization Based on Previous Search History

    Directory of Open Access Journals (Sweden)

    Danping Wang

    2017-01-01

    Full Text Available A hybrid coevolution particle swarm optimization algorithm with dynamic multispecies strategy based on K-means clustering and nonrevisit strategy based on Binary Space Partitioning fitness tree (called MCPSO-PSH is proposed. Previous search history memorized into the Binary Space Partitioning fitness tree can effectively restrain the individuals’ revisit phenomenon. The whole population is partitioned into several subspecies and cooperative coevolution is realized by an information communication mechanism between subspecies, which can enhance the global search ability of particles and avoid premature convergence to local optimum. To demonstrate the power of the method, comparisons between the proposed algorithm and state-of-the-art algorithms are grouped into two categories: 10 basic benchmark functions (10-dimensional and 30-dimensional, 10 CEC2005 benchmark functions (30-dimensional, and a real-world problem (multilevel image segmentation problems. Experimental results show that MCPSO-PSH displays a competitive performance compared to the other swarm-based or evolutionary algorithms in terms of solution accuracy and statistical tests.

  5. CMCpy: Genetic Code-Message Coevolution Models in Python.

    Science.gov (United States)

    Becich, Peter J; Stark, Brian P; Bhat, Harish S; Ardell, David H

    2013-01-01

    Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes ("messages"). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/.

  6. Improving automatic cooperation between UAVs through co-evolution

    Science.gov (United States)

    Smith, James F., III

    2008-04-01

    A fuzzy logic resource manager (RM) that enables a collection of unmanned aerial vehicles (UAVs) to automatically cooperate to make meteorological measurements will be discussed. The RM renders the UAVs autonomous allowing them to change paths and cooperate without human intervention. Innovations related to the "priority for helping" (PH) fuzzy decision tree (FDT) used by the RM will be discussed. The PH FDT permits three types of automatic cooperation between the UAVs. A subroutine of the communications routing algorithm (CRA) used by the RM is also examined. The CRA allows the UAVs to reestablish communications if needed by changing their behavior. A genetic program (GP) based procedure for automatically creating FDTs is briefly described. A GP is an algorithm based on the theory of evolution that automatically evolves mathematical expressions or computer algorithms. The GP data mines a scenario database to automatically create the FDTs. A recently invented co-evolutionary process that allows improvement of the initially data mined FDT will be discussed. Co-evolution uses a genetic algorithm (GA) to evolve scenarios to augment the GP's scenario database. The GP data mines the augmented database to discover an improved FDT. The process is iterated ultimately evolving a very robust FDT. Improvements to the PH FDT offered through co-evolution are discussed. UAV simulations using the improved PH FDT and CRA are provided.

  7. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Kimbrel

    2013-02-01

    Full Text Available Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.

  8. Targeted sequencing of venom genes from cone snail genomes improves understanding of conotoxin molecular evolution.

    Science.gov (United States)

    Phuong, Mark A; Mahardika, Gusti N

    2018-03-05

    To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100X coverage) and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are composed of 1-6 exons and are typically short in length (mean = ∼85bp). Second, we expanded our understanding of the following genetic features of conotoxin evolution: (a) positive selection, where exons coding the mature toxin region were often three times more divergent than their adjacent noncoding regions, (b) expression regulation, with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome (24%-63%), and (c) extensive gene turnover, where Conidae species varied from 120-859 conotoxin gene copies. Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. Overall, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.

  9. Understanding the genetic and molecular pathogenesis of Friedreich’s ataxia through animal and cellular models

    Science.gov (United States)

    Martelli, Alain; Napierala, Marek; Puccio, Hélène

    2012-01-01

    In 1996, a link was identified between Friedreich’s ataxia (FRDA), the most common inherited ataxia in men, and alterations in the gene encoding frataxin (FXN). Initial studies revealed that the disease is caused by a unique, most frequently biallelic, expansion of the GAA sequence in intron 1 of FXN. Since the identification of this link, there has been tremendous progress in understanding frataxin function and the mechanism of FRDA pathology, as well as in developing diagnostics and therapeutic approaches for the disease. These advances were the subject of the 4th International Friedreich’s Ataxia Conference held on 5th–7th May in the Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. More than 200 scientists gathered from all over the world to present the results of research spanning all areas of investigation into FRDA (including clinical aspects, FRDA pathogenesis, genetics and epigenetics of the disease, development of new models of FRDA, and drug discovery). This review provides an update on the understanding of frataxin function, developments of animal and cellular models of the disease, and recent advances in trying to uncover potential molecules for therapy. PMID:22382366

  10. Newtonian chimpanzees? A molecular dynamics approach to understanding decision-making by wild chimpanzees

    Science.gov (United States)

    Westley, Matthew; Sen, Surajit; Sinha, Anindya

    2014-07-01

    In this study, we computationally investigate decision-making by individuals and the ensuing social structure of a primate species, chimpanzees, using Newton's equations of classical mechanics, as opposed to agentbased analyses in which individual chimpanzees make independent decisions. Our model uses molecular dynamics simulation techniques to solve Newton's equations and is able to approximate the movements of female and male chimpanzees, especially in relation to the available food resources, in a manner that is consistent with their observed behavior in natural habitats. It is noteworthy that our Newtonian dynamics-based model may allow us to make certain specific observations of their behaviour, some of which may be difficult to achieve through agent-based modelling exercises or even field studies. Chimpanzees tend to live in fission-fusion social groups, with varying number of individuals, in which both females and males tend to display intrasexual competition for valuable food resources while the males also compete for oestrus females. Most populations of the species are also restricted to a small range of habitats, a clear indication that they are especially vulnerable to the availability and distribution of food sources. With reasonable assumptions of chimpanzee behaviour, we have been able to analyse the clustering behaviour of individuals in relation to local food sources as also patterns of their migration across groups. Our simulated results are qualitatively consistent with field observations conducted on a particular semi-isolated population of chimpanzees in Bossou, Guinea, in western Africa.

  11. Progress in understanding the molecular oxygen paradox - function of mitochondrial reactive oxygen species in cell signaling.

    Science.gov (United States)

    Kuksal, Nidhi; Chalker, Julia; Mailloux, Ryan J

    2017-10-26

    The molecular oxygen (O2) paradox was coined to describe its essential nature and toxicity. The latter characteristic of O2 is associated with the formation of reactive oxygen species (ROS), which can damage structures vital for cellular function. Mammals are equipped with antioxidant systems to fend off the potentially damaging effects of ROS. However, under certain circumstances antioxidant systems can become overwhelmed leading to oxidative stress and damage. Over the past few decades, it has become evident that ROS, specifically H2O2, are integral signaling molecules complicating the previous logos that oxyradicals were unfortunate by-products of oxygen metabolism that indiscriminately damage cell structures. To avoid its potential toxicity whilst taking advantage of its signaling properties, it is vital for mitochondria to control ROS production and degradation. H2O2 elimination pathways are well characterized in mitochondria. However, less is known about how H2O2 production is controlled. The present review examines the importance of mitochondrial H2O2 in controlling various cellular programs and emerging evidence for how production is regulated. Recently published studies showing how mitochondrial H2O2 can be used as a secondary messenger will be discussed in detail. This will be followed with a description of how mitochondria use S-glutathionylation to control H2O2 production.

  12. Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

    Science.gov (United States)

    Mather, Alison E; Vaughan, Timothy G; French, Nigel P

    2015-11-01

    Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. Understanding homogeneous nucleation in solidification of aluminum by molecular dynamics simulations

    Science.gov (United States)

    Mahata, Avik; Asle Zaeem, Mohsen; Baskes, Michael I.

    2018-02-01

    Homogeneous nucleation from aluminum (Al) melt was investigated by million-atom molecular dynamics simulations utilizing the second nearest neighbor modified embedded atom method potentials. The natural spontaneous homogenous nucleation from the Al melt was produced without any influence of pressure, free surface effects and impurities. Initially isothermal crystal nucleation from undercooled melt was studied at different constant temperatures, and later superheated Al melt was quenched with different cooling rates. The crystal structure of nuclei, critical nucleus size, critical temperature for homogenous nucleation, induction time, and nucleation rate were determined. The quenching simulations clearly revealed three temperature regimes: sub-critical nucleation, super-critical nucleation, and solid-state grain growth regimes. The main crystalline phase was identified as face-centered cubic, but a hexagonal close-packed (hcp) and an amorphous solid phase were also detected. The hcp phase was created due to the formation of stacking faults during solidification of Al melt. By slowing down the cooling rate, the volume fraction of hcp and amorphous phases decreased. After the box was completely solid, grain growth was simulated and the grain growth exponent was determined for different annealing temperatures.

  14. Understanding the effect of polylysine architecture on DNA binding using molecular dynamics simulations.

    Science.gov (United States)

    Elder, Robert M; Emrick, Todd; Jayaraman, Arthi

    2011-11-14

    Polycations with varying chemistries and architectures have been synthesized and used in DNA transfection. In this paper we connect poly-L-lysine (PLL) architecture to DNA-binding strength, and in turn transfection efficiency, since experiments have shown that graft-type oligolysine architectures [e.g., poly(cyclooctene-g-oligolysine)] exhibit higher transfection efficiency than linear PLL. We use atomistic molecular dynamics simulations to study structural and thermodynamic effects of polycation-DNA binding for linear PLL and grafted oligolysines of varying graft lengths. Structurally, linear PLL binds in a concerted manner, while each oligolysine graft binds independently of its neighbors in the grafted architecture. Additionally, the presence of a hydrophobic backbone in the grafted architecture weakens binding to DNA compared to linear PLL. The binding free energy varies nonmonotonically with the graft length primarily due to entropic contributions. The binding free energy normalized to the number of bound amines is similar between the grafted and linear architectures at the largest (Poly5) and smallest (Poly2) graft length and stronger than the intermediate graft lengths (Poly3 and Poly4). These trends agree with experimental results that show higher transfection efficiency for Poly3 and Poly4 grafted oligolysines than for Poly5, Poly2, and linear PLL.

  15. [Achieving pathogenesis understanding of ocular diseases by deciphering the underlying molecular pathways].

    Science.gov (United States)

    Huang, Qian

    2005-10-01

    The field of ophthalmology research has experienced a revolution since the 1970's, when molecular biology techniques were gradually and widely adopted. Many of the developments generated impact that went far beyond the field of ophthalmology. A classic case was the identification and characterization of the Retinoblastoma susceptibility gene (Rb), whose impact went far beyond the rare and obscure disease, as it provides key evidence for the concept of tumor suppressor gene and the "two hit" theory of tumor formation. The identification of scores of genes involved in retinitis pigmentosum (pigmentosa), on the other hand, show cases the complexity of multi-factorial diseases. Ophthalmology researchers in China have been quick in integrating these novel tools into their research. However, the field still lags behind in the effective use of these technologies to carry out in-depth inquiries into key disease mechanisms. The advent of "omics" technologies heralded a new era in biomedical research that allows for the global and rapid survey of genetic and biochemical profiles. Effective integration of these novel technologies into ophthalmology research will have far-reaching impact for the whole field.

  16. Current Understanding of Molecular Pathology and Treatment of Cardiomyopathy in Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Tirsa L. E. van Westering

    2015-05-01

    Full Text Available Duchenne muscular dystrophy (DMD is a genetic muscle disorder caused by mutations in the Dmd gene resulting in the loss of the protein dystrophin. Patients do not only experience skeletal muscle degeneration, but also develop severe cardiomyopathy by their second decade, one of the main causes of death. The absence of dystrophin in the heart renders cardiomyocytes more sensitive to stretch-induced damage. Moreover, it pathologically alters intracellular calcium (Ca2+ concentration, neuronal nitric oxide synthase (nNOS localization and mitochondrial function and leads to inflammation and necrosis, all contributing to the development of cardiomyopathy. Current therapies only treat symptoms and therefore the need for targeting the genetic defect is immense. Several preclinical therapies are undergoing development, including utrophin up-regulation, stop codon read-through therapy, viral gene therapy, cell-based therapy and exon skipping. Some of these therapies are undergoing clinical trials, but these have predominantly focused on skeletal muscle correction. However, improving skeletal muscle function without addressing cardiac aspects of the disease may aggravate cardiomyopathy and therefore it is essential that preclinical and clinical focus include improving heart function. This review consolidates what is known regarding molecular pathology of the DMD heart, specifically focusing on intracellular Ca2+, nNOS and mitochondrial dysregulation. It briefly discusses the current treatment options and then elaborates on the preclinical therapeutic approaches currently under development to restore dystrophin thereby improving pathology, with a focus on the heart.

  17. Understanding trophic interactions of Orius spp. (Hemiptera: Anthocoridae) in lettuce crops by molecular methods.

    Science.gov (United States)

    Gomez-Polo, Priscila; Alomar, Oscar; Castañé, Cristina; Aznar-Fernández, Thaïs; Lundgren, Jonathan G; Piñol, Josep; Agustí, Nuria

    2016-02-01

    The aphid Nasonovia ribisnigri (Mosley) (Hemiptera: Aphididae) and the thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) are common pests in Mediterranean lettuce crops, where Orius spp. are common generalist predators. Predation by Orius spp. was studied in a lettuce plot by conventional polymerase chain reaction (PCR) and real-time PCR analyses using specific primers of both main pests. Also, high-throughput sequencing was used to have a wider approach of the diet of these predators in natural field conditions. Molecular analyses indicated a higher predation on N. ribisnigri in spring and on F. occidentalis in summer. Predation on alternative prey, like Collembola, was also found in both seasons. Real-time PCR was more sensitive than conventional PCR in showing the target trophic links, whereas high-throughput sequencing revealed predation on other natural enemies - intraguild predation (IGP), showing other trophic interactions of Orius majusculus within the studied ecosystem. This study gives important information about the trophic relationships present in Mediterranean lettuce crops in different periods of the year. The detected predation by Orius spp. on alternative prey, as well as on other natural enemies, should be further investigated to clarify whether it adds or detracts to the biological control of N. ribisnigri and F. occidentalis. © 2015 Society of Chemical Industry.

  18. Nanomedicine and personalised medicine: understanding the personalisation of health care in the molecular era.

    Science.gov (United States)

    Noury, Mathieu; López, José

    2017-05-01

    Globally supported by public policy and investment, nanomedicine is presented as an ongoing medical revolution that will radically change the practice of health care from diagnostic to therapeutic, and everything in between. One of nanomedicine's major promises is that of personalised medicine, enabling diagnostics and therapeutics tailored to individual needs and developing a truly 'patient-friendly' medical approach. Based on qualitative interviews with nanomedicine researchers in Canada, this article explores the emerging concept of personalised medicine as it becomes entangled with nanomedical research. More precisely, drawing on insights from science studies and the sociology of expectations, it analyses researchers' perceptions of personalised medicine in the cutting edge of current nanomedicine research. Two perceptions of personalisation are identified; a molecular conception of individuality and a technical conception of personalisation. The article concludes by examining the relationship between the two conceptions and contrasts them with the normative reflex of a more expansive conception of personalised medicine. © 2016 Foundation for the Sociology of Health & Illness.

  19. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction.

    Science.gov (United States)

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Leinweber, Peter; Kühn, Oliver

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy: An analytical technique to understand therapeutic responses at the molecular level.

    Science.gov (United States)

    Kalmodia, Sushma; Parameswaran, Sowmya; Yang, Wenrong; Barrow, Colin J; Krishnakumar, Subramanian

    2015-11-16

    Rapid monitoring of the response to treatment in cancer patients is essential to predict the outcome of the therapeutic regimen early in the course of the treatment. The conventional methods are laborious, time-consuming, subjective and lack the ability to study different biomolecules and their interactions, simultaneously. Since; mechanisms of cancer and its response to therapy is dependent on molecular interactions and not on single biomolecules, an assay capable of studying molecular interactions as a whole, is preferred. Fourier Transform Infrared (FTIR) spectroscopy has become a popular technique in the field of cancer therapy with an ability to elucidate molecular interactions. The aim of this study, was to explore the utility of the FTIR technique along with multivariate analysis to understand whether the method has the resolution to identify the differences in the mechanism of therapeutic response. Towards achieving the aim, we utilized the mouse xenograft model of retinoblastoma and nanoparticle mediated targeted therapy. The results indicate that the mechanism underlying the response differed between the treated and untreated group which can be elucidated by unique spectral signatures generated by each group. The study establishes the efficiency of non-invasive, label-free and rapid FTIR method in assessing the interactions of nanoparticles with cellular macromolecules towards monitoring the response to cancer therapeutics.

  1. Genetic and genomic perspective to understand the molecular pathogenesis of keratoconus

    Science.gov (United States)

    Jeyabalan, Nallathambi; Shetty, Rohit; Ghosh, Anuprita; Anandula, Venkata Ramana; Ghosh, Arka Subhra; Kumaramanickavel, Govindasamy

    2013-01-01

    Keratoconus (KC; Mendelian Inheritance in Man (OMIM) 14830) is a bilateral, progressive corneal defect affecting all ethnic groups around the world. It is the leading cause of corneal transplantation. The age of onset is at puberty, and the disorder is progressive until the 3rd–4th decade of life when it usually arrests. It is one of the major ocular problems with significant social and economic impacts as the disease affects young generation. Although genetic and environmental factors are associated with KC, but the precise etiology is still elusive. Results from complex segregation analysis suggests that genetic abnormalities may play an essential role in the susceptibility to KC. Due to genetic heterogeneity, a recent study revealed 17 different genomic loci identified in KC families by linkage mapping in various populations. The focus of this review is to provide a concise update on the current knowledge of the genetic basis of KC and genomic approaches to understand the disease pathogenesis. PMID:23925319

  2. Genetic and genomic perspective to understand the molecular pathogenesis of keratoconus

    Directory of Open Access Journals (Sweden)

    Nallathambi Jeyabalan

    2013-01-01

    Full Text Available Keratoconus (KC; Mendelian Inheritance in Man (OMIM 14830 is a bilateral, progressive corneal defect affecting all ethnic groups around the world. It is the leading cause of corneal transplantation. The age of onset is at puberty, and the disorder is progressive until the 3 rd -4 th decade of life when it usually arrests. It is one of the major ocular problems with significant social and economic impacts as the disease affects young generation. Although genetic and environmental factors are associated with KC, but the precise etiology is still elusive. Results from complex segregation analysis suggests that genetic abnormalities may play an essential role in the susceptibility to KC. Due to genetic heterogeneity, a recent study revealed 17 different genomic loci identified in KC families by linkage mapping in various populations. The focus of this review is to provide a concise update on the current knowledge of the genetic basis of KC and genomic approaches to understand the disease pathogenesis.

  3. Application of molecular epidemiology to understanding campylobacteriosis in the Canterbury region of New Zealand.

    Science.gov (United States)

    Gilpin, B J; Walshe, G; Walsh, G; On, S L; Smith, D; Marshall, J C; French, N P

    2013-06-01

    Pulsed-field gel electrophoresis genotypes of Campylobacter isolates from 603 human patients were compared with 485 isolates from retail offal (primarily chicken and lamb) to identify temporal clusters and possible sources of campylobacteriosis. Detailed epidemiological information was collected from 364 of the patients, and when combined with genotyping data allowed a putative transmission pathway of campylobacteriosis to be assigned for 88% of patients. The sources of infection were 47% food, 28% direct animal contact, 7% overseas travel, 4% person-to-person transmission and 3% water-related. A significant summer increase in campylobacteriosis cases was primarily attributed to an increase in food-related cases. Genotyping of isolates was essential for identifying the likely cause of infection for individuals. However, a more rapid and cheaper typing tool for Campylobacter is needed, which if applied to human and animal isolates on a routine basis could advance greatly our understanding of the ongoing problem of Campylobacter infection in New Zealand.

  4. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Ashour A., E-mail: ashour.ahmed@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany); Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Cairo, Faculty of Science, Department of Chemistry, 12613 Giza (Egypt); Thiele-Bruhn, Sören, E-mail: thiele@uni-trier.de [University of Trier, Soil Science, D-54286 Trier (Germany); Leinweber, Peter, E-mail: peter.leinweber@uni-rostock.de [Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Rostock, Soil Science, D-18051 Rostock (Germany); Kühn, Oliver, E-mail: oliver.kuehn@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany)

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. - Highlights: • Experiment and theory showed that SAA obeys a site-specific sorption on soil surfaces. • SAA-SOM-interaction increases by increasing polarity of SOM sorption site. • H-bonds, dispersion, and π-π-interactions were observed for SAA-SOM-interaction. • Dipole moment and atomic charges of SOM sorption sites control SAA-SOM-interaction. • The Freundlich unit capacities were estimated from the calculated binding energies. • The current SOM model is flexible to describe interactions of SOM with other pollutants.

  5. [Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions

    Science.gov (United States)

    Smith, Grant

    2004-01-01

    The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation

  6. Understanding the cephalopod immune system based on functional and molecular evidence.

    Science.gov (United States)

    Gestal, C; Castellanos-Martínez, S

    2015-09-01

    Cephalopods have the most advanced circulatory and nervous system among the mollusks. Recently, they have been included in the European directive which state that suffering and pain should be minimized in cephalopods used in experimentation. The knowledge about cephalopod welfare is still limited and several gaps are yet to be filled, especially in reference to pathogens, pathologies and immune response of these mollusks. In light of the requirements of the normative, in addition to the ecologic and economic importance of cephalopods, in this review we update the work published to date concerning cephalopod immune system. Significant advances have been reached in relation to the characterization of haemocytes and defensive mechanisms comprising cellular and humoral factors mainly, but not limited, in species of high economic value like Sepia officinalis and Octopus vulgaris. Moreover, the improvement of molecular approaches has helped to discover several immune-related genes/proteins. These immune genes/proteins include antimicrobial peptides, phenoloxidases, antioxidant enzymes, serine protease inhibitor, lipopolysaccharide-induced TNF-α factor, Toll-like receptors, lectins, even clusters of differentiation among others. Most of them have been found in haemocytes but also in gills and digestive gland, and the characterization as well as their precise role in the immune response of cephalopods is still pending to be elucidated. The assessment of immune parameters in cephalopods exposed to contaminants is just starting, but the negative impact of some pollutants on the immune response of the common octopus has been reported. This review summarizes the current status of our knowledge about the cephalopod immune system that seems to be far from simply. On the contrary, the advances gained to date point out a complex innate immunity in cephalopods. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Robustness of coevolution in resolving prisoner's dilemma games on interdependent networks subject to attack

    Science.gov (United States)

    Liu, Penghui; Liu, Jing

    2017-08-01

    Recently, coevolution between strategy and network structure has been established as a rule to resolve social dilemmas and reach optimal situations for cooperation. Many follow-up researches have focused on studying how coevolution helps networks reorganize to deter the defectors and many coevolution methods have been proposed. However, the robustness of the coevolution rules against attacks have not been studied much. Since attacks may directly influence the original evolutionary process of cooperation, the robustness should be an important index while evaluating the quality of a coevolution method. In this paper, we focus on investigating the robustness of an elementary coevolution method in resolving the prisoner's dilemma game upon the interdependent networks. Three different types of time-independent attacks, named as edge attacks, instigation attacks and node attacks have been employed to test its robustness. Through analyzing the simulation results obtained, we find this coevolution method is relatively robust against the edge attack and the node attack as it successfully maintains cooperation in the population over the entire attack range. However, when the instigation probability of the attacked individuals is large or the attack range of instigation attack is wide enough, coevolutionary rule finally fails in maintaining cooperation in the population.

  8. The coevolution of genes and genetic codes: Crick's frozen accident revisited.

    Science.gov (United States)

    Sella, Guy; Ardell, David H

    2006-09-01

    The standard genetic code is the nearly universal system for the translation of genes into proteins. The code exhibits two salient structural characteristics: it possesses a distinct organization that makes it extremely robust to errors in replication and translation, and it is highly redundant. The origin of these properties has intrigued researchers since the code was first discovered. One suggestion, which is the subject of this review, is that the code's organization is the outcome of the coevolution of genes and genetic codes. In 1968, Francis Crick explored the possible implications of coevolution at different stages of code evolution. Although he argues that coevolution was likely to influence the evolution of the code, he concludes that it falls short of explaining the organization of the code we see today. The recent application of mathematical modeling to study the effects of errors on the course of coevolution, suggests a different conclusion. It shows that coevolution readily generates genetic codes that are highly redundant and similar in their error-correcting organization to the standard code. We review this recent work and suggest that further affirmation of the role of coevolution can be attained by investigating the extent to which the outcome of coevolution is robust to other influences that were present during the evolution of the code.

  9. The evolution of reduced antagonism--A role for host-parasite coevolution.

    Science.gov (United States)

    Gibson, A K; Stoy, K S; Gelarden, I A; Penley, M J; Lively, C M; Morran, L T

    2015-11-01

    Why do some host-parasite interactions become less antagonistic over evolutionary time? Vertical transmission can select for reduced antagonism. Vertical transmission also promotes coevolution between hosts and parasites. Therefore, we hypothesized that coevolution itself may underlie transitions to reduced antagonism. To test the coevolution hypothesis, we selected for reduced antagonism between the host Caenorhabditis elegans and its parasite Serratia marcescens. This parasite is horizontally transmitted, which allowed us to study coevolution independently of vertical transmission. After 20 generations, we observed a response to selection when coevolution was possible: reduced antagonism evolved in the copassaged treatment. Reduced antagonism, however, did not evolve when hosts or parasites were independently selected without coevolution. In addition, we found strong local adaptation for reduced antagonism between replicate host/parasite lines in the copassaged treatment. Taken together, these results strongly suggest that coevolution was critical to the rapid evolution of reduced antagonism. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  10. Plant cell walls throughout evolution: towards a molecular understanding of their design principles

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Purbasha; Bosneaga, Elena; Auer, Manfred

    2009-02-16

    Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche,which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are constantly remodelled and reconstructed during the development of an individual plant, and in response to environmental stress or pathogen attacks. Carbohydrate-rich cell walls display complex designs, which together with the presence of phenolic polymers constitutes a barrier for microbes, fungi, and animals. Throughout evolution microbes have co-evolved strategies for efficient breakdown of cell walls. Our current understanding of cell walls and their evolutionary changes are limited as our knowledge is mainly derived from biochemical and genetic studies, complemented by a few targeted yet very informative imaging studies. Comprehensive plant cell wall models will aid in the re-design of plant cell walls for the purpose of commercially viable lignocellulosic biofuel production as well as for the timber, textile, and paper industries. Such knowledge will also be of great interest in the context of agriculture and to plant biologists in general. It is expected that detailed plant cell wall models will require integrated correlative multimodal, multiscale imaging and modelling approaches, which are currently underway.

  11. Extremal Optimization: Methods Derived from Co-Evolution

    Energy Technology Data Exchange (ETDEWEB)

    Boettcher, S.; Percus, A.G.

    1999-07-13

    We describe a general-purpose method for finding high-quality solutions to hard optimization problems, inspired by self-organized critical models of co-evolution such as the Bak-Sneppen model. The method, called Extremal Optimization, successively eliminates extremely undesirable components of sub-optimal solutions, rather than ''breeding'' better components. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, Extremal Optimization improves on a single candidate solution by treating each of its components as species co-evolving according to Darwinian principles. Unlike Simulated Annealing, its non-equilibrium approach effects an algorithm requiring few parameters to tune. With only one adjustable parameter, its performance proves competitive with, and often superior to, more elaborate stochastic optimization procedures. We demonstrate it here on two classic hard optimization problems: graph partitioning and the traveling salesman problem.

  12. Cosmological coevolution of Yang-Mills fields and perfect fluids

    International Nuclear Information System (INIS)

    Barrow, John D.; Jin, Yoshida; Maeda, Kei-ichi

    2005-01-01

    We study the coevolution of Yang-Mills fields and perfect fluids in Bianchi type I universes. We investigate numerically the evolution of the universe and the Yang-Mills fields during the radiation and dust eras of a universe that is almost isotropic. The Yang-Mills field undergoes small amplitude chaotic oscillations, as do the three expansion scale factors which are also displayed by the expansion scale factors of the universe. The results of the numerical simulations are interpreted analytically and compared with past studies of the cosmological evolution of magnetic fields in radiation and dust universes. We find that, whereas magnetic universes are strongly constrained by the microwave background anisotropy, Yang-Mills universes are principally constrained by primordial nucleosynthesis but the bound is comparatively weak with Ω YM rad

  13. Lotka-Volterra dynamics kills the Red Queen: population size fluctuations and associated stochasticity dramatically change host-parasite coevolution.

    Science.gov (United States)

    Gokhale, Chaitanya S; Papkou, Andrei; Traulsen, Arne; Schulenburg, Hinrich

    2013-11-19

    Host-parasite coevolution is generally believed to follow Red Queen dynamics consisting of ongoing oscillations in the frequencies of interacting host and parasite alleles. This belief is founded on previous theoretical work, which assumes infinite or constant population size. To what extent are such sustained oscillations realistic? Here, we use a related mathematical modeling approach to demonstrate that ongoing Red Queen dynamics is unlikely. In fact, they collapse rapidly when two critical pieces of realism are acknowledged: (i) population size fluctuations, caused by the antagonism of the interaction in concordance with the Lotka-Volterra relationship; and (ii) stochasticity, acting in any finite population. Together, these two factors cause fast allele fixation. Fixation is not restricted to common alleles, as expected from drift, but also seen for originally rare alleles under a wide parameter space, potentially facilitating spread of novel variants. Our results call for a paradigm shift in our understanding of host-parasite coevolution, strongly suggesting that these are driven by recurrent selective sweeps rather than continuous allele oscillations.

  14. A role for habitat area in the geographic mosaic of coevolution between red crossbills and lodgepole pine.

    Science.gov (United States)

    Siepielski, A M; Benkman, C W

    2005-07-01

    Understanding how resource abundance limits adaptive evolution and influences species interactions is an important step towards developing insight into the role of microevolutionary processes in establishing macroevolutionary patterns. We examined how variation in resource abundance (forest area of lodgepole pine Pinus contorta ssp. latifolia) influenced patterns of co-adaptation and coevolution between red crossbill (Loxia curvirostra complex) and lodgepole pine populations. First, we found that crossbill abundance increased logarithmically as forest area increased in mountain ranges lacking a preemptive competitor (pine squirrels Tamiasciurus hudsonicus). Second, seed defences against predation by crossbills increased with increases in crossbill density, suggesting that seed defences have likely evolved in proportion to the intensity of selection that crossbills exert. Third, the average bill size of crossbill populations increased with increasing seed defences, which implies that crossbill offenses increased with increases in seed defences. The large bill size on the largest range is the result of coevolution with lodgepole pine with this crossbill population perhaps speciating. Local adaptation of crossbill populations on smaller ranges, however, is more likely the result of resident crossbills representing a subset of the potential colonists (phenotypic sorting) than of local evolution. In the smallest range, migration and possibly more frequent extinction likely impede local adaptation and may result in maladaptation.

  15. Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-D8 Liquid. Understanding Measurements with Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    de Almeida, Valmor F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Hongjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Herwig, Kenneth W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kidder, Michelle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-01-25

    understand measurements or calibrate/validate molecular dynamics models.

  16. Towards a Molecular Understanding of the Biosynthesis of Amaryllidaceae Alkaloids in Support of Their Expanding Medical Use

    Directory of Open Access Journals (Sweden)

    Adam M. Takos

    2013-05-01

    Full Text Available The alkaloids characteristically produced by the subfamily Amaryllidoideae of the Amaryllidaceae, bulbous plant species that include well know genera such as Narcissus (daffodils and Galanthus (snowdrops, are a source of new pharmaceutical compounds. Presently, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used to treat symptoms of Alzheimer’s disease, is produced commercially as a drug from cultivated plants. However, several Amaryllidaceae alkaloids have shown great promise as anti-cancer drugs, but their further clinical development is restricted by their limited commercial availability. Amaryllidaceae species have a long history of cultivation and breeding as ornamental bulbs, and phytochemical research has focussed on the diversity in alkaloid content and composition. In contrast to the available pharmacological and phytochemical data, ecological, physiological and molecular aspects of the Amaryllidaceae and their alkaloids are much less explored and the identity of the alkaloid biosynthetic genes is presently unknown. An improved molecular understanding of Amaryllidaceae alkaloid biosynthesis would greatly benefit the rational design of breeding programs to produce cultivars optimised for the production of pharmaceutical compounds and enable biotechnology based approaches.

  17. Understanding the Formation of the Self-Assembly of Colloidal Copper Nanoparticles by Surfactant: A Molecular Velcro

    Directory of Open Access Journals (Sweden)

    Raquel Kely Bortoleto-Bugs

    2013-01-01

    Full Text Available Self-assembly procedure is employed to synthesize colloidal copper nanoparticles (ccNPs with cationic surfactant in an environmentally friendly method. Scanning electron microscopy images provide a clear view of the ccNPs formed having an approximate size of 15 nm. The X-ray diffraction reveals that the ccNPs have the two types of copper oxide as well as the metallic copper. The new procedure shows that the cationic surfactant CTAB plays an important role in the understanding and development of self-assembly. There is a strong relationship between the ccNPs formation with the critical micelle concentration of the CTAB which influences both shape and size. The outcomes allowed the development of a molecular model for the ccNPs synthesis showing that the CTAB monomer on the surface has the function of a molecular velcro making the linkage of ccNPs to form an agglomerate with size around 600 nm. Finally, with the emerging new technologies, the synthesis of copper oxide takes a new perspective for their applicability in diverse integrated areas such as the flexible electronics and energy.

  18. Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface.

    Science.gov (United States)

    Penna, M J; Mijajlovic, M; Tamerler, C; Biggs, M J

    2015-07-14

    The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).

  19. Determination of LFER descriptors of 30 cations of ionic liquids--progress in understanding their molecular interaction potentials.

    Science.gov (United States)

    Cho, Chul-Woong; Jungnickel, Christian; Stolte, Stefan; Preiss, Ulrich; Arning, Jürgen; Ranke, Johannes; Krossing, Ingo; Thöming, Jorg

    2012-02-01

    In order to understand molecular interaction potentials of 30 cations of ionic liquids (ILs), the well-known linear free energy relationship concept (LFER) was applied. The LFER descriptors for the excess molar refractivity and the molar volume were calculated in silico and for hydrogen-bonding acidity and basicity, and the polarizability/dipolarity of IL cations were experimentally determined through high performance liquid chromatography (HPLC) measurements. For the study, three different columns (RP-select B, Cyan, and Diol) and buffered mobile phases, based on two organic solvents acetonitrile (ACN) and methanol (MeOH), were selectively combined to the HPLC separation systems RP-select B-ACN, RP-select B-MeOH, Cyan-MeOH, Diol-ACN, and Diol-MeOH. By measuring the retention factors of 45 neutral calibration compounds and calculating LFER descriptors of three cations in the HPLC systems, the system parameters, including an ionic z coefficient, were determined. Conversely, the LFER descriptors of 30 ionic liquid cations were determined, based on the parameters of five systems and their retention factors in the HPLC systems. The results showed that the type of head group, alkyl chain length and further substituents of the cation have a significant influence on the dipolarity/polarizability and the hydrogen-bonding acidity, and functionalized groups (hydroxyl, ether, and dimethylamino) lead to hydrogen-bonding basicity of the cation. The characterization of cationic LFER descriptors opens up the chance for a more quantitative understanding of molecular interaction potentials and physicochemical properties of ILs. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons.

    Directory of Open Access Journals (Sweden)

    Soledad Sacristán

    2009-10-01

    Full Text Available Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1 powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1 gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1 the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2 the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.

  1. Origins of coevolution between residues distant in protein 3D structures

    OpenAIRE

    Anishchenko, Ivan; Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

    2017-01-01

    Coevolution-derived contact predictions are enabling accurate protein structure modeling. However, coevolving residues are not always in contact, and this is a potential source of error in such modeling efforts. To investigate the sources of such errors and, more generally, the origins of coevolution in protein structures, we provide a global overview of the contributions to the “exceptions” to the general rule that coevolving residues are close in protein three-dimensional structures.

  2. ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL

    International Nuclear Information System (INIS)

    FITTS, J.P.; KALB, P.D.; FRANCIS, A.J.; FUHRMANN, M.; DODGE, C.J.; GILLOW, J.B.

    2004-01-01

    Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants with

  3. Coevolution of network structure and cooperation in the public goods game

    International Nuclear Information System (INIS)

    Wang Lei; Xia Chengyi; Wang Juan

    2013-01-01

    Recently, the emergence of cooperation has become a central topic in the evolutionary game field, and coevolution of game dynamics and network topology structure can give us a fresh viewpoint of how the network evolves and cooperation arises. In this paper, we show in detail a picture of the co-evolutionary behaviors between the microscopic structure of the network and cooperation promotion in the public goods game (PGG). Based on a mechanism named after evolutionary preferential attachment (EPA), in which the growth of the network depends on the outcome of PGG dynamics, we explore the structural properties of networks and cooperative behaviors taking place on the networks created by EPA rules. Extensive simulation results indicate that the structure of the resulting networks displays a transition from homogeneous to heterogeneous properties as the selection strength ϵ increases, and the cooperative behaviors have a non-trivial state in which cooperators and defectors can simultaneously occupy the hub nodes in the network. Current results are of interest for us to further understand the cooperation persistence and structure evolution in many natural, social and economical systems. (paper)

  4. Coevolution between positive reciprocity, punishment, and partner switching in repeated interactions.

    Science.gov (United States)

    Wubs, Matthias; Bshary, Redouan; Lehmann, Laurent

    2016-06-15

    Cooperation based on mutual investments can occur between unrelated individuals when they are engaged in repeated interactions. Individuals then need to use a conditional strategy to deter their interaction partners from defecting. Responding to defection such that the future payoff of a defector is reduced relative to cooperating with it is called a partner control mechanism. Three main partner control mechanisms are (i) to switch from cooperation to defection when being defected ('positive reciprocity'), (ii) to actively reduce the payoff of a defecting partner ('punishment'), or (iii) to stop interacting and switch partner ('partner switching'). However, such mechanisms to stabilize cooperation are often studied in isolation from each other. In order to better understand the conditions under which each partner control mechanism tends to be favoured by selection, we here analyse by way of individual-based simulations the coevolution between positive reciprocity, punishment, and partner switching. We show that random interactions in an unstructured population and a high number of rounds increase the likelihood that selection favours partner switching. In contrast, interactions localized in small groups (without genetic structure) increase the likelihood that selection favours punishment and/or positive reciprocity. This study thus highlights the importance of comparing different control mechanisms for cooperation under different conditions. © 2016 The Author(s).

  5. Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family.

    Directory of Open Access Journals (Sweden)

    Ying Liu

    Full Text Available In mammals, IFIT (Interferon [IFN]-induced proteins with Tetratricopeptide Repeat [TPR] motifs family genes are involved in many cellular and viral processes, which are tightly related to mammalian IFN response. However, little is known about non-mammalian IFIT genes. In the present study, IFIT genes are identified in the genome databases from the jawed vertebrates including the cartilaginous elephant shark but not from non-vertebrates such as lancelet, sea squirt and acorn worm, suggesting that IFIT gene family originates from a vertebrate ancestor about 450 million years ago. IFIT family genes show conserved gene structure and gene arrangements. Phylogenetic analyses reveal that this gene family has expanded through lineage-specific and species-specific gene duplication. Interestingly, IFN gene family seem to share a common ancestor and a similar evolutionary mechanism; the function link of IFIT genes to IFN response is present early since the origin of both gene families, as evidenced by the finding that zebrafish IFIT genes are upregulated by fish IFNs, poly(I:C and two transcription factors IRF3/IRF7, likely via the IFN-stimulated response elements (ISRE within the promoters of vertebrate IFIT family genes. These coevolution features creates functional association of both family genes to fulfill a common biological process, which is likely selected by viral infection during evolution of vertebrates. Our results are helpful for understanding of evolution of vertebrate IFN system.

  6. Understanding the effect of secondary structure on molecular interactions of poly-L-lysine with different substrates by SFA.

    Science.gov (United States)

    Binazadeh, Mojtaba; Faghihnejad, Ali; Unsworth, Larry D; Zeng, Hongbo

    2013-10-14

    Nonspecific adsorption of proteins on biomaterial surfaces challenges the widespread application of engineered materials, and understanding the impact of secondary structure of proteins and peptides on their adsorption process is of both fundamental and practical importance in bioengineering. In this work, poly-L-lysine (PLL)-based α-helices and β-sheets were chosen as a model system to investigate the effect of secondary structure on peptide interactions with substrates of various surface chemistries. Circular dichroism (CD) was used to confirm the presence of both α-helix and β-sheet structured PLL in aqueous solutions and upon adsorption to quartz, where these secondary structures seemed to be preserved. Atomic force microscopy (AFM) imaging showed different surface patterns for adsorbed α-helix and β-sheet PLL. Interactions between PLL of different secondary structures and various substrates (i.e., PLL, Au, mica, and poly(ethylene glycol) (PEG)) were directly measured using a surface forces apparatus (SFA). It was found that β-sheet PLL films showed higher adsorbed layer thicknesses in general. Adhesion energies of β-sheet versus Au and β-sheet versus β-sheet were considerably higher than that of α-helix versus Au and α-helix versus α-helix systems, respectively. Au and β-sheet PLL interactions seemed to be more dependent on the salt concentration than that of α-helix, while the presence of a grafted PEG layer greatly diminished any attraction with either PLL structure. The molecular interaction mechanism of peptide in different secondary structures is discussed in terms of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, Alexander-de Gennes (AdG) steric model and hydrogen bonding, which provides important insight into the fundamental understanding of the interaction mechanism between proteins and biomaterials.

  7. Molecular Level Understanding of Sodium Dodecyl Sulfate (SDS) Induced Sol-Gel Transition of Pluronic F127 Using Fisetin as a Fluorescent Molecular Probe.

    Science.gov (United States)

    Mishra, Jhili; Swain, Jitendriya; Mishra, Ashok Kumar

    2018-01-11

    The thermoreversible sol-gel transition of pluronic F127 is markedly altered even with addition of submicellar concentration of sodium dodecyl sulfate (SDS) surfactant. Multiple fluorescence parameters like fluorescence intensity, fluorescence anisotropy and fluorescence lifetime of both the prototropic forms (anion (A - *) and phototautomer FT*) of the photoprototropic fluorescent probe fisetin has been efficiently used to understand the molecular level properties like polarity and microviscosity of the PF127-SDS system as a function of temperature. The SDS-induced increase in the interfacial hydrophobicity level is seen to affect the sol-gel phase transition of PF127 (21-18 °C). The E T (30) polarity parameter value of anionic emission of fisetin suggests that there is a considerable decrease in the polarity of the PF127 medium with increase in temperature and with the addition of SDS. The microviscosity progressively increases from ∼5 mPa s (sol state, 10 °C) to ∼22.01 mPa s (gel state 35 °C) in aqueous solution of PF127. The variation in microviscosity with addition of SDS in PF127-SDS mixed system is significant in sol phase whereas in gel phase this variation is significantly less. Temperature dependent fluorescence lifetime of FT* indicates that there is heterogeneity in distribution of fisetin molecules at different domains of PF127. This work also show-cases the sensitivity of fisetin toward change in polarity and change in sol-gel transition temperature of copolymer PF127 with variation in temperature (both forward and reverse directions) and SDS.

  8. Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae).

    Science.gov (United States)

    Sotero-Caio, Cibele G; Volleth, Marianne; Hoffmann, Federico G; Scott, LuAnn; Wichman, Holly A; Yang, Fengtang; Baker, Robert J

    2015-10-06

    Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniqueness of natural history attributes of each taxon. Ideally, detailed investigation of the chromosome architecture of an organism and related groups, placed within a phylogenetic context, is required. We used multiple approaches to investigate the dynamics of chromosomal evolution in lineages of bats with considerable karyotypic variation, focusing on the different facets contributing to fixation of the exceptional chromosomal changes in Tonatia saurophila. Integration of empirical data with proposed models of chromosome evolution was performed to understand the probable conditions for Tonatia's karyotypic evolution. The trajectory of reorganization of chromosome blocks since the common ancestor of Glossophaginae and Phyllostominae subfamilies suggests that multiple tandem fusions, as well as disruption and fusions of conserved phyllostomid chromosomes were major drivers of karyotypic reshuffling in Tonatia. Considerable variation in the rates of chromosomal evolution between phyllostomid lineages was observed. Thirty-nine unique fusions and fission events reached fixation in Tonatia over a short period of time, followed by ~12 million years of chromosomal stasis. Physical mapping of repetitive DNA revealed an unusual accumulation of LINE-1 sequences on centromeric regions, probably associated with the chromosomal dynamics of this genus. Multiple rearrangements have reached fixation in a wave-like fashion in phyllostomid bats. Different biological features of Tonatia support distinct models of rearrangement fixation, and it is unlikely that the fixations were a result of solely stochastic processes in small ancient populations. Increased recombination rates were probably facilitated by expansion of repetitive DNA, reinforced by aspects of taxon reproduction and

  9. Chaotic Red Queen coevolution in three-species food chains.

    Science.gov (United States)

    Dercole, Fabio; Ferriere, Regis; Rinaldi, Sergio

    2010-08-07

    Coevolution between two antagonistic species follows the so-called 'Red Queen dynamics' when reciprocal selection results in an endless series of adaptation by one species and counteradaptation by the other. Red Queen dynamics are 'genetically driven' when selective sweeps involving new beneficial mutations result in perpetual oscillations of the coevolving traits on the slow evolutionary time scale. Mathematical models have shown that a prey and a predator can coevolve along a genetically driven Red Queen cycle. We found that embedding the prey-predator interaction into a three-species food chain that includes a coevolving superpredator often turns the genetically driven Red Queen cycle into chaos. A key condition is that the prey evolves fast enough. Red Queen chaos implies that the direction and strength of selection are intrinsically unpredictable beyond a short evolutionary time, with greatest evolutionary unpredictability in the superpredator. We hypothesize that genetically driven Red Queen chaos could explain why many natural populations are poised at the edge of ecological chaos. Over space, genetically driven chaos is expected to cause the evolutionary divergence of local populations, even under homogenizing environmental fluctuations, and thus to promote genetic diversity among ecological communities over long evolutionary time.

  10. Critical mass of public goods and its coevolution with cooperation

    Science.gov (United States)

    Shi, Dong-Mei; Wang, Bing-Hong

    2017-07-01

    In this study, the enhancing parameter represented the value of the public goods to the public in public goods game, and was rescaled to a Fermi-Dirac distribution function of critical mass. Public goods were divided into two categories, consumable and reusable public goods, and their coevolution with cooperative behavior was studied. We observed that for both types of public goods, cooperation was promoted as the enhancing parameter increased when the value of critical mass was not very large. An optimal value of critical mass which led to the best cooperation was identified. We also found that cooperations emerged earlier for reusable public goods, and defections became extinct earlier for the consumable public goods. Moreover, we observed that a moderate depreciation rate for public goods resulted in an optimal cooperation, and this range became wider as the enhancing parameter increased. The noise influence on cooperation was studied, and it was shown that cooperation density varied non-monotonically as noise amplitude increased for reusable public goods, whereas decreased monotonically for consumable public goods. Furthermore, existence of the optimal critical mass was also identified in other three regular networks. Finally, simulation results were utilized to analyze the provision of public goods in detail.

  11. Niche construction, sources of selection and trait coevolution.

    Science.gov (United States)

    Laland, Kevin; Odling-Smee, John; Endler, John

    2017-10-06

    Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

  12. Paternal care and litter size coevolution in mammals.

    Science.gov (United States)

    Stockley, Paula; Hobson, Liane

    2016-04-27

    Biparental care of offspring occurs in diverse mammalian genera and is particularly common among species with socially monogamous mating systems. Despite numerous well-documented examples, however, the evolutionary causes and consequences of paternal care in mammals are not well understood. Here, we investigate the evolution of paternal care in relation to offspring production. Using comparative analyses to test for evidence of evolutionary associations between male care and life-history traits, we explore if biparental care is likely to have evolved because of the importance of male care to offspring survival, or if evolutionary increases in offspring production are likely to result from the evolution of biparental care. Overall, we find no evidence that paternal care has evolved in response to benefits of supporting females to rear particularly costly large offspring or litters. Rather, our findings suggest that increases in offspring production are more likely to follow the evolution of paternal care, specifically where males contribute depreciable investment such as provisioning young. Through coevolution with litter size, we conclude that paternal care in mammals is likely to play an important role in stabilizing monogamous mating systems and could ultimately promote the evolution of complex social behaviours. © 2016 The Authors.

  13. Microeconomic co-evolution model for financial technical analysis signals

    Science.gov (United States)

    Rotundo, G.; Ausloos, M.

    2007-01-01

    Technical analysis (TA) has been used for a long time before the availability of more sophisticated instruments for financial forecasting in order to suggest decisions on the basis of the occurrence of data patterns. Many mathematical and statistical tools for quantitative analysis of financial markets have experienced a fast and wide growth and have the power for overcoming classical TA methods. This paper aims to give a measure of the reliability of some information used in TA by exploring the probability of their occurrence within a particular microeconomic agent-based model of markets, i.e., the co-evolution Bak-Sneppen model originally invented for describing species population evolutions. After having proved the practical interest of such a model in describing financial index so-called avalanches, in the prebursting bubble time rise, the attention focuses on the occurrence of trend line detection crossing of meaningful barriers, those that give rise to some usual TA strategies. The case of the NASDAQ crash of April 2000 serves as an illustration.

  14. Coevolution of quantum and classical strategies on evolving random networks.

    Directory of Open Access Journals (Sweden)

    Qiang Li

    Full Text Available We study the coevolution of quantum and classical strategies on weighted and directed random networks in the realm of the prisoner's dilemma game. During the evolution, agents can break and rewire their links with the aim of maximizing payoffs, and they can also adjust the weights to indicate preferences, either positive or negative, towards their neighbors. The network structure itself is thus also subject to evolution. Importantly, the directionality of links does not affect the accumulation of payoffs nor the strategy transfers, but serves only to designate the owner of each particular link and with it the right to adjust the link as needed. We show that quantum strategies outperform classical strategies, and that the critical temptation to defect at which cooperative behavior can be maintained rises, if the network structure is updated frequently. Punishing neighbors by reducing the weights of their links also plays an important role in maintaining cooperation under adverse conditions. We find that the self-organization of the initially random network structure, driven by the evolutionary competition between quantum and classical strategies, leads to the spontaneous emergence of small average path length and a large clustering coefficient.

  15. Biclustering of the Gene Expression Data by Coevolution Cuckoo Search

    Directory of Open Access Journals (Sweden)

    Lu Yin

    2015-06-01

    Full Text Available Biclustering has a potential to discover the local expression patterns analyzing the gene expression data which provide clues about biological processes. However, since it is proven that the biclustering problem is NP-hard, it is necessary to seek more effective algorithm. Cuckoo Search (CS models the brood parasitism behavior of cuckoo to solve the optimization problem and outperforms the other existing algorithms. In this paper, we introduce a new algorithm for biclustering gene expression data, called cuckoo search biclustering (CSB, which adopts CS to solve the biclustering problem. For further improving the performance of CSB, three modifications to CSB are made with the aim of increasing the convergence rate and the coevolution cuckoo search biclustering (COCSB is designed. CSB and COCSB are tested on the six gene expression data and their results are compared to those of CC, FLOC, ISA, SEBI, BIC-aiNet, PSOB, SAB and SSB. The comparison shows that CSB and COCSB have achieved great success in biological significance and time performance.

  16. Coevolution of competingCallosobruchusspecies does not stabilize coexistence.

    Science.gov (United States)

    Hausch, Stephen J; Fox, Jeremy W; Vamosi, Steven M

    2017-08-01

    Interspecific resource competition is expected to select for divergence in resource use, weakening interspecific relative to intraspecific competition, thus promoting stable coexistence. More broadly, because interspecific competition reduces fitness, any mechanism of interspecific competition should generate selection favoring traits that weaken interspecific competition. However, species also can adapt to competition by increasing their competitive ability, potentially destabilizing coexistence. We reared two species of bean beetles, the specialist Callosobruchus maculatus and the generalist C. chinensis , in allopatry and sympatry on a mixture of adzuki beans and lentils, and assayed mutual invasibility after four, eight, and twelve generations of evolution. Contrary to the expectation that coevolution of competitors will weaken interspecific competition, the rate of mutual invasibility did not differ between sympatry and allopatry. Rather, the invasion rate of C. chinensis , but not C. maculatus , increased with duration of evolution, as C. chinensis adapted to lentils without experiencing reduced adaptation to adzuki beans, and regardless of the presence or absence of C. maculatus . Our results highlight that evolutionary responses to interspecific competition promote stable coexistence only under specific conditions that can be difficult to produce in practice.

  17. Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

    Science.gov (United States)

    Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Švedas, Vytas

    2014-01-01

    Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties. PMID:24959852

  18. Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions.

    Directory of Open Access Journals (Sweden)

    Dmitry Suplatov

    Full Text Available Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties.

  19. Towards a molecular understanding of the apicomplexan actin motor: on a road to novel targets for malaria remedies?

    Energy Technology Data Exchange (ETDEWEB)

    Kumpula, Esa-Pekka [University of Oulu, PO Box 3000, 90014 Oulu (Finland); Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg (Germany); German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg (Germany); Kursula, Inari, E-mail: inari.kursula@helmholtz-hzi.de [University of Oulu, PO Box 3000, 90014 Oulu (Finland); Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg (Germany); German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg (Germany); University of Bergen, Jonas Lies vei 91, 5009 Bergen (Norway)

    2015-04-16

    In this review, current structural understanding of the apicomplexan glideosome and actin regulation is described. Apicomplexan parasites are the causative agents of notorious human and animal diseases that give rise to considerable human suffering and economic losses worldwide. The most prominent parasites of this phylum are the malaria-causing Plasmodium species, which are widespread in tropical and subtropical regions, and Toxoplasma gondii, which infects one third of the world’s population. These parasites share a common form of gliding motility which relies on an actin–myosin motor. The components of this motor and the actin-regulatory proteins in Apicomplexa have unique features compared with all other eukaryotes. This, together with the crucial roles of these proteins, makes them attractive targets for structure-based drug design. In recent years, several structures of glideosome components, in particular of actins and actin regulators from apicomplexan parasites, have been determined, which will hopefully soon allow the creation of a complete molecular picture of the parasite actin–myosin motor and its regulatory machinery. Here, current knowledge of the function of this motor is reviewed from a structural perspective.

  20. Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti-resonances

    DEFF Research Database (Denmark)

    Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevincli, Haldun

    2013-01-01

    Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple...... rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method...

  1. FIB and MIP: understanding nanoscale porosity in molecularly imprinted polymers via 3D FIB/SEM tomography.

    Science.gov (United States)

    Neusser, G; Eppler, S; Bowen, J; Allender, C J; Walther, P; Mizaikoff, B; Kranz, C

    2017-10-05

    We present combined focused ion beam/scanning electron beam (FIB/SEM) tomography as innovative method for differentiating and visualizing the distribution and connectivity of pores within molecularly imprinted polymers (MIPs) and non-imprinted control polymers (NIPs). FIB/SEM tomography is used in cell biology for elucidating three-dimensional structures such as organelles, but has not yet been extensively applied for visualizing the heterogeneity of nanoscopic pore networks, interconnectivity, and tortuosity in polymers. To our best knowledge, the present study is the first application of this strategy for analyzing the nanoscale porosity of MIPs. MIPs imprinted for propranolol - and the corresponding NIPs - were investigated establishing FIB/SEM tomography as a viable future strategy complementing conventional isotherm studies. For visualizing and understanding the properties of pore networks in detail, polymer particles were stained with osmium tetroxide (OsO 4 ) vapor, and embedded in epoxy resin. Staining with OsO 4 provides excellent contrast during high-resolution SEM imaging. After optimizing the threshold to discriminate between the stained polymer matrix, and pores filled with epoxy resin, a 3D model of the sampled volume may be established for deriving not only the pore volume and pore surface area, but also to visualize the interconnectivity and tortuosity of the pores within the sampled polymer volume. Detailed studies using different types of cross-linkers and the effect of hydrolysis on the resulting polymer properties have been investigated. In comparison of MIP and NIP, it could be unambiguously shown that the interconnectivity of the visualized pores in MIPs is significantly higher vs. the non-imprinted polymer, and that the pore volume and pore area is 34% and approx. 35% higher within the MIP matrix. This confirms that the templating process not only induces selective binding sites, but indeed also affects the physical properties of such

  2. Genetic and Linguistic Coevolution in Northern Island Melanesia

    Science.gov (United States)

    Hunley, Keith; Dunn, Michael; Lindström, Eva; Reesink, Ger; Terrill, Angela; Healy, Meghan E.; Koki, George; Friedlaender, Françoise R.; Friedlaender, Jonathan S.

    2008-01-01

    Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may

  3. Coevolution of Supermassive Black Holes and Their Host Galaxies

    Science.gov (United States)

    Hiner, Kyle Devon

    The role of black holes in galaxy evolution has come under intense scrutiny since it was discovered that every galaxy in the local universe contains a supermassive black hole (SMBH) at its nucleus. The existence of scaling relations between the SMBH and its host galaxy show that their presence is not coincidental, but rather that SMBHs and their hosts have a shared evolution. The nature of this coevolution is still debated with some proposing it to be a natural result of hierarchical merging models, while others invoke SMBH feedback mechanisms that couple BH growth with that of the host galaxy. In this dissertation, I examine different regimes of SMBH activity and host galaxy properties. I investigate a sample of post-starburst galaxies to gain insight into the morphological and spectrophotometric evolution of galaxies through galaxy interactions and mergers. I plot detailed comparisons of the galaxy kinematics as measured from different stellar populations. I also investigate post-starburst galaxies that simultaneously host an AGN. I develop a technique to study the properties of both the host galaxy and the SMBH in these objects, directly investigating the scaling relation between the two. I describe analysis performed on red quasars in another study that directly probes the scaling relations in the non-local universe. Lastly, I conduct SED fitting of quasars to illuminate the differences between two major spectral types, and investigate host galaxy properties including star formation. All of these projects focus on the relationship between the SMBH and host galaxy. I show that a range of galaxy interactions can lead to black hole growth and are part of galaxy evolution over cosmic time.

  4. Co-evolution and thresholds in arid floodplain wetland ecosystems.

    Science.gov (United States)

    Sandi, Steven; Rodriguez, Jose; Riccardi, Gerardo; Wen, Li; Saintilan, Neil

    2017-04-01

    Vegetation in arid floodplain wetlands consist of water dependent and flood tolerant species that rely on periodical floods in order to maintain healthy conditions. The floodplain often consist of a complex system of marshes, swamps and lagoons interconnected by a network of streams and poorly defined rills. Over time, feedbacks develop between vegetation and flow paths producing areas of flow obstruction and flow concentration, which combined with depositional and erosional process lead to a continuous change on the position and characteristics of inundation areas. This coevolution of flow paths and vegetation can reach a threshold that triggers major channel transformations and abandonment of wetland areas, in a process that is irreversible. The Macquarie Marshes is a floodplain wetland complex in the semi-arid region of north western NSW, Australia. The site is characterised by a low-gradient topography that leads to channel breakdown processes where the river network becomes practically non-existent and the flow extends over large areas of wetland that later re-join and reform channels exiting the system. Due to a combination of climatic and anthropogenic pressures, the wetland ecosystem in the Macquarie Marshes has deteriorated over the past few decades. This has been linked to decreasing inundation frequencies and extent, with whole areas of flood dependent species such as Water Couch and Common Reed undergoing complete succession to terrestrial species and dryland. In this presentation we provide an overview of an ecogeomorphological model that we have developed in order to simulate the complex dynamics of the marshes. The model combines hydrodynamic, vegetation and channel evolution modules. We focus on the vegetation component of the model and the transitional rules to predict wetland invasion by terrestrial vegetation.

  5. Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects.

    Science.gov (United States)

    Luan, Jun-Bo; Chen, Wenbo; Hasegawa, Daniel K; Simmons, Alvin M; Wintermantel, William M; Ling, Kai-Shu; Fei, Zhangjun; Liu, Shu-Sheng; Douglas, Angela E

    2015-09-15

    Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Coevolution and divergence in the Joshua tree/yucca moth mutualism.

    Science.gov (United States)

    Godsoe, William; Yoder, Jeremy B; Smith, Christopher Irwin; Pellmyr, Olle

    2008-06-01

    Theory suggests that coevolution drives diversification in obligate pollination mutualism, but it has been difficult to disentangle the effects of coevolution from other factors. We test the hypothesis that differential selection by two sister species of pollinating yucca moths (Tegeticula spp.) drove divergence between two varieties of the Joshua tree (Yucca brevifolia) by comparing measures of differentiation in floral and vegetative features. We show that floral features associated with pollination evolved more rapidly than vegetative features extrinsic to the interaction and that a key floral feature involved in the mutualism is more differentiated than any other and matches equivalent differences in the morphology of the pollinating moths. A phylogenetically based, ancestral states reconstruction shows that differences in moth morphology arose in the time since they first became associated with Joshua trees. These results suggest that coevolution, rather than extrinsic environmental factors, has driven divergence in this obligate pollination mutualism.

  7. Studying the co-evolution of protein families with the Mirrortree web server.

    Science.gov (United States)

    Ochoa, David; Pazos, Florencio

    2010-05-15

    The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

  8. Using analyses of amino Acid coevolution to understand protein structure and function.

    Science.gov (United States)

    Ashenberg, Orr; Laub, Michael T

    2013-01-01

    Determining which residues of a protein contribute to a specific function is a difficult problem. Analyses of amino acid covariation within a protein family can serve as a useful guide by identifying residues that are functionally coupled. Covariation analyses have been successfully used on several different protein families to identify residues that work together to promote folding, enable protein-protein interactions, or contribute to an enzymatic activity. Covariation is a statistical signal that can be measured in a multiple sequence alignment of homologous proteins. As sequence databases have expanded dramatically, covariation analyses have become easier and more powerful. In this chapter, we describe how functional covariation arises during the evolution of proteins and how this signal can be distinguished from various background signals. We discuss the basic methodology for performing amino acid covariation analysis, using bacterial two-component signal transduction proteins as an example. We provide practical suggestions for each step of the process including assembly of protein sequences, construction of a multiple sequence alignment, measurement of covariation, and analysis of results. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

    Science.gov (United States)

    Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

    2013-03-01

    Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

  10. Coevolution of bed surface patchiness and channel morphology: 1. Mechanisms of forced patch formation

    Science.gov (United States)

    Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

    2015-01-01

    Riverbeds frequently display a spatial structure where the sediment mixture composing the channel bed has been sorted into discrete patches of similar grain size. Even though patches are a fundamental feature in gravel bed rivers, we have little understanding of how patches form, evolve, and interact. Here we present a two-dimensional morphodynamic model that is used to examine in greater detail the mechanisms responsible for the development of forced bed surface patches and the coevolution of bed morphology and bed surface patchiness. The model computes the depth-averaged channel hydrodynamics, mixed-grain-size sediment transport, and bed evolution by coupling the river morphodynamic model Flow and Sediment Transport with Morphological Evolution of Channels (FaSTMECH) with a transport relation for gravel mixtures and the mixed-grain-size Exner equation using the active layer assumption. To test the model, we use it to simulate a flume experiment in which the bed developed a sequence of alternate bars and temporally and spatially persistent forced patches with a general pattern of coarse bar tops and fine pools. Cross-stream sediment flux causes sediment to be exported off of bars and imported into pools at a rate that balances downstream gradients in the streamwise sediment transport rate, allowing quasi-steady bar-pool topography to persist. The relative importance of lateral gravitational forces on the cross-stream component of sediment transport is a primary control on the amplitude of the bars. Because boundary shear stress declines as flow shoals over the bars, the lateral sediment transport is increasingly size selective and leads to the development of coarse bar tops and fine pools.

  11. The RNA-world and co-evolution hypothesis and the origin of life: Implications, research strategies and perspectives

    Science.gov (United States)

    Lahav, Noam

    1993-01-01

    The applicability of the RNA-world and co-evolution hypothesis to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficultites. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activites of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypothesis under consideration. It is suggested that the novel directed molecular evolution technology, and molecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a `Primordial Darwinian entity'.

  12. Interlocus sexually antagonistic coevolution can create indirect selection for increased recombination.

    Science.gov (United States)

    Dapper, Amy L; Lively, Curtis M

    2014-04-01

    The ubiquity of recombination in nature is a paradox because it breaks up combinations of alleles favored by natural selection. Theoretical work has shown that antagonistic coevolution between hosts and parasites can result in rapid fluctuations in epistasis that can create a short-term advantage to recombination. Here, we show that another kind of antagonistic coevolution, interlocus sexually antagonistic coevolution (SAC), can also create indirect selection for modifiers that increase the rate of recombination, and that it can lead to very high levels of recombination at equilibrium. Recombination is favored because interlocus SAC creates heterogeneity in the strength and direction of selection, both within and between generations, which maintains an excess of disadvantageous haplotypes in the population. This result is similar to and consistent with dynamics of fluctuating epistasis produced in models of host-parasite coevolution. However, the conditions under which interlocus SAC provides an advantage to recombination are more permissive. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  13. The Coevolution of "Tyrannosaurus" & Its Prey: Could "Tyrannosaurus" Chase down & Kill a "Triceratops" for Lunch?

    Science.gov (United States)

    May, S. Randolph

    2014-01-01

    Students will analyze the coevolution of the predator-prey relationships between "Tyrannosaurus rex" and its prey species using analyses of animal speeds from fossilized trackways, prey-animal armaments, adaptive behaviors, bite marks on prey-animal fossils, predator-prey ratios, and scavenger competition. The students will be asked to…

  14. Insect-plant coevolution in the mountains of Sinai | Gilbert | Egyptian ...

    African Journals Online (AJOL)

    Insect-plant coevolution in the mountains of Sinai. Francis Gilbert, Samy Zalat, Fayez Semida. Abstract. Egyptian Journal of Biology Vol.1 1999: 142-152. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online. HOW TO USE AJOL.

  15. NEMS Oscillators as Sensors and Actuators: Understanding the Mechanical Properties of Nanoresonators and Their Applications for Molecular Sensing

    Data.gov (United States)

    National Aeronautics and Space Administration — Development of nanotechnology and enhancement of nanostructures for future applications requires a good understanding of a material's behavior at the nanoscale, as...

  16. Understanding the molecular target therapy and it's approved synchronous use with radiation therapy in current Indian oncology practice

    International Nuclear Information System (INIS)

    Gupta, Puneet; Dohhen, Umesh Kumar; Romana; Srivastava, Priyanka

    2012-01-01

    The molecular targeted drugs (MTD) are of two types; large and small. The large molecular targeted drugs (LMTD) cannot cross the cancer cell membrane whereas those that cross the cancer cell membrane are nicknamed small molecular target drugs (SMTD). India has availability of almost all MTD originals approved by USA Food and Drug administration. However a few LMTD like inj vectibix, inj Zevalin, Inj Bexar etc.; and SMTD like cap Tipifarnib approved for AML, are not available in India currently although approved and available in USA. The MTD may he used alone as singlet; along with chemotherapy as doublet or triplet; or along with radiation and chemotherapy combo (nicknamed chemo-radiation-bio therapy). The molecular target therapy approved by USA and/or European FDA and currently available in India and used along with radiation therapy with or without chemotherapy, indication wise are; Brain Tumor Inj Nimotuzumab (LMTD) and Inj bevacizumab (LMTD) in Glioblasoma Multiforme; for Carcinoma Head and neck Inj Cetuximab and Inj Nimotuzumab (LMTT), Tab Geftinib (SMTD). (author)

  17. Understanding the influence of buckwheat bran on wheat dough baking performance: Mechanistic insights from molecular and material science approaches

    NARCIS (Netherlands)

    Zanoletti, M.; Marti, A.; Marengo, M.; Iametti, S.; Pagani, M.A.; Renzetti, S.

    2017-01-01

    A molecular and material science approach is used to describe the influence of coarse and fine buckwheat bran on wheat dough properties and bread textural quality. Focus is given on (i) gluten solvation and structural arrangements in presence of bran as studied by front-face fluorescence; (ii)

  18. Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

    Science.gov (United States)

    Adhikari, Badri; Hou, Jie; Cheng, Jianlin

    2018-03-01

    In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure, and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts. The third method (MULTICOM-CLUSTER) is a consensus combination of the predictions of the first two methods. We evaluated our methods on 94 CASP12 domains. On a subset of 38 free-modeling domains, our methods achieved an average precision of up to 41.7% for top L/5 long-range contact predictions. The comparison of the three methods shows that the quality and effective depth of multiple sequence alignments, coevolution-based features, and machine learning integration of coevolution-based features and traditional features drive the quality of predicted protein contacts. On the full CASP12 dataset, the coevolution-based features alone can improve the average precision from 28.4% to 41.6%, and the machine learning integration of all the features further raises the precision to 56.3%, when top L/5 predicted long-range contacts are evaluated. And the correlation between the precision of contact prediction and the logarithm of the number of effective sequences in alignments is 0.66. © 2017 Wiley Periodicals, Inc.

  19. The evolutionary response of predators to dangerous prey: hotspots and coldspots in the geographic mosaic of coevolution between garter snakes and newts.

    Science.gov (United States)

    Brodie, Edmund D; Ridenhour, B J; Brodie, E D

    2002-10-01

    The "geographic mosaic" approach to understanding coevolution is predicated on the existence of variable selection across the landscape of an interaction between species. A range of ecological factors, from differences in resource availability to differences in community composition, can generate such a mosaic of selection among populations, and thereby differences in the strength of coevolution. The result is a mixture of hotspots, where reciprocal selection is strong, and coldspots, where reciprocal selection is weak or absent, throughout the ranges of species. Population subdivision further provides the opportunity for nonadaptive forces, including gene flow, drift, and metapopulation dynamics, to influence the coevolutionary interaction between species. Some predicted results of this geographic mosaic of coevolution include maladapted or mismatched phenotypes, maintenance of high levels of polymorphism, and prevention of stable equilibrium trait combinations. To evaluate the potential for the geographic mosaic to influence predator-prey coevolution, we investigated the geographic pattern of genetically determined TTX resistance in the garter snake Thamnophis sirtalis over much of the range of its ecological interaction with toxic newts of genus Taricha. We assayed TTX resistance in over 2900 garter snakes representing 333 families from 40 populations throughout western North America. Our results provide dramatic evidence that geographic structure is an important component in coevolutionary interactions between predators and prey. Resistance levels vary substantially (over three orders of magnitude) among populations and over short distances. The spatial array of variation is consistent with two areas of intense evolutionary response by predators ("hotspots") surrounded by clines of decreasing resistance. Some general predictions of the geographic mosaic process are supported, including clinal variation in phenotypes, polymorphism in some populations, and

  20. Review on the Molecular Tools for the Understanding of the Epidemiology of Animal Trypanosomosis in West Africa

    Directory of Open Access Journals (Sweden)

    Duvallet G

    1999-01-01

    Full Text Available The epidemiology of animal trypanosomosis around Bobo-Dioulasso (Burkina Faso, West Africa benefited a lot in the last years from the progress of molecular tools. The two most used molecular techniques were the polymerase chain reaction for the diagnosis of the disease in cattle and the characterization of the trypanosomes in the host and the vector on one hand, and the microsatellite DNA polymorphism in tsetse flies to study the intraspecific genetic variability of the vector on the other hand. The results obtained in the Sideradougou area during a recent two year survey with these techniques, associated with many other georeferenced informations concerning vector and cattle distribution, natural environment, landuse, ground occupation, livestock management, were combined in a Geographical Information System. This new approach of a complex pathogenic system led to a better evaluation of the risk of trypanosome transmission.

  1. Qualitative and quantitative approach towards the molecular understanding of structural, vibrational and optical features of urea ninhydrin monohydrate

    Energy Technology Data Exchange (ETDEWEB)

    Sasikala, V. [Department of Physics, Bishop Moore College, Mavelikara, Alappuzha, Kerala 690110 (India); Sajan, D., E-mail: drsajanbmc@gmail.com [Department of Physics, Bishop Moore College, Mavelikara, Alappuzha, Kerala 690110 (India); Chaitanya, K. [Department of Chemistry, Nanjing University of Science and Technology, Xialingwei 200, Nanjing (China); Sundius, Tom [Department of Physics, University of Helsinki (Finland); Devi, T. Uma [Department of Physics, Government Arts College for Women (Autonomous), Pudukottai (India)

    2017-04-15

    In this study, single crystals of urea ninhydrin monohydrate (UNMH) have been grown by slow evaporation method. The grown crystals were characterized by FT-IR, FT-Raman and UV-Vis-NIR spectroscopies. The Kurtz and Perry powder method was employed to confirm the near-zero SHG efficiency of the as-grown centrosymmetric UNMH crystal. The third order nonlinearity of the crystal has been studied by the open aperture Z-scan method. The nonlinear absorption coefficient is calculated and the potentiality of UNMH in optical limiting applications is identified. The molecular geometry and the origin of optical non-linearity at the molecular level have been investigated by the density functional theory. The normal coordinate analysis was carried out to assign the molecular vibrational modes. Vibrational spectral studies confirms the presence of weak O-H⋯O and moderate O-H⋯O type hydrogen bonds in the molecule as well as O-H⋯O, N-H⋯O and blue-shifted C-H⋯O type H-bonds in the crystal. The intramolecular charge transfer interactions and the electronic absorption mechanisms have been discussed. The static and the dynamic values of hyperpolarizabilities for UNMH were estimated theoretically by DFT methods. - Highlights: • Molecular geometric and NBO interaction features of UNMH were analyzed. • Vibrational spectral features and types of H-bonding in isolated gaseous phase molecule were discussed. • Electronic absorption maxima of different phases of UNMH were found out. • The non-linear absorption behaviour of UNMH is investigated using z-scan. • First- and second- order hyperpolarizability values were estimated theoretically.

  2. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Science.gov (United States)

    Kumar, Sonu; Frank, Martin; Schwartz-Albiez, Reinhard

    2013-01-01

    Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  3. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sonu Kumar

    Full Text Available Human Galectin-8 (Gal-8 is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76. Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.

  4. Streamflow recession patterns can help unravel the role of climate and humans in landscape co-evolution

    NARCIS (Netherlands)

    Bogaart, Patrick W.; Van Der Velde, Ype; Lyon, Steve W.; Dekker, Stefan C.

    2016-01-01

    Traditionally, long-term predictions of river discharges and their extremes include constant relationships between landscape properties and model parameters. However, due to the co-evolution of many landscape properties more sophisticated methods are necessary to quantify future

  5. Taming a wild beast: Developing molecular tools and new methods to understand the biology of Zymoseptoria tritici.

    Science.gov (United States)

    Talbot, Nicholas J

    2015-06-01

    Septoria blotch of wheat is one of the world's most serious plant diseases, which is difficult to control due to the absence of durable host resistance and the increasing frequency of fungicide-resistance. The ascomycete fungus that causes the disease, Zymoseptoria tritici, has been very challenging to study. This special issue of Fungal Genetics and Biology showcases an integrated approach to method development and the innovation of new molecular tools to study the biology of Z. tritici. When considered together, these new methods will have a rapid and dramatic effect on our ability to combat this significant disease. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Adaptive co-evolution of strategies and network leading to optimal cooperation level in spatial prisoner's dilemma game

    International Nuclear Information System (INIS)

    Han-Shuang, Chen; Zhong-Huai, Hou; Hou-Wen, Xin; Ji-Qian, Zhang

    2010-01-01

    We study evolutionary prisoner's dilemma game on adaptive networks where a population of players co-evolves with their interaction networks. During the co-evolution process, interacted players with opposite strategies either rewire the link between them with probability p or update their strategies with probability 1 – p depending on their payoffs. Numerical simulation shows that the final network is either split into some disconnected communities whose players share the same strategy within each community or forms a single connected network in which all nodes are in the same strategy. Interestingly, the density of cooperators in the final state can be maximised in an intermediate range of p via the competition between time scale of the network dynamics and that of the node dynamics. Finally, the mean-field analysis helps to understand the results of numerical simulation. Our results may provide some insight into understanding the emergence of cooperation in the real situation where the individuals' behaviour and their relationship adaptively co-evolve. (general)

  7. The RNA-world and co-evolution hypotheses and the origin of life: Implications, research strategies and perspectives

    Science.gov (United States)

    Lahav, Noam

    1993-12-01

    The applicability of the RNA-world and co-evolution hypotheses to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficulties. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activities of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypotheses under consideration. It is suggested that the noveldirected molecular evolution technology, andmolecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a ‘Primordial Darwinian entity’.

  8. Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study.

    Science.gov (United States)

    Singh, Tanya; Adekoya, Olayiwola Adedotun; Jayaram, B

    2015-04-01

    Matrix metalloproteinases (MMPs) consist of a class of proteins required for normal tissue function. Their over expression is associated with many disease states and hence the interest in MMPs as drug targets. Almost all MMP inhibitors have been reported to fail in clinical trials due to lack of specificity. Zinc in the binding site of metalloproteinases performs essential biological functions and contributes to the binding affinity of inhibitors. The multiple possibilities for coordination geometry and the consequent charge on the zinc atom indicate that parameters developed are not directly transferable across different families of zinc metalloproteinases with different zinc coordination geometries, active sites and ligand architectures which makes it difficult to evaluate metal-ligand interactions. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising docking of small molecule inhibitors against the target MMPs, derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, molecular dynamics simulations on the docked ligand-MMP complexes and evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted binding free energies and experiment, suggesting the potential applicability of the pathway. We then proceeded to formulate a few design principles which identify the key protein residues for generating molecules with high affinity and specificity against each of the MMPs.

  9. Enhanced Electrical Conductivity of Molecularly p-Doped Poly(3-hexylthiophene) through Understanding the Correlation with Solid-State Order

    KAUST Repository

    Hynynen, Jonna

    2017-10-11

    Molecular p-doping of the conjugated polymer poly(3-hexylthiophene) (P3HT) with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) is a widely studied model system. Underlying structure–property relationships are poorly understood because processing and doping are often carried out simultaneously. Here, we exploit doping from the vapor phase, which allows us to disentangle the influence of processing and doping. Through this approach, we are able to establish how the electrical conductivity varies with regard to a series of predefined structural parameters. We demonstrate that improving the degree of solid-state order, which we control through the choice of processing solvent and regioregularity, strongly increases the electrical conductivity. As a result, we achieve a value of up to 12.7 S cm–1 for P3HT:F4TCNQ. We determine the F4TCNQ anion concentration and find that the number of (bound + mobile) charge carriers of about 10–4 mol cm–3 is not influenced by the degree of solid-state order. Thus, the observed increase in electrical conductivity by almost 2 orders of magnitude can be attributed to an increase in charge-carrier mobility to more than 10–1 cm2 V–1 s–1. Surprisingly, in contrast to charge transport in undoped P3HT, we find that the molecular weight of the polymer does not strongly influence the electrical conductivity, which highlights the need for studies that elucidate structure–property relationships of strongly doped conjugated polymers.

  10. A model of designing as the intersection between uncertainty perception, information processing, and coevolution

    DEFF Research Database (Denmark)

    Lasso, Sarah Venturim; Cash, Philip; Daalhuizen, Jaap

    2016-01-01

    transformation process. Here the aim of the activity is to reduce the perceived uncertainty through identifying and integrating external information and knowledge within the design team. For2example, when perceiving uncertainty the designer might seek new information online, process this information, and share......A number of fundamental perspectives on designing have been described in the literature, in particular problem/solution coevolution and information use. However, these different perspectives have to-date been modelled separately, making holistic description of design activity difficult. This paper...... takes the first steps towards linking these disparate perspectives in a model of designing that synthesises coevolution and information processing. How designers act has been shown to play an important role in the process of New Product Development (NPD) (See e.g. Badke-Schaub and Frankenberger, 2012...

  11. Molecular Analysis of Flood Deposits in the Tennessee River Valley: Implications for Understanding Carbon Cycling in Fluvial Environments and Anthropogenic Impacts

    Science.gov (United States)

    Blackaby, E.; Craven, O. D.; Hockaday, W. C.; Forman, S. L.; Stinchcomb, G. E.

    2017-12-01

    The middle Tennessee River Valley contains both historic and prehistoric (>AD 1600) flood deposits. Stratigraphic sequences of stacked flood deposits that often bury soils provide new insights on organic matter transported and preserved prior to and after European colonization. This study focused on understanding carbon cycling within a dynamic fluvial system and quantifying the anthropogenic effect on flood processes through the analysis of molecular components of the organic matter. The data may be helpful in discerning the organic geochemical fingerprint for historic and prehistoric flood deposits. Ten samples were collected from three sites at varying depths and dated using optically stimulated luminescence (OSL). All samples underwent solid-state cross polar 13C NMR analysis at twelve kilohertz, and a molecular mixing model (MMM) was used to determine the molecular components of the organic matter present in each sample. The MMM categorized carbon molecules present in each sample in terms of carbohydrate, protein, lipid, lignin, char, or pure carbonyl. Char was the most prominent molecular component of all ten samples ranging from 28.7 to 55.9% and comprised larger percentages in prehistoric deposits. The historic deposits, while still char dominated, showed more molecular diversity with higher percentages in non-char carbon groups. The carbonyl, lipid, and carbohydrate groups are present throughout all the samples with the carbonyl ranging from 9.3 to 31.4%, the lipid from 5.5 to 16.7%, and the carbohydrate from 4.4 to 16.9%. The high amount of carbonyl throughout the samples indicates that the deposits existed in a highly oxidizing environment. Differences in the presence and amount of carbon groups between historic and prehistoric flood deposits potentially reflect diagenic alternation of organic matter through time, changes in human land use, or some combination processes. These preliminary results possibly indicate changes in carbon pools accessed with

  12. Contrasting patterns in mammal-bacteria coevolution: bartonella and leptospira in bats and rodents.

    Directory of Open Access Journals (Sweden)

    Bonnie R Lei

    2014-03-01

    Full Text Available Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host-pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model.We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001. Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001. In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629. Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731, while Bartonella and rodents had the fewest (0.264.In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover

  13. Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents

    Science.gov (United States)

    Lei, Bonnie R.; Olival, Kevin J.

    2014-01-01

    Background Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model. Methodology/Principal Findings We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264). Conclusions/Significance In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and

  14. Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants.

    Science.gov (United States)

    Woo, Jeongmin; Robertson, David L; Lovell, Simon C

    2014-04-01

    A major challenge for developing effective treatments for HIV-1 is the viruses' ability to generate new variants. Inter-strain recombination is a major contributor to this high evolutionary rate, since at least 20% of viruses are observed to be recombinant. However, the patterns of recombination vary across the viral genome. A number of factors influence recombination, including sequence identity and secondary RNA structure. In addition the recombinant genome must code for a functional virus, and expressed proteins must fold to stable and functional structures. Any intragenic recombination that disrupts internal residue contacts may therefore produce an unfolded protein. Here we find that contact maps based on protein structures predict recombination breakpoints observed in the HIV-1 pandemic. Moreover, many pairs of contacting residues that are unlikely to be disrupted by recombination are coevolving. We conclude that purifying selection arising from protein structure and intramolecular coevolutionary changes shapes the observed patterns of recombination in HIV-1. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Molecular diversity of entodiniomorphid ciliate Troglodytella abrassarti and its coevolution with chimpanzees

    Czech Academy of Sciences Publication Activity Database

    Vallo, Peter; Petrželková, Klára Judita; Profousová, Ilona; Petrášová, J.; Pomajbíková, K.; Leendertz, F.; Hashimoto, C.; Simmons, N.; Babweteera, F.; Machanda, Z.; Piel, A.; Robbins, M. M.; Boesch, C.; Sanz, C.; Morgan, D.; Sommer, V.; Furuichi, T.; Fujita, S.; Matsuzawa, T.; Kaur, T.; Huffman, M. A.; Modrý, David

    2012-01-01

    Roč. 148, č. 4 (2012), s. 525-533 ISSN 0002-9483 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : SSU rDNA * ITS * entodiniomorphida * Troglodytellidae * Pan troglodytes Subject RIV: EG - Zoology Impact factor: 2.481, year: 2012

  16. Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification.

    Science.gov (United States)

    Althoff, David M; Segraves, Kari A; Smith, Christopher I; Leebens-Mack, James; Pellmyr, Olle

    2012-03-01

    Coevolution is thought to be especially important in diversification of obligate mutualistic interactions such as the one between yuccas and pollinating yucca moths. We took a three-step approach to examine if plant and pollinator speciation events were likely driven by coevolution. First, we tested whether there has been co-speciation between yuccas and pollinator yucca moths in the genus Tegeticula (Prodoxidae). Second, we tested whether co-speciation also occurred between yuccas and commensalistic yucca moths in the genus Prodoxus (Prodoxidae) in which reciprocal evolutionary change is unlikely. Finally, we examined the current range distributions of yuccas in relationship to pollinator speciation events to determine if plant and moth speciation events likely occurred in sympatry or allopatry. Co-speciation analyses of yuccas with their coexisting Tegeticula pollinator and commensalistic Prodoxus lineages demonstrated phylogenetic congruence between both groups of moths and yuccas, even though moth lineages differ in the type of interaction with yuccas. Furthermore, Yucca species within a lineage occur primarily in allopatry rather than sympatry. We conclude that biogeographic factors are the overriding force in plant and pollinator moth speciation and significant phylogenetic congruence between the moth and plant lineages is likely due to shared biogeography rather than coevolution. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease

    Directory of Open Access Journals (Sweden)

    Jui-Yu eChou

    2015-05-01

    Full Text Available Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA, including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA. Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.

  18. The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease.

    Science.gov (United States)

    Chou, Jui-Yu; Leu, Jun-Yi

    2015-01-01

    Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.

  19. Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

    Science.gov (United States)

    Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

    2017-12-01

    Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the

  20. Understanding the interface between silicon-based materials and water: Molecular-dynamics exploration of infrared spectra

    Directory of Open Access Journals (Sweden)

    José A. Martinez-Gonzalez

    2017-11-01

    Full Text Available Molecular-dynamics simulations for silicon, hydrogen- and hydroxyl-terminated silicon in contact with liquid water, at 220 and 300 K, display water-density ‘ordering’ along the laboratory z-axis, emphasising the hydrophobicity of the different systems and the position of this first adsorbed layer. Density of states (DOS of the oxygen and proton velocity correlation functions (VACFs and infrared (IR spectra of the first monolayer of adsorbed water, calculated via Fourier transformation, indicate similarities to more confined, ice-like dynamical behaviour (redolent of ice. It was observed that good qualitative agreement is obtained between the DOS for this first layer in all systems. The DOS for the lower-frequency zone indicates that for the interface studied (i.e., the first layer near the surface, the water molecules try to organise in a similar form, and that this form is intermediate between liquid water and ice. For IR spectra, scrutiny of the position of the highest-intensity peaks for the stretching and bending bands indicate that such water molecules in the first solvating layer are organised in an intermediate fashion between ice and liquid water.

  1. Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling

    Directory of Open Access Journals (Sweden)

    Thiruvengadam Raguchander

    2009-12-01

    Full Text Available Abstract Background Plant Growth Promoting Rhizobacteria (PGPR, Pseudomonas fluorescens strain KH-1 was found to exhibit plant growth promotional activity in rice under both in-vitro and in-vivo conditions. But the mechanism underlying such promotional activity of P. fluorescens is not yet understood clearly. In this study, efforts were made to elucidate the molecular responses of rice plants to P. fluorescens treatment through protein profiling. Two-dimensional polyacrylamide gel electrophoresis strategy was adopted to identify the PGPR responsive proteins and the differentially expressed proteins were analyzed by mass spectrometry. Results Priming of P. fluorescens, 23 different proteins found to be differentially expressed in rice leaf sheaths and MS analysis revealed the differential expression of some important proteins namely putative p23 co-chaperone, Thioredoxin h- rice, Ribulose-bisphosphate carboxylase large chain precursor, Nucleotide diPhosphate kinase, Proteosome sub unit protein and putative glutathione S-transferase protein. Conclusion Functional analyses of the differential proteins were reported to be directly or indirectly involved in growth promotion in plants. Thus, this study confirms the primary role of PGPR strain KH-1 in rice plant growth promotion.

  2. Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling.

    Science.gov (United States)

    Kandasamy, Saveetha; Loganathan, Karthiba; Muthuraj, Raveendran; Duraisamy, Saravanakumar; Seetharaman, Suresh; Thiruvengadam, Raguchander; Ponnusamy, Balasubramanian; Ramasamy, Samiyappan

    2009-12-24

    Plant Growth Promoting Rhizobacteria (PGPR), Pseudomonas fluorescens strain KH-1 was found to exhibit plant growth promotional activity in rice under both in-vitro and in-vivo conditions. But the mechanism underlying such promotional activity of P. fluorescens is not yet understood clearly. In this study, efforts were made to elucidate the molecular responses of rice plants to P. fluorescens treatment through protein profiling. Two-dimensional polyacrylamide gel electrophoresis strategy was adopted to identify the PGPR responsive proteins and the differentially expressed proteins were analyzed by mass spectrometry. Priming of P. fluorescens, 23 different proteins found to be differentially expressed in rice leaf sheaths and MS analysis revealed the differential expression of some important proteins namely putative p23 co-chaperone, Thioredoxin h- rice, Ribulose-bisphosphate carboxylase large chain precursor, Nucleotide diPhosphate kinase, Proteosome sub unit protein and putative glutathione S-transferase protein. Functional analyses of the differential proteins were reported to be directly or indirectly involved in growth promotion in plants. Thus, this study confirms the primary role of PGPR strain KH-1 in rice plant growth promotion.

  3. Understanding the lid movements of LolA in Escherichia coli using molecular dynamics simulation and in silico point mutation.

    Science.gov (United States)

    Murahari, Priyadarshini; Anishetty, Sharmila; Pennathur, Gautam

    2013-12-01

    The Lol system in Escherichia coli is involved in localization of lipoproteins and hence is essential for growth of the organism. LolA is a periplasmic chaperone that binds to outer-membrane specific lipoproteins and transports them from inner membrane to outer membrane through LolB. The hydrophobic lipid-binding cavity of LolA consists of α-helices which act as a lid in regulating the transfer of lipoproteins from LolA to LolB. The current study aims to investigate the structural changes observed in LolA during the transition from open to closed conformation in the absence of lipoprotein. Molecular dynamics (MD) simulations were carried out for two LolA crystal structures; LolA(R43L), and in silico mutated MsL43R for a simulation time of 50 ns in water environment. We have performed an in silico point mutation of leucine to arginine in MsL43R to evaluate the importance of arginine to induce structural changes and impact the stability of protein structure. A complete dynamic analysis of open to closed conformation reveals the existence of two distinct levels; closing of lid and closing of entrance of hydrophobic cavity. Our analysis reveals that the structural flexibility of LolA is an important factor for its role as a periplasmic chaperone. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. The evolution of viviparity: molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes.

    Science.gov (United States)

    Van Dyke, James U; Brandley, Matthew C; Thompson, Michael B

    2014-01-01

    Squamate reptiles (lizards and snakes) are an ideal model system for testing hypotheses regarding the evolution of viviparity (live birth) in amniote vertebrates. Viviparity has evolved over 100 times in squamates, resulting in major changes in reproductive physiology. At a minimum, all viviparous squamates exhibit placentae formed by the appositions of maternal and embryonic tissues, which are homologous in origin with the tissues that form the placenta in therian mammals. These placentae facilitate adhesion of the conceptus to the uterus as well as exchange of oxygen, carbon dioxide, water, sodium, and calcium. However, most viviparous squamates continue to rely on yolk for nearly all of their organic nutrition. In contrast, some species, which rely on the placenta for at least a portion of organic nutrition, exhibit complex placental specializations associated with the transport of amino acids and fatty acids. Some viviparous squamates also exhibit reduced immunocompetence during pregnancy, which could be the result of immunosuppression to protect developing embryos. Recent molecular studies using both candidate-gene and next-generation sequencing approaches have suggested that at least some of the genes and gene families underlying these phenomena play similar roles in the uterus and placenta of viviparous mammals and squamates. Therefore, studies of the evolution of viviparity in squamates should inform hypotheses of the evolution of viviparity in all amniotes, including mammals.

  5. Quantitative Fermi level tuning in amorphous organic semiconductor by molecular doping: Toward full understanding of the doping mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jin-Peng, E-mail: yangjp@yzu.edu.cn, E-mail: uenon@faculty.chiba-u.jp; Wang, Wen-Qing; Cheng, Li-Wen; Zeng, Xiang-Hua [College of Physical Science and Technology, Yangzhou University, Jiangsu 225009 (China); Bussolotti, Fabio [Institute for Molecular Science, Okazaki 444-8585 (Japan); Li, Yan-Qing; Tang, Jian-Xin [Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou 215123 (China); Kera, Satoshi [Institute for Molecular Science, Okazaki 444-8585 (Japan); Graduate School of Advanced Integration Science, Chiba University, Chiba 263–8522 (Japan); Ueno, Nobuo, E-mail: yangjp@yzu.edu.cn, E-mail: uenon@faculty.chiba-u.jp [Graduate School of Advanced Integration Science, Chiba University, Chiba 263–8522 (Japan)

    2016-08-29

    The doping mechanism in organic-semiconductor films has been quantitatively studied via ultrahigh-sensitivity ultraviolet photoelectron spectroscopy of N,N-bis(1-naphthyl)-N,N-diphenyl-1,1-biphenyl-4,4-diamine (α-NPD) films doped with hexaazatriphenylene-hexacarbonitrile [HAT(CN){sub 6}]. We observed that HOMO of α-NPD shifts to the Fermi level (E{sub F}) in two different rates with the doping concentration of HAT(CN){sub 6}, but HOMO distributions of both pristine and doped amorphous α-NPD films are excellently approximated with a same Gaussian distribution without exponential tail states over ∼5 × 10{sup 18} cm{sup −3} eV{sup −1}. From the theoretical simulation of the HAT(CN){sub 6}-concentration dependence of the HOMO in doped films, we show that the passivation of Gaussian-distributed hole traps, which peak at 1.1 eV above the HOMO onset, occurs at ultralow doping [HAT(CN){sub 6} molecular ratio (MR) < 0.01], leading to a strong HOMO shift of ∼0.40 eV towards E{sub F}, and MR dependence of HOMO changes abruptly at MR ∼ 0.01 to a weaker dependence for MR > 0.01 due to future of the dopant acceptor level.

  6. Towards further understanding of stacking fault tetrahedron absorption and defect-free channels – A molecular dynamics study

    International Nuclear Information System (INIS)

    Fan, Haidong; El-Awady, Jaafar A.; Wang, Qingyuan

    2015-01-01

    Highlights: • Stacking fault tetrahedron (SFT) is fully absorbed by screw dislocation. • Absorbed SFT becomes moveable with the aid of Lomer dislocations. • Finally SFT is removed from the specimen or from defect-free channels. • Two scenarios responsible for the formation of defect-free channels were proposed. - Abstract: The mechanisms leading to stacking fault tetrahedron (SFT) absorption via interactions with dislocations, and subsequent formation of plastic flow localization in defect-free channels, which were frequently observed in irradiated materials in transmission electron microscopy experiments, are still unclear. To address this, screw dislocation interactions with SFTs in copper were investigated using molecular dynamics (MD) simulations. The interaction details reveal that a screw dislocation can fully absorb an SFT through the thermally activated transformation of Lomer–Cottrell lock into Lomer dislocations. After absorption, almost all the vacancies in the SFT are transferred into Lomer dislocations, which are able to move transversely under complex loading conditions. As a result, SFTs can be removed from the material (for SFTs near surface) or from defect-free channels (for SFTs in the bulk) with the aid of Lomer dislocations. In addition, it was shown that this absorption process is favorable only at high temperature, low applied shear stress and/or high SFT density. These results are in good agreement with in situ TEM observations. The current simulations and analyses provide useful insights into the formation mechanisms of defect-free channels in irradiated materials

  7. A Decade of Molecular Understanding of Withanolide Biosynthesis and In vitro Studies in Withania somnifera (L.) Dunal: Prospects and Perspectives for Pathway Engineering

    Science.gov (United States)

    Dhar, Niha; Razdan, Sumeer; Rana, Satiander; Bhat, Wajid W.; Vishwakarma, Ram; Lattoo, Surrinder K.

    2015-01-01

    Withania somnifera, a multipurpose medicinal plant is a rich reservoir of pharmaceutically active triterpenoids that are steroidal lactones known as withanolides. Though the plant has been well-characterized in terms of phytochemical profiles as well as pharmaceutical activities, limited attempts have been made to decipher the biosynthetic route and identification of key regulatory genes involved in withanolide biosynthesis. This scenario limits biotechnological interventions for enhanced production of bioactive compounds. Nevertheless, recent emergent trends vis-à-vis, the exploration of genomic, transcriptomic, proteomic, metabolomics, and in vitro studies have opened new vistas regarding pathway engineering of withanolide production. During recent years, various strategic pathway genes have been characterized with significant amount of regulatory studies which allude toward development of molecular circuitries for production of key intermediates or end products in heterologous hosts. Another pivotal aspect covering redirection of metabolic flux for channelizing the precursor pool toward enhanced withanolide production has also been attained by deciphering decisive branch point(s) as robust targets for pathway modulation. With these perspectives, the current review provides a detailed overview of various studies undertaken by the authors and collated literature related to molecular and in vitro approaches employed in W. somnifera for understanding various molecular network interactions in entirety. PMID:26640469

  8. A decade of molecular understanding of withanolide biosynthesis and in vitro studies in Withania somnifera (L. Dunal: Prospects and perspectives for pathway engineering

    Directory of Open Access Journals (Sweden)

    Niha eDhar

    2015-11-01

    Full Text Available Withania somnifera, a multipurpose medicinal plant is a rich reservoir of pharmaceutically active triterpenoids that are steroidal lactones known as withanolides. Though the plant has been well characterized in terms of phytochemical profiles as well as pharmaceutical activities, limited attempts have been made to decipher the biosynthetic route and identification of key regulatory genes involved in withanolide biosynthesis. This scenario limits biotechnological interventions for enhanced production of bioactive compounds. Nevertheless, recent emergent trends vis-à-vis, the exploration of genomic, transcriptomic, proteomic, metabolomic and in vitro studies have opened new vistas regarding pathway engineering of withanolide production. During recent years, various strategic pathway genes have been characterized with significant amount of regulatory studies which allude towards development of molecular circuitries for production of key intermediates or end products in heterologous hosts. Another pivotal aspect covering redirection of metabolic flux for channelizing the precursor pool towards enhanced withanolide production has also been attained by deciphering decisive branch point(s as robust targets for pathway modulation. With these perspectives, the current review provides a detailed overview of various studies undertaken by the authors and collated literature related to molecular and in vitro approaches employed in W. Somnifera for understanding various molecular network interactions in entirety.

  9. Design as co-evolution of problem, solution, and audience

    DEFF Research Database (Denmark)

    Halstrøm, Per Liljenberg; Galle, Per

    2014-01-01

    design beyond the level of definitions, reviewing canonical theories about design as a professional enterprise. We find that the well-established theoretical notion of ‘co-evolution’ of problem and solution in design has its merits in regard to understanding design deliberations; but also that existing......The meaning of ‘design’ can be captured in a general way by a good definition, but even the best definition cannot provide an understanding sufficiently deep to guide the professional designer or the student of design in the intricate deliberations of doing design in practice. Therefore we explore...

  10. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices.

    Science.gov (United States)

    Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

    2012-01-01

    Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography.

  11. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

    Science.gov (United States)

    Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

    2013-01-01

    Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography. PMID:23403722

  12. Current understanding of PrnP Genetics: A tool for Molecular Assisted Selection in Sheep Populations (A review

    Directory of Open Access Journals (Sweden)

    Viorica Cosier

    2016-04-01

    Full Text Available Scrapie is a neurodegenerative prion disease of sheep, goats and mouflons, belonging to the group of transmissible spongiform encephalopathies (TSEs, which affects humans as well. Even though classical scrapie has been known for over 250 years, the 1985 BSE crisis related to the advent of new forms of the Creutzfeldt-Jakob disease (vCJD in humans imposed the implementation of rapid coercive legal measures of prevention, control and eradication of TSEs. According to the prion hypothesis, the transmissible agent is the pathological isoform (PrPSc of cellular prion protein (PrPC. Specific polymorphisms of the gene that encodes cell prion protein (PrnP in sheep have been associated with resistance / natural susceptibility to the development and progression of the disease. Combinations of alleles at three adjacent codons (136 [A/V], 154 [H/R], 171 [H/Q/R] underpin the classification of 15 possible genotypes in risk classes, applicable in selection schemes where the maximum resistance is conferred by ARR allele, and the minimum by the VRQ allele. Although, after applying these programmes, the genetic structure of sheep populations has changed favourably, genotype association studies showed that no genotype is completely resistant to the infection, including homozygote ARR / ARR. With the discovery of atypical scrapie (Nor98, it became evident that the connection between the genetics of prion protein gene polymorphisms and susceptibility to the disease must be re-evaluated individually for each breed. In scrapie monitoring and control programmes, three diagnostic categories of the disease are observed: classical scrapie, atypical scrapie and BSE scrapie in small ruminant. This review shows the chronology of progress in the fight for the eradication of TSEs in sheep, 30 years after the BSE epidemic outburst, focusing especially on the link between the molecular diagnostic forms and the genetics of the disease.

  13. Molecular Understanding of Growth Inhibitory Effect from Irradiated to Bystander Tumor Cells in Mouse Fibrosarcoma Tumor Model.

    Directory of Open Access Journals (Sweden)

    Sejal Desai

    Full Text Available Even though bystander effects pertaining to radiation risk assessment has been extensively studied, the molecular players of radiation induced bystander effect (RIBE in the context of cancer radiotherapy are poorly known. In this regard, the present study is aimed to investigate the effect of irradiated tumor cells on the bystander counterparts in mouse fibrosarcoma (WEHI 164 cells tumor model. Mice co-implanted with WEHI 164 cells γ-irradiated with a lethal dose of 15 Gy and unirradiated (bystander WEHI 164 cells showed inhibited tumor growth, which was measured in terms of tumor volume and Luc+WEHI 164 cells based bioluminescence in vivo imaging. Histopathological analysis and other assays revealed decreased mitotic index, increased apoptosis and senescence in these tumor tissues. In addition, poor angiogenesis was observed in these tumor tissues, which was further confirmed by fluorescence imaging of tumor vascularisation and CD31 expression by immuno-histochemistry. Interestingly, the growth inhibitory bystander effect was exerted more prominently by soluble factors obtained from the irradiated tumor cells than the cellular fraction. Cytokine profiling of the supernatants obtained from the irradiated tumor cells showed increased levels of VEGF, Rantes, PDGF, GMCSF and IL-2 and decreased levels of IL-6 and SCF. Comparative proteomic analysis of the supernatants from the irradiated tumor cells showed differential expression of total 24 protein spots (21 up- and 3 down-regulated when compared with the supernatant from the unirradiated control cells. The proteins which showed substantially higher level in the supernatant from the irradiated cells included diphosphate kinase B, heat shock cognate, annexin A1, angiopoietin-2, actin (cytoplasmic 1/2 and stress induced phosphoprotein 1. However, the levels of proteins like annexin A2, protein S100 A4 and cofilin was found to be lower in this supernatant. In conclusion, our results provided deeper

  14. Understanding the influence of buckwheat bran on wheat dough baking performance: Mechanistic insights from molecular and material science approaches.

    Science.gov (United States)

    Zanoletti, Miriam; Marti, Alessandra; Marengo, Mauro; Iametti, Stefania; Pagani, M Ambrogina; Renzetti, Stefano

    2017-12-01

    A molecular and material science approach is used to describe the influence of coarse and fine buckwheat bran on wheat dough properties and bread textural quality. Focus is given on (i) gluten solvation and structural arrangements in presence of bran as studied by front-face fluorescence; (ii) thermo-mechanical behavior of dough during heating studied by dynamic mechanical thermal analysis and (iii) texture of bread crumb analyzed in terms of a cellular solid. The thermo-mechanical behavior of dough was found to be largely related to starch phase transitions during heating. The use of thermodynamic approaches to biopolymer melting revealed that key transitions such as the onset of starch gelatinization were function of the interplay of water and bran volume fractions in the dough. Front-face fluorescence studies in wheat dough revealed that gluten solvation and structural arrangements were delayed by increasing bran addition level and reduction in particle size, as indicated by the drastic decrease in the protein surface hydrophobicity index. Variations in gluten structure could be strongly related to dough baking performance, i.e. specific volume. With regards to texture, the approach revealed that crumb texture was controlled by variations in density, moisture and bran volume fractions. Overall, this study elucidates a number of physical mechanisms describing the influence of buckwheat bran addition to dough and bread quality. These mechanisms strongly pointed at the influence of bran on water partitioning among the main polymeric components. In the future, these mechanisms should be investigated with bran material of varying source, composition and structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Information-triggered Co-evolution: A Combined Process Perspective

    DEFF Research Database (Denmark)

    Cash, Philip; Gonçalves, Milene

    2017-01-01

    Core elements of design work include the development of problem/solution understanding, as well as information and knowledge sharing activities. However, their interrelationships have been little explored. As such, this work aims to take the first steps towards a more integrated evaluation and de...

  16. Taxonomy, phylogeny, and coevolution of pines and their stem rusts

    Science.gov (United States)

    C. I. Millar; B. B. Kinloch

    1991-01-01

    We review and reinterpret major events in the evolution of pines and their stem rusts using information from their taxonomy, genetics, biogeography, and fossil history. Understanding of pine evolution has been significantly revised in the last 20 years. Pines appear to have evolved early in the Mesozoic and to have diversified and migrated throughout middle latitudes...

  17. Molecular Profiling of the Phytophthora plurivora Secretome: A Step towards Understanding the Cross-Talk between Plant Pathogenic Oomycetes and Their Hosts

    Science.gov (United States)

    Fleischmann, Frank; Dalio, Ronaldo J. D.; Di Maro, Antimo; Scognamiglio, Monica; Fiorentino, Antonio; Parente, Augusto; Osswald, Wolfgang; Chambery, Angela

    2014-01-01

    The understanding of molecular mechanisms underlying host–pathogen interactions in plant diseases is of crucial importance to gain insights on different virulence strategies of pathogens and unravel their role in plant immunity. Among plant pathogens, Phytophthora species are eliciting a growing interest for their considerable economical and environmental impact. Plant infection by Phytophthora phytopathogens is a complex process coordinated by a plethora of extracellular signals secreted by both host plants and pathogens. The characterization of the repertoire of effectors secreted by oomycetes has become an active area of research for deciphering molecular mechanisms responsible for host plants colonization and infection. Putative secreted proteins by Phytophthora species have been catalogued by applying high-throughput genome-based strategies and bioinformatic approaches. However, a comprehensive analysis of the effective secretome profile of Phytophthora is still lacking. Here, we report the first large-scale profiling of P. plurivora secretome using a shotgun LC-MS/MS strategy. To gain insight on the molecular signals underlying the cross-talk between plant pathogenic oomycetes and their host plants, we also investigate the quantitative changes of secreted protein following interaction of P. plurivora with the root exudate of Fagus sylvatica which is highly susceptible to the root pathogen. We show that besides known effectors, the expression and/or secretion levels of cell-wall-degrading enzymes were altered following the interaction with the host plant root exudate. In addition, a characterization of the F. sylvatica root exudate was performed by NMR and amino acid analysis, allowing the identification of the main released low-molecular weight components, including organic acids and free amino acids. This study provides important insights for deciphering the extracellular network involved in the highly susceptible P. plurivora-F. sylvatica interaction

  18. Molecular biomineralization: toward an understanding of the biogenic origin of polymetallic nodules, seamount crusts, and hydrothermal vents.

    Science.gov (United States)

    Wang, Xiaohong; Wiens, Matthias; Schröder, Heinz C; Schloßmacher, Ute; Müller, Werner E G

    2011-01-01

    Polymetallic nodules and crusts, hydrothermal vents from the Deep Sea are economically interesting, since they contain alloying components, e.g., manganese or cobalt, that are used in the production of special steels; in addition, they contain rare metals applied for plasma screens, for magnets in hard disks, or in hybrid car motors. While hydrothermal vents can regenerate in weeks, polymetallic nodules and seamount crusts grow slowly. Even though the geochemical basis for the growth of the nodules and crusts has been well studied, the contribution of microorganisms to the formation of these minerals remained obscure. Recent HR-SEM (high-resolution scanning electron microscopy) analyses of nodules and crusts support their biogenic origin. Within the nodules, bacteria with surface S-layers are arranged on biofilm-like structures, around which Mn deposition starts. In crusts, coccoliths represent the dominant biologically formed structures that act as bio-seeds for an initial Mn deposition. In contrast, hydrothermal vents have apparently an abiogenic origin; however, their minerals are biogenically transformed by bacteria. In turn, strategies can now be developed for biotechnological enrichment as well as selective dissolution of metals from such concretions. We are convinced that the recent discoveries will considerably contribute to our understanding of the participation of organic matrices in the enrichment of those metals and will provide the basis for feasibility studies for biotechnological applications.

  19. Understanding the molecular biology of intervertebral disc degeneration and potential gene therapy strategies for regeneration: a review.

    Science.gov (United States)

    Sampara, Prasanthi; Banala, Rajkiran Reddy; Vemuri, Satish Kumar; Av, Gurava Reddy; Gpv, Subbaiah

    2018-03-22

    Intervertebral disc degeneration (IVDD) is a multi-factorial process characterized by phenotypic and genotypic changes, which leads to low back pain and disability. Prolonged imbalance between anabolism and catabolism in discs alters their composition resulting in progressive loss of proteoglycans and hydration leading to IVDD. The current managements for IVDD are only able to relieve the symptoms but do not address the underlying pathology of degeneration. Researchers have tried to find out differences between the aging and degeneration of the disc. Intense attempts are in progress for identifying the various factors responsible for disc degeneration, as well as strategies for regeneration. Recently biological approaches have gained thrust in the field of IVDD. The present review illustrates the current understanding of intervertebral disc degeneration and aims to put forth recent advancements in regeneration strategies involving different biological therapies such as growth factor, cell, and gene therapy. The potentials and consequences of these therapies are also extensively discussed along with citing the most suitable method, that is, the gene therapy in detail. Initially, gene therapy was mediated by viral vectors but recent progress has enabled researchers to opt for non-virus-mediated gene therapy methods, which ensure that there are no risks of mutagenicity and infection in target cells. With constant efforts, non-virus-mediated gene therapy may prove to be an extremely powerful tool in treatment of IVDD in future.

  20. Ecological mechanisms for the coevolution of mating systems and defence.

    Science.gov (United States)

    Campbell, Stuart A

    2015-02-01

    The diversity of flowering plants is evident in two seemingly unrelated aspects of life history: sexual reproduction, exemplified by the stunning variation in flower form and function, and defence, often in the form of an impressive arsenal of secondary chemistry. Researchers are beginning to appreciate that plant defence and reproduction do not evolve independently, but, instead, may have reciprocal and interactive (coevolutionary) effects on each other. Understanding the mechanisms for mating-defence interactions promises to broaden our understanding of how ecological processes can generate these two rich sources of angiosperm diversity. Here, I review current research on the role of herbivory as a driver of mating system evolution, and the role of mating systems in the evolution of defence strategies. I outline different ecological mechanisms and processes that could generate these coevolutionary patterns, and summarize theoretical and empirical support for each. I provide a conceptual framework for linking plant defence with mating system theory to better integrate these two research fields.

  1. Rod monochromacy and the coevolution of cetacean retinal opsins.

    Directory of Open Access Journals (Sweden)

    Robert W Meredith

    2013-04-01

    Full Text Available Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1, short-wavelength sensitive opsin 1 (SWS1, and long-wavelength sensitive opsin (LWS in selected cetaceans, but have not examined the full complement of opsin genes across the complete range of cetacean families. Here, we report protein-coding sequences for RH1 and both color opsin genes (SWS1, LWS from representatives of all extant cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some cetaceans are rod monochomats. Molecular evolutionary analyses contradict the "coastal" hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti and in toothed whales (Odontoceti. Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1 Balaenidae (bowhead and right whales, (2 Balaenopteroidea (rorquals plus gray whale, (3 Mesoplodon bidens (Sowerby's beaked whale, (4 Physeter macrocephalus (giant sperm whale, and (5 Kogia breviceps (pygmy sperm whale. All of these cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple cetacean lineages renders these taxa rod monochromats, a condition previously unknown among

  2. Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times.

    Science.gov (United States)

    Hoyal Cuthill, Jennifer F; Charleston, Michael

    2015-12-01

    Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  3. Kingian Co-Evolution of the Water and Mineral/Rock Components for Earth and Mars: Implications for Planetary Habitability (Invited)

    Science.gov (United States)

    Baker, V. R.

    2013-12-01

    Planetary habitability may fluctuate episodically against a background provided by the co-evolution of a planet's mineral/rock (geosphere) components and its water (hydrosphere) in relation to its position in a circumstellar system. The water/rock (geosphere/hydrosphere) co-evolution can be inferred from the geological histories of the terrestrial planets of the solar system, particularly from the very extensive understanding of Earth and Mars. Habitability and water/rock co-evolution have components that are tychistic (i.e., driven by chance) and anancastic (i.e., dynamically driven largely by deterministic forces). They also have a final, end-directed (i.e., teleomatic) aspect that operates in accordance with natural laws. This is a larger perspective on the idea of planetary habitability than is generally associated with an astronomical approach, and it incorporates additional insights from a geological perspective on the issue. The geological histories of Mars and Earth are punctuated with critical, short-term epochs of extreme change, which for Earth are known to be associated with major disruptions of its biosphere. These catastrophic epochs can be described as a type of non-Darwinian evolution that was envisioned by the geologist Clarence King. In an 1877 paper King proposed that accelerated evolutionary change occurs during sudden environmental disruptions. Such Kingian disruptions in mineral/rock and water evolution mark the planetary histories of Mars and Earth, including the early formation and condensation of a steam atmosphere, an impacting cataclysm at about 3.9 to 4 Ga, episodes of concentrated volcanism and tectonism, and associated rapid changes in the linked atmosphere and hydrosphere. These disruptions are closely tied to migrations of water between different planetary reservoirs, the nature of planetary accretion, the origin of a physically coupled atmosphere and ocean, the prospects for initiating plate tectonics, and punctuated greenhouse

  4. Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.

    Science.gov (United States)

    Berezovskaya, Faina S; Wolf, Yuri I; Koonin, Eugene V; Karev, Georgy P

    2014-07-02

    The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The recent development of powerful genome engineering tools on the basis of CRISPR-Cas has sharply increased the interest in the diversity and evolution of these systems. Comparative genomic data indicate that during evolution of prokaryotes CRISPR-Cas loci are lost and acquired via horizontal gene transfer at high rates. Mathematical modeling and initial experimental studies of CRISPR-carrying microbes and viruses reveal complex coevolutionary dynamics. We performed a bifurcation analysis of models of coevolution of viruses and microbial host that possess CRISPR-Cas hereditary adaptive immunity systems. The analyzed Malthusian and logistic models display complex, and in particular, quasi-chaotic oscillation regimes that have not been previously observed experimentally or in agent-based models of the CRISPR-mediated immunity. The key factors for the appearance of the quasi-chaotic oscillations are the non-linear dependence of the host immunity on the virus load and the partitioning of the hosts into the immune and susceptible populations, so that the system consists of three components. Bifurcation analysis of CRISPR-host coevolution model predicts complex regimes including quasi-chaotic oscillations. The quasi-chaotic regimes of virus-host coevolution are likely to be biologically relevant given the evolutionary instability of the CRISPR-Cas loci revealed by comparative genomics. The results of this analysis might have implications beyond the CRISPR-Cas systems, i.e. could describe the behavior of any adaptive immunity system with a heritable component, be it genetic or epigenetic. These predictions are experimentally testable. This manuscript was reviewed by

  5. Social evolution. Oxytocin-gaze positive loop and the coevolution of human-dog bonds.

    Science.gov (United States)

    Nagasawa, Miho; Mitsui, Shouhei; En, Shiori; Ohtani, Nobuyo; Ohta, Mitsuaki; Sakuma, Yasuo; Onaka, Tatsushi; Mogi, Kazutaka; Kikusui, Takefumi

    2015-04-17

    Human-like modes of communication, including mutual gaze, in dogs may have been acquired during domestication with humans. We show that gazing behavior from dogs, but not wolves, increased urinary oxytocin concentrations in owners, which consequently facilitated owners' affiliation and increased oxytocin concentration in dogs. Further, nasally administered oxytocin increased gazing behavior in dogs, which in turn increased urinary oxytocin concentrations in owners. These findings support the existence of an interspecies oxytocin-mediated positive loop facilitated and modulated by gazing, which may have supported the coevolution of human-dog bonding by engaging common modes of communicating social attachment. Copyright © 2015, American Association for the Advancement of Science.

  6. Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants

    DEFF Research Database (Denmark)

    Munkacsi, A B; Pan, J J; Villesen, Palle

    2004-01-01

    of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral-mushroom...... family Pterulaceae using phylogenetic reconstructions based on broad taxon sampling, including the first mushroom collected from the garden of an ant species in the A. pilosum group. The domestication of the pterulaceous cultivar is independent from the domestication of the gilled mushrooms cultivated...

  7. The co-evolution of language and emotions

    Science.gov (United States)

    Jablonka, Eva; Ginsburg, Simona; Dor, Daniel

    2012-01-01

    We argue that language evolution started like the evolution of reading and writing, through cultural evolutionary processes. Genuinely new behavioural patterns emerged from collective exploratory processes that individuals could learn because of their brain plasticity. Those cultural–linguistic innovative practices that were consistently socially and culturally selected drove a process of genetic accommodation of both general and language-specific aspects of cognition. We focus on the affective facet of this culture-driven cognitive evolution, and argue that the evolution of human emotions co-evolved with that of language. We suggest that complex tool manufacture and alloparenting played an important role in the evolution of emotions, by leading to increased executive control and inter-subjective sensitivity. This process, which can be interpreted as a special case of self-domestication, culminated in the construction of human-specific social emotions, which facilitated information-sharing. Once in place, language enhanced the inhibitory control of emotions, enabled the development of novel emotions and emotional capacities, and led to a human mentality that departs in fundamental ways from that of other apes. We end by suggesting experimental approaches that can help in evaluating some of these proposals and hence lead to better understanding of the evolutionary biology of language and emotions. PMID:22734058

  8. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation.

    Science.gov (United States)

    Koza, Anna; Kusmierska, Anna; McLaughlin, Kimberley; Moshynets, Olena; Spiers, Andrew J

    2017-07-03

    Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. A hypothesis of coevolution between cooperation and responses to inequity

    Directory of Open Access Journals (Sweden)

    Sarah F Brosnan

    2011-04-01

    Full Text Available Recent evidence demonstrates that humans are not the only species to respond negatively to inequitable outcomes which are to their disadvantage. Several species respond negatively if they subsequently receive a less good reward than a social partner for completing the same task. While these studies suggest that the negative response to inequity is not a uniquely human behavior, they do not provide a functional explanation for the emergence of these responses due to similar characteristics among these species. Emerging data support the hypothesis that an aversion to inequity is a mechanism to promote successful long-term cooperative relationships amongst non-kin. In this paper, I discuss several converging lines of evidence which illustrate the need to further evaluate this relationship. First, cooperation can survive modest inequity; in explicitly cooperative interactions, individuals are willing to continue to cooperate despite inequitable outcomes as long as the partner’s overall behavior is equitable. Second, the context of inequity affects reactions to it in ways which support the idea that joint efforts lead to an expectation of joint payoffs. Finally, comparative studies indicate a link between the degree and extent of cooperation between unrelated individuals in a species and that species’ response to inequitable outcomes. This latter line of evidence indicates that this behavior evolved in conjunction with cooperation and may represent an adaptation to increase the payoffs associated with cooperative interactions. Together these data inform a testable working hypothesis for understanding decision-making in the context of inequity and provide a new, comparative framework for evaluating decision-making behavior.

  10. The Co-evolution of Bullying Perpetration, Homophobic Teasing, and a School Friendship Network.

    Science.gov (United States)

    Merrin, Gabriel J; Haye, Kayla de la; Espelage, Dorothy L; Ewing, Brett; Tucker, Joan S; Hoover, Matthew; Green, Harold D

    2018-03-01

    Bullying and homophobic teasing behaviors affect the lives of many school aged children, often co-occur, and tend to peak in middle school. While bullying and homophobic teasing behaviors are known to be peer group phenomena, studies typically examine the associations at the individual or school levels. An examination of these behaviors at the peer group level can aid in our understanding of the formation and maintenance of peer groups that engage in these forms of aggressive behavior (selection), and the extent to which friends and the peer group impact individual rates of these aggressive behaviors (influence). In this longitudinal study, we assess the co-evolution of friendship networks, bullying perpetration, and homophobic teasing among middle school students (n = 190) using a Stochastic Actor-Based Model (SABM) for longitudinal networks. Data were collected from 6-8th-grade students (Baseline age 12-15; 53% Female; 47% Male) across three waves of data. The sample was diverse with 58% African American, 31% White, and 11% Hispanic. Since bullying and homophobic teasing behaviors are related yet distinct forms of peer aggression, to capture the unique and combined effects of these behaviors we ran models separately and then together in a competing model. Results indicated that on average individuals with higher rates of bullying perpetration and homophobic teasing were associated with becoming increasingly popular as a friend. However, the effects were not linear, and individuals with the highest rates of bullying perpetration and homophobic teasing were less likely to receive friendship nominations. There was no evidence that bullying perpetration or homophobic teasing were associated with the number of friendship nominations made. Further, there was a preference for individuals to form or maintain friendships with peers who engaged in similar rates of homophobic name-calling; however, this effect was not found for bullying perpetration. Additionally

  11. Dust in the first quasars as a powerful probe of galaxy/BH co-evolution

    Science.gov (United States)

    Valiante, R.; Schneider, R.

    The origin of the large dust masses (> 108 M ) revealed by millimetre (mm) and sub-mm observations of z > 5 quasars is still hotly debated and interpreting/understanding the strong connection between the formation and growth of the first quasars and their host galaxies represents a challenge for both models and observations. By means of the semi-analytical model GAMETE/QSOdust (Valiante et al. 2011), we reconstruct the hierarchical build-up of high redshift QSOs and their host galaxies in a cosmological context. In addition, the chemical properties of the host galaxies, namely the mass of gas, stars, metals and dust are consistently followed in the model. As a pilot study, we have applied the model to SDSS J1148+5152 (J1148) at z = 6.4, using this source as a template for the general population of high-z QSOs. We show how dust formation and evolution may provide insights on the physical processes driving and regulating the co-evolution of quasars and their hosts in the early Universe: the dust mass produced by stars depends on the stellar initial mass function (IMF) and on the shape of the star formation history (SFH), which is controlled by the evolution of the gas content through mergers and outflows driven by Supernovae (SNe) and by the active galactic nucleus (AGN); the total mass of metals is a tracer of the integrated star formation history (total stellar mass) and it is sensitive to the strength and frequencies of merger-driven starbursts, metal-rich outflows, as well as to the detrimental effect of accretion onto grains in the dense interstellar medium. The above findings, complemented by a detailed analysis of the spectral energy distribution (SED) of J1148 by means of a radiative transfer code, point to an evolutionary scenario where the nuclear BH and the stellar bulge grow hand-in-hand by means of merger-driven gas inflows; when the BH mass exceeds ˜ 108 M , a strong AGNdriven wind drives a powerful outflow that is able to clear-up the ISM of its dust

  12. Light-induced structural changes in a short light, oxygen, voltage (LOV protein revealed by molecular dynamics simulations – implications for the understanding of LOV photoactivation.

    Directory of Open Access Journals (Sweden)

    Marco eBocola

    2015-10-01

    Full Text Available The modularity of light, oxygen, voltage (LOV blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state and Hβ strand (light state, while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96, which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved flipping glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.

  13. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

    Science.gov (United States)

    Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

    2016-05-01

    A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

  14. Towards Co-evolution of Membranes and Metabolism

    Science.gov (United States)

    Wei, Chenyu; Wilson, Michael A.; Pohorille, Andrew

    2014-01-01

    Conceptually, the most robust way to explain how primitive cell-like structures acquired and increased their capabilities is on the basis of Darwinian evolution. A population of protocells containing material that produced more environmentally fit progeny would increase in time at the expense of other protocells. In this scenario, protocellular boundaries were inextricably connected to the metabolism they encapsulated: to be inheritable, early metabolism must have led to an increased rate of growth and division of vesicles and, similarly, transport through vesicle boundaries must have supported the evolution of metabolism. Everything that could not be delivered from the environment had to be produced and retained inside protocells. Despite their importance to the understanding of the origin of life, only a few cases of coupling between metabolism and membrane-related processes have been identified so far. For example, reactions inside fatty-acid vesicles have been linked to their competitive growth and division, and mechanisms by which membrane permeability might have coupled to information polymers have been proposed and explained. Most recently, it has been shown that a dipeptide inside fatty-acid vesicles catalyzes the formation of another dipeptide that binds to vesicle walls and, by doing so, promotes their growth at the expense of other vesicles, thus demonstrating evolutionary advantage of small, membrane-bound peptides. It has been shown that the appearance of phospholipids imparted selective advantage to protocells bound by phospholipid-containing membranes, eventually driving fatty-acid vesicles to extinction. Phospholipid membranes, however, are nearly impermeable to charged species. Yet, the ability to transport ions across membranes was vital for regulating cellular volume, pH homeostasis, generating energy and sensing the environment. To account for this, evolutionary scenarios for the emergence of simple ion channels, protein structures surrounding

  15. Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (Phthiraptera, Anoplura)

    Czech Academy of Sciences Publication Activity Database

    Hypša, Václav; Křížek, J.

    2007-01-01

    Roč. 54, č. 2 (2007), s. 242-251 ISSN 0095-3628 Grant - others:GA ČR(CZ) GA206/04/0520 Institutional research plan: CEZ:AV0Z60220518 Keywords : Anoplura * endosymbionts * coevolution * molecular phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 2.558, year: 2007

  16. Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

    Science.gov (United States)

    Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

    2017-12-12

    Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.

  17. The potential for arms race and Red Queen coevolution in a protist host-parasite system.

    Science.gov (United States)

    Råberg, Lars; Alacid, Elisabet; Garces, Esther; Figueroa, Rosa

    2014-12-01

    The dynamics and consequences of host-parasite coevolution depend on the nature of host genotype-by-parasite genotype interactions (G × G) for host and parasite fitness. G × G with crossing reaction norms can yield cyclic dynamics of allele frequencies ("Red Queen" dynamics) while G × G where the variance among host genotypes differs between parasite genotypes results in selective sweeps ("arms race" dynamics). Here, we investigate the relative potential for arms race and Red Queen coevolution in a protist host-parasite system, the dinoflagellate Alexandrium minutum and its parasite Parvilucifera sinerae. We challenged nine different clones of A. minutum with 10 clones of P. sinerae in a fully factorial design and measured infection success and host and parasite fitness. Each host genotype was successfully infected by four to ten of the parasite genotypes. There were strong G × Gs for infection success, as well as both host and parasite fitness. About three quarters of the G × G variance components for host and parasite fitness were due to crossing reaction norms. There were no general costs of resistance or infectivity. We conclude that there is high potential for Red Queen dynamics in this host-parasite system.

  18. Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

    Science.gov (United States)

    Shen, Chen; Chu, Chen; Geng, Yini; Jin, Jiahua; Chen, Fei; Shi, Lei

    2018-01-01

    Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.

  19. Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

    Directory of Open Access Journals (Sweden)

    Chen Shen

    Full Text Available Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.

  20. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.

    Directory of Open Access Journals (Sweden)

    Tábita Hünemeier

    Full Text Available Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905 to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.

  1. Incipient speciation of sea star populations by adaptive gamete recognition coevolution.

    Science.gov (United States)

    Hart, Michael W; Sunday, Jennifer M; Popovic, Iva; Learning, Kevin J; Konrad, Christine M

    2014-05-01

    Reproductive isolation--the key event in speciation--can evolve when sexual conflict causes selection favoring different combinations of male and female adaptations in different populations. Likely targets of such selection include genes that encode proteins on the surfaces of sperm and eggs, but no previous study has demonstrated intraspecific coevolution of interacting gamete recognition genes under selection. Here, we show that selection drives coevolution between an egg receptor for sperm (OBi1) and a sperm acrosomal protein (bindin) in diverging populations of a sea star (Patiria miniata). We found positive selection on OBi1 in an exon encoding part of its predicted substrate-binding protein domain, the ligand for which is found in bindin. Gene flow was zero for the parts of bindin and OBi1 in which selection for high rates of amino acid substitution was detected; higher gene flow for other parts of the genome indicated selection against immigrant alleles at bindin and OBi1. Populations differed in allele frequencies at two key positively selected sites (one in each gene), and differences at those sites predicted fertilization rate variation among male-female pairs. These patterns suggest adaptively evolving loci that influence reproductive isolation between populations. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  2. Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites.

    Science.gov (United States)

    Medina, Iliana; Langmore, Naomi E

    2015-12-22

    Coevolution is often invoked as an engine of biological diversity. Avian brood parasites and their hosts provide one of the best-known examples of coevolution. Brood parasites lay their eggs in the nests of other species, selecting for host defences and reciprocal counteradaptations in parasites. In theory, this arms race should promote increased rates of speciation and phenotypic evolution. Here, we use recently developed methods to test whether the three largest avian brood parasitic lineages show changes in rates of phenotypic diversity and speciation relative to non-parasitic lineages. Our results challenge the accepted paradigm, and show that there is little consistent evidence that lineages of brood parasites have higher speciation or extinction rates than non-parasitic species. However, we provide the first evidence that the evolution of brood parasitic behaviour may affect rates of evolution in morphological traits associated with parasitism. Specifically, egg size and the colour and pattern of plumage have evolved up to nine times faster in parasitic than in non-parasitic cuckoos. Moreover, cuckoo clades of parasitic species that are sympatric (and share similar host genera) exhibit higher rates of phenotypic evolution. This supports the idea that competition for hosts may be linked to the high phenotypic diversity found in parasitic cuckoos. © 2015 The Author(s).

  3. Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture Coevolution

    Science.gov (United States)

    Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira

    2012-01-01

    Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele. PMID:22768049

  4. Coevolution of antibiotic production and counter-resistance in soil bacteria.

    Science.gov (United States)

    Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

    2010-03-01

    We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

  5. The evolution of floral scent and olfactory preferences in pollinators: coevolution or pre-existing bias?

    Science.gov (United States)

    Schiestl, Florian P; Dötterl, Stefan

    2012-07-01

    Coevolution is thought to be a major factor in shaping plant-pollinator interactions. Alternatively, plants may have evolved traits that fitted pre-existing preferences or morphologies in the pollinators. Here, we test these two scenarios in the plant family of Araceae and scarab beetles (Coleoptera, Scarabaeidae) as pollinators. We focused on floral volatile organic compounds (VOCs) and production/detection of VOCs by scarab beetles. We found phylogenetic structure in the production/detection of methoxylated aromatics in scarabs, but not plants. Within the plants, most of the compounds showed a well-supported pattern of correlated evolution with scarab-beetle pollination. In contrast, the scarabs showed no correlation between VOC production/detection and visitation to Araceae flowers, with the exception of the VOC skatole. Moreover, many VOCs were found in nonpollinating beetle groups (e.g., Melolonthinae) that are ancestors of pollinating scarabs. Importantly, none of the tested VOCs were found to have originated in pollinating taxa. Our analysis indicates a Jurassic origin of VOC production/detection in scarabs, but a Cretaceous/Paleocene origin of floral VOCs in plants. Therefore, we argue against coevolution, instead supporting the scenario of sequential evolution of floral VOCs in Araceae driven by pre-existing bias of pollinators. © 2012 The Author(s).

  6. Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration.

    Directory of Open Access Journals (Sweden)

    Antoine Barrière

    2012-09-01

    Full Text Available Phenotypes that appear to be conserved could be maintained not only by strong purifying selection on the underlying genetic systems, but also by stabilizing selection acting via compensatory mutations with balanced effects. Such coevolution has been invoked to explain experimental results, but has rarely been the focus of study. Conserved expression driven by the unc-47 promoters of Caenorhabditis elegans and C. briggsae persists despite divergence within a cis-regulatory element and between this element and the trans-regulatory environment. Compensatory changes in cis and trans are revealed when these promoters are used to drive expression in the other species. Functional changes in the C. briggsae promoter, which has experienced accelerated sequence evolution, did not lead to alteration of gene expression in its endogenous environment. Coevolution among promoter elements suggests that complex epistatic interactions within cis-regulatory elements may facilitate their divergence. Our results offer a detailed picture of regulatory evolution in which subtle, lineage-specific, and compensatory modifications of interacting cis and trans regulators together maintain conserved gene expression patterns.

  7. Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm-egg binding partners.

    Science.gov (United States)

    Grayson, Phil

    2015-12-01

    Reproductive proteins are among the most rapidly evolving classes of proteins. For a subset of these, rapid evolution is driven by positive Darwinian selection despite vital, well-conserved, reproductive functions. Izumo1 is the only essential sperm-egg fusion protein currently known on mammalian sperm, and its egg receptor (Juno; formerly Folr4) was recently discovered. Male knockout mice for Izumo1 and female knockout mice for Juno are both healthy but sterile. Here, both sperm-egg binding proteins are shown to be evolving under positive selection. Within mammals, coevolution of Izumo1 and Juno is also uncovered, suggesting that similar forces have shaped the evolutionary histories of these binding partners within Mammalia. Additionally, genomic analyses reveal an ancient origin for the Izumo gene family, initially reported as conserved exclusively in mammals. Newly identified Izumo1 orthologues could serve reproductive functions in birds, fish and reptiles. Surprisingly, these same analyses support Juno's presence in mammals alone, suggesting a recent mammalian-specific duplication and neofunctionalization of the ancestral folate receptor. Despite the indispensability of their reproductive interaction, and their apparent coevolution within Mammalia, this binding pair arose through strikingly different evolutionary forces.

  8. Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm–egg binding partners

    Science.gov (United States)

    Grayson, Phil

    2015-01-01

    Reproductive proteins are among the most rapidly evolving classes of proteins. For a subset of these, rapid evolution is driven by positive Darwinian selection despite vital, well-conserved, reproductive functions. Izumo1 is the only essential sperm–egg fusion protein currently known on mammalian sperm, and its egg receptor (Juno; formerly Folr4) was recently discovered. Male knockout mice for Izumo1 and female knockout mice for Juno are both healthy but sterile. Here, both sperm–egg binding proteins are shown to be evolving under positive selection. Within mammals, coevolution of Izumo1 and Juno is also uncovered, suggesting that similar forces have shaped the evolutionary histories of these binding partners within Mammalia. Additionally, genomic analyses reveal an ancient origin for the Izumo gene family, initially reported as conserved exclusively in mammals. Newly identified Izumo1 orthologues could serve reproductive functions in birds, fish and reptiles. Surprisingly, these same analyses support Juno's presence in mammals alone, suggesting a recent mammalian-specific duplication and neofunctionalization of the ancestral folate receptor. Despite the indispensability of their reproductive interaction, and their apparent coevolution within Mammalia, this binding pair arose through strikingly different evolutionary forces. PMID:27019721

  9. BIS2Analyzer: a server for co-evolution analysis of conserved protein families.

    Science.gov (United States)

    Oteri, Francesco; Nadalin, Francesca; Champeimont, Raphaël; Carbone, Alessandra

    2017-07-03

    Along protein sequences, co-evolution analysis identifies residue pairs demonstrating either a specific co-adaptation, where changes in one of the residues are compensated by changes in the other during evolution or a less specific external force that affects the evolutionary rates of both residues in a similar magnitude. In both cases, independently of the underlying cause, co-evolutionary signatures within or between proteins serve as markers of physical interactions and/or functional relationships. Depending on the type of protein under study, the set of available homologous sequences may greatly differ in size and amino acid variability. BIS2Analyzer, openly accessible at http://www.lcqb.upmc.fr/BIS2Analyzer/, is a web server providing the online analysis of co-evolving amino-acid pairs in protein alignments, especially designed for vertebrate and viral protein families, which typically display a small number of highly similar sequences. It is based on BIS2, a re-implemented fast version of the co-evolution analysis tool Blocks in Sequences (BIS). BIS2Analyzer provides a rich and interactive graphical interface to ease biological interpretation of the results. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Coevolution Trumps Pleiotropy: Carbon Assimilation Traits Are Independent of Metabolic Network Structure in Budding Yeast

    Science.gov (United States)

    Opulente, Dana A.; Morales, Christopher M.; Carey, Lucas B.; Rest, Joshua S.

    2013-01-01

    Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution). However, the extent to which network pleiotropy versus environmental coevolution shapes shared responses has not been addressed. To test these alternatives, we took advantage of the fact that the genus Saccharomyces has variation in habitat usage and diversity in the carbon sources that a given strain can metabolize. We examined patterns of gain and loss in carbon utilization traits across 488 strains of Saccharomyces to investigate whether the structure of metabolic pathways or selection pressure from common environments may have caused carbon utilization traits to be gained and lost together. While most carbon sources were gained and lost independently of each other, we found four clusters that exhibit non-random patterns of gain and loss across strains. Contrary to the network pleiotropy hypothesis, we did not find that these patterns are explained by the structure of metabolic pathways or shared enzymes. Consistent with the hypothesis that common environments shape suites of phenotypes, we found that the environment a strain was isolated from partially predicts the carbon sources it can assimilate. PMID:23326606

  11. Self-organization towards optimally interdependent networks by means of coevolution

    International Nuclear Information System (INIS)

    Wang, Zhen; Szolnoki, Attila; Perc, Matjaž

    2014-01-01

    Coevolution between strategy and network structure is established as a means to arrive at the optimal conditions needed to resolve social dilemmas. Yet recent research has highlighted that the interdependence between networks may be just as important as the structure of an individual network. We therefore introduce the coevolution of strategy and network interdependence to see whether this can give rise to elevated levels of cooperation in the prisoner's dilemma game. We show that the interdependence between networks self-organizes so as to yield optimal conditions for the evolution of cooperation. Even under extremely adverse conditions, cooperators can prevail where on isolated networks they would perish. This is due to the spontaneous emergence of a two-class society, with only the upper class being allowed to control and take advantage of the interdependence. Spatial patterns reveal that cooperators, once arriving at the upper class, are much more competent than defectors in sustaining compact clusters of followers. Indeed, the asymmetric exploitation of interdependence confers to them a strong evolutionary advantage that may resolve even the toughest of social dilemmas. (paper)

  12. Understanding primate brain evolution

    OpenAIRE

    Dunbar, R.I.M; Shultz, Susanne

    2007-01-01

    We present a detailed reanalysis of the comparative brain data for primates, and develop a model using path analysis that seeks to present the coevolution of primate brain (neocortex) and sociality within a broader ecological and life-history framework. We show that body size, basal metabolic rate and life history act as constraints on brain evolution and through this influence the coevolution of neocortex size and group size. However, they do not determine either of these variables, which ap...

  13. Understanding Supply Networks from Complex Adaptive Systems

    Directory of Open Access Journals (Sweden)

    Jamur Johnas Marchi

    2014-10-01

    Full Text Available This theoretical paper is based on complex adaptive systems (CAS that integrate dynamic and holistic elements, aiming to discuss supply networks as complex systems and their dynamic and co-evolutionary processes. The CAS approach can give clues to understand the dynamic nature and co-evolution of supply networks because it consists of an approach that incorporates systems and complexity. This paper’s overall contribution is to reinforce the theoretical discussion of studies that have addressed supply chain issues, such as CAS.

  14. Terrestrial Particulate Organic Matter Degradation in Estuarine and Coastal Areas: Coupling Lipid Tracers and Molecular Tools to Better Understand Deltaic Biogeochemical Cycles

    Science.gov (United States)

    Galeron, M. A.; Volkman, J. K.; Rontani, J. F.; Radakovitch, O.; Charriere, B.; Amiraux, R.

    2016-02-01

    Deltaic and coastal areas have been studied extensively worldwide, due to their high economic and ecosystemic value. It was long thought that terrestrial particulate organic matter (TPOM) degraded during river transport was refractory to further degradation upon its arrival at sea. But studies on coastal sediments and in the Mackenzie delta (Canada) showed that, on the contrary, TPOM was undergoing intense degradation upon reaching seawater. In order to generalize these results to worldwide river basins, we propose to trace degradation processes impacting TPOM during in-stream transport as well as coastal distribution. We selected the Rhône River (France) for its differences with the Mackenzie River (latitude, temperature, coastal salinity) and carefully researched lipid tracers to help us pinpoint both the origin of the POM and the degradative processes undergone. Betulin, α-/β-amyrins, dehydroabietic acid, sitosterol and their specific degradation products were selected. While the Rhône delta has been studied for decades, there is very little research on its in-stream processes, and how they can be linked with coastal cycles and fluxes. Coupling new specific lipid tracers especially selected for the monitoring of higher plant degradation and molecular biology tools, we were able to better trace the origin of TPOM transported along the Rhône River, as well as better understand its degradation state in the river, the delta, and upon its arrival at sea. We show here that autoxidation (free radical induced oxidation), long overlooked, is a major degradation process impacting TPOM transported along the Rhone River, and is even more intense upon the arrival of TPOM at sea. Salinity, metal ion desorption, bacterial and biochemical activity are amongst the factors studied as inducers of such an intense degradation. This understanding is crucial if we want a truly extensive knowledge of terrestrial particulate organic matter transport and deposition, as well as

  15. Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology

    Directory of Open Access Journals (Sweden)

    Orkid Coskuner-Weber

    2018-01-01

    Full Text Available Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs, which are at the center of Alzheimer’s and Parkinson’s disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer’s and Parkinson’s diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer’s and Parkinson’s diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer’s and Parkinson’s diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer’s and Parkinson’s diseases. This information represents an important foundation for the successful and

  16. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

    Science.gov (United States)

    2018-01-01

    Abstract Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology—Biosignatures—Coevolution of Earth and life—Mars. Astrobiology 18, 1–27. PMID:29252008

  17. Streamflow recession patterns can help unravel the role of climate and humans in landscape co-evolution

    Science.gov (United States)

    Bogaart, Patrick W.; van der Velde, Ype; Lyon, Steve W.; Dekker, Stefan C.

    2016-04-01

    Traditionally, long-term predictions of river discharges and their extremes include constant relationships between landscape properties and model parameters. However, due to the co-evolution of many landscape properties more sophisticated methods are necessary to quantify future landscape-hydrological model relationships. As a first step towards such an approach we use the Brutsaert and Nieber (1977) analysis method to characterize streamflow recession behaviour of ≈ 200 Swedish catchments within the context of global change and landscape co-evolution. Results suggest that the Brutsaert-Nieber parameters are strongly linked to the climate, soil, land use, and their interdependencies. Many catchments show a trend towards more non-linear behaviour, meaning not only faster initial recession but also slower recession towards base flow. This trend has been found to be independent from climate change. Instead, we suggest that land cover change, both natural (restoration of natural soil profiles in forested areas) and anthropogenic (reforestation and optimized water management), is probably responsible. Both change types are characterised by system adaptation and change, towards more optimal ecohydrological conditions, suggesting landscape co-evolution is at play. Given the observed magnitudes of recession changes during the past 50 years, predictions of future river discharge critically need to include the effects of landscape co-evolution. The interconnections between the controls of land cover and climate on river recession behaviour, as we have quantified in this paper, provide first-order handles to do so.

  18. Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

    Science.gov (United States)

    Verin, Mélissa; Tellier, Aurélien

    2018-04-20

    Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  19. Complex adaptive responses during antagonistic coevolution between Tribolium castaneum and its natural parasite Nosema whitei revealed by multiple fitness components

    Directory of Open Access Journals (Sweden)

    Bérénos Camillo

    2012-01-01

    Full Text Available Abstract Background Host-parasite coevolution can lead to local adaptation of either parasite or host if there is specificity (GxG interactions and asymmetric evolutionary potential between host and parasite. This has been demonstrated both experimentally and in field studies, but a substantial proportion of studies fail to detect such clear-cut patterns. One explanation for this is that adaptation can be masked by counter-adaptation by the antagonist. Additionally, genetic architecture underlying the interaction is often highly complex thus preventing specific adaptive responses. Here, we have employed a reciprocal cross-infection experiment to unravel the adaptive responses of two components of fitness affecting both parties with different complexities of the underlying genetic architecture (i.e. mortality and spore load. Furthermore, our experimental coevolution of hosts (Tribolium castaneum and parasites (Nosema whitei included paired replicates of naive hosts from identical genetic backgrounds to allow separation between host- and parasite-specific responses. Results In hosts, coevolution led to higher resistance and altered resistance profiles compared to paired control lines. Host genotype × parasite genotype interactions (GH × GP were observed for spore load (the trait of lower genetic complexity, but not for mortality. Overall parasite performance correlated with resistance of its matching host coevolution background reflecting a directional and unspecific response to strength of selection during coevolution. Despite high selective pressures exerted by the obligatory killing parasite, and host- and parasite-specific mortality profiles, no general pattern of local adaptation was observed, but one case of parasite maladaptation was consistently observed on both coevolved and control host populations. In addition, the use of replicate control host populations in the assay revealed one case of host maladaptation and one case of parasite

  20. Interspecific interactions drive cultural co-evolution and acoustic convergence in syntopic species.

    Science.gov (United States)

    Laiolo, Paola

    2012-05-01

    1. Antagonistic interactions have been favourite subjects of studies on species co-evolution, because coexistence among competing species often results in quantifiable character displacement. A common output for competitive interactions is trait divergence, although the opposite phenomenon, convergence, has been proposed to evolve in some instances, for example in the communication behaviour of species that maintain mutually exclusive territories. 2. I use here experimental and observational evidence to study how species interactions drive heterospecific signal convergence and analyse how convergence feeds back to the interaction itself, in the form of aggressive behaviour. I recorded the learned territorial signals of two non-hybridizing larks, Galerida cristata and G. theklae, and used allopatric populations as controls for evaluating acoustic convergence in syntopy. Acoustic variation was analysed with respect to social conditions controlling for other potential agents of natural selection, habitat and climate. 3. Interspecific convergence of Galerida calls peaked in syntopy. Although call acoustic structure was affected by climate and habitat, it matched gradients of density and proximity to congeners even at small local scales. The process of cultural transmission, in which individuals may acquire components of behaviour by copying neighbours, enhances the correlation between call acoustics and the local social milieu. 4. Territories were defended against both species, but playback stimuli of convergent congener calls elicited a stronger aggressive reaction than congener calls from allopatric locations. 5. This study shows that learned behaviours may co-evolve as a consequence of antagonistic interactions, determining reciprocal cultural evolution or cultural co-evolution. As for (biological) co-evolution, the distribution of competing species influences whether a particular area becomes a syntopic environment in which convergence is occurring, or

  1. Molecular and Neuroendocrine Approaches to Understanding Trade-offs: Food, Sex, Aggression, Stress, and Longevity-An Introduction to the Symposium.

    Science.gov (United States)

    Schneider, Jill E; Deviche, Pierre

    2017-12-01

    Life history strategies are composed of multiple fitness components, each of which incurs costs and benefits. Consequently, organisms cannot maximize all fitness components simultaneously. This situation results in a dynamic array of trade-offs in which some fitness traits prevail at the expense of others, often depending on context. The identification of specific constraints and trade-offs has helped elucidate physiological mechanisms that underlie variation in behavioral and physiological life history strategies. There is general recognition that trade-offs are made at the individual and population level, but much remains to be learned concerning the molecular neuroendocrine mechanisms that underlie trade-offs. For example, we still do not know whether the mechanisms that underlie trade-offs at the individual level relate to trade-offs at the population level. To advance our understanding of trade-offs, we organized a group of speakers who study neuroendocrine mechanisms at the interface of traits that are not maximized simultaneously. Speakers were invited to represent research from a wide range of taxa including invertebrates (e.g., worms and insects), fish, nonavian reptiles, birds, and mammals. Three general themes emerged. First, the study of trade-offs requires that we investigate traditional endocrine mechanisms that include hormones, neuropeptides, and their receptors, and in addition, other chemical messengers not traditionally included in endocrinology. The latter group includes growth factors, metabolic intermediates, and molecules of the immune system. Second, the nomenclature and theory of neuroscience that has dominated the study of behavior is being re-evaluated in the face of evidence for the peripheral actions of so-called neuropeptides and neurotransmitters and the behavioral repercussions of these actions. Finally, environmental and ecological contexts continue to be critical in unmasking molecular mechanisms that are hidden when study animals

  2. Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.

    Science.gov (United States)

    Suardíaz, Reynier; Jambrina, Pablo G; Masgrau, Laura; González-Lafont, Àngels; Rosta, Edina; Lluch, José M

    2016-04-12

    . Overall, a different binding mode from the one accepted for 15-LOX-1 is proposed, which provides a molecular basis for 15-LOX-2 exclusive 15-HPETE production in front of the double (although highly 15-) 12/15 regiospecificity of 15-LOX-1. Understanding how these different isoenzymes achieve their regiospecificity is expected to help in specific inhibitor design.

  3. Teaching Teaching & Understanding Understanding

    DEFF Research Database (Denmark)

    2006-01-01

    "Teaching Teaching & Understanding Understanding" is a 19-minute award-winning short-film about teaching at university and higher-level educational institutions. It is based on the "Constructive Alignment" theory developed by Prof. John Biggs. The film delivers a foundation for understanding what...

  4. The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere.

    Science.gov (United States)

    Jelen, Benjamin I; Giovannelli, Donato; Falkowski, Paul G

    2016-09-08

    All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.

  5. The role of local adaptation in shaping fish-mussel coevolution

    DEFF Research Database (Denmark)

    Douda, Karel; Liu, Huan-Zhang; Yu, Dan

    2017-01-01

    -host association varies temporally (between areas of ancient and recent sympatry) and spatially (at a sub-basin level in its native range).3. Results revealed the ability of S.woodiana to widely exploit non-bitterling host fishes at a global scale. In contrast, the ability of S.woodiana to exploit closely...... impact on the persistence of local populations. Bivalves of the order Unionida (freshwater mussels) are a functionally important but declining group of affiliate species, which are dependent on freshwater fish to host their parasitic larvae. The role of local adaptations and host fish resistance...... in shaping freshwater mussel host relationships remains poorly understood.2. We used an invasive East Asian unionid bivalve, Sinanodonta woodiana, and its potential host fishes to study the mechanisms shaping fish-mussel coevolution using a combination of laboratory cross-exposure methods and field...

  6. A non-classical phase diagram for virus-bacterial co-evolution mediated by CRISPR

    Science.gov (United States)

    Han, Pu; Deem, Michael

    CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. Due to the cost of CRISPR, bacteria can lose the acquired immunity. We will show an intriguing phase diagram of the virus extinction probability, which when the rate of losing the acquired immunity is small, is more complex than that of the classic predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape the recognition by CRISPR, and this co-evolution leads to a non-trivial phase structure that cannot be explained by the classical predator-prey model.

  7. The Co-evolution of Business Incubators and National Incubator Networks in Emerging Markets

    Directory of Open Access Journals (Sweden)

    David F. Robinson

    2010-11-01

    Full Text Available The study proposes a three stage model of the development of business incubation practices in emerging markets. The model addresses the diffusion of incubation practices to new markets, the institutionalization of those practices and the co-evolution of incubators and national networks of incubation. The model is based on interviews conducted in Bolivia, Peru, Chile, Argentina, and Brazil. New incubators in emerging markets often face strong cultural norms and institutional impediments to helping entrepreneurs start new businesses. As incubation becomes better established in a country, incubators provide more advanced technical, legal and market-based advice. Networks of incubators form to share specialized services across many incubators, to allocate government funding to incubators, and to lobby for public and private support of innovation.

  8. Limited ability driven phase transitions in the coevolution process in Axelrod's model

    International Nuclear Information System (INIS)

    Wang Bing; Han Yuexing; Chen Luonan; Aihara, Kazuyuki

    2009-01-01

    We study the coevolution process in Axelrod's model by taking into account of agents' abilities to access information, which is described by a parameter α to control the geographical range of communication. We observe two kinds of phase transitions in both cultural domains and network fragments, which depend on the parameter α. By simulation, we find that not all rewiring processes pervade the dissemination of culture, that is, a very limited ability to access information constrains the cultural dissemination, while an exceptional ability to access information aids the dissemination of culture. Furthermore, by analyzing the network characteristics at the frozen states, we find that there exists a stage at which the network develops to be a small-world network with community structures.

  9. Immune loss as a driver of coexistence during host-phage coevolution

    Science.gov (United States)

    Weissman, Jake L; Holmes, Rayshawn; Barrangou, Rodolphe; Moineau, Sylvain; Fagan, William F; Levin, Bruce; Johnson, Philip L F

    2018-01-01

    Bacteria and their viral pathogens face constant pressure for augmented immune and infective capabilities, respectively. Under this reciprocally imposed selective regime, we expect to see a runaway evolutionary arms race, ultimately leading to the extinction of one species. Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose that the regular loss of immunity by the bacterial host can also produce host-phage coexistence. We pair a general model of immunity with an experimental and theoretical case study of the CRISPR-Cas immune system to contrast the behavior of tradeoff and loss mechanisms in well-mixed systems. We find that, while both mechanisms can produce stable coexistence, only immune loss does so robustly within realistic parameter ranges. PMID:29328063

  10. Coevolution of patch-type dependent emigration and patch-type dependent immigration.

    Science.gov (United States)

    Weigang, Helene C

    2017-08-07

    The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model. The dispersing population inhabits a landscape structured into many patches of two types and disperses during a continuous-time season. The trait under consideration is a four dimensional vector consisting of two values for emigration probability from the patches and two values for immigration probability into the patches of each type. Using the adaptive dynamics approach I show that four qualitatively different dispersal strategies may evolve in different parameter regions, including a counterintuitive strategy, where patches of one type are fully dispersed from (emigration probability is one) but individuals nevertheless always immigrate into them during the dispersal season (immigration probability is one). I present examples of evolutionary branching in a wide parameter range, when the patches with high local death rate during the dispersal season guarantee a high expected disperser output. I find that two dispersal strategies can coexist after evolutionary branching: a strategy with full immigration only into the patches with high expected disperser output coexists with a strategy that immigrates into any patch. Stochastic simulations agree with the numerical predictions. Since evolutionary branching is also found when immigration evolves alone, the present study is adding coevolutionary constraints on the emigration traits and hence finds that the coevolution of a higher dimensional trait sometimes hinders evolutionary diversification. Copyright © 2017

  11. Cross-Resistance: A Consequence of Bi-partite Host-Parasite Coevolution

    Directory of Open Access Journals (Sweden)

    Tilottama Biswas

    2018-02-01

    Full Text Available Host-parasite coevolution can influence interactions of the host and parasite with the wider ecological community. One way that this may manifest is in cross-resistance towards other parasites, which has been observed to occur in some host-parasite evolution experiments. In this paper, we test for cross-resistance towards Bacillus thuringiensis and Pseudomonas entomophila in the red flour beetle Tribolium castaneum, which was previously allowed to coevolve with the generalist entomopathogenic fungus Beauveria bassiana. We combine survival and gene expression assays upon infection to test for cross-resistance and underlying mechanisms. We show that larvae of T. castaneum that evolved with B. bassiana under coevolutionary conditions were positively cross-resistant to the bacterium B. thuringiensis, but not P. entomophila. Positive cross-resistance was mirrored at the gene expression level with markers that were representative of the oral route of infection being upregulated upon B. bassiana exposure. We find that positive cross-resistance towards B. thuringiensis evolved in T. castaneum as a consequence of its coevolutionary interactions with B. bassiana. This cross-resistance appears to be a consequence of resistance to oral toxicity. The fact that coevolution with B. bassiana results in resistance to B. thuringiensis, but not P. entomophila implies that B. thuringiensis and B. bassiana may share mechanisms of infection or toxicity not shared by P. entomophila. This supports previous suggestions that B. bassiana may possess Cry-like toxins, similar to those found in B. thuringiensis, which allow it to infect orally.

  12. A biologia molecular contribuindo para a compreensão e a prevenção das doenças hereditárias Molecular biology contribution to the understanding and prevention of genetic disorders

    Directory of Open Access Journals (Sweden)

    Mayana Zatz

    2002-01-01

    Full Text Available O fim do seqüenciamento do genoma humano levanta inúmeras questões: Como o projeto genoma humano vai influenciar nossas vidas? Como a medicina tem se beneficiado do estudo dos genes? Quais são as aplicações práticas imediatas e o que se espera para o futuro? Quais são as implicações éticas? Este capítulo ilustra como as doenças genéticas têm contribuído para a compreensão do genoma humano. Ajuda-nos a entender como nossos genes funcionam quando normais e por que causam doenças quando alterados. Do ponto de vista prático, o estudo dos genes tem permitido o diagnóstico molecular para um número crescente de patologias, o que é fundamental para evitar outros exames invasivos, identificar casais em risco, e prevenir o nascimento de novos afetados. Além disso, discute-se quais são as perspectivas futuras em relação ao tratamento destas e de outras patologias genéticas incluindo a clonagem para fins terapêuticos e a utilização de células-tronco. Finalmente aborda as implicações éticas relacionadas ao uso de testes genéticos. Os benefícios de cada teste, principalmente para doenças de início tardio para as quais ainda não há tratamento, têm que ser discutidos exaustivamente com os consulentes antes de sua aplicação.The sequencing of the human genome raised many questions such as: How the human genome project will influence our lives? How the medicine will benefit from the study of genes ? What are the application in practice and what can we expect from the future? What are the ethical implications? This chapter illustrates how genetic diseases, such as neuromuscular disorders are contributing to our understanding of the human genome. It helps us to start to understand how our genes work and why they cause diseases when mutated. One of the practical application of studying genes is the improvement of molecular diagnosis for a growing number of disorders which is of utmost importance to avoid other invasive exams

  13. Understanding the molecular mechanisms underlying the effects of light intensity on flavonoid production by RNA-seq analysis in Epimedium pseudowushanense B.L.Guo.

    Directory of Open Access Journals (Sweden)

    Junqian Pan

    Full Text Available Epimedium pseudowushanense B.L.Guo, a light-demanding shade herb, is used in traditional medicine to increase libido and strengthen muscles and bones. The recognition of the health benefits of Epimedium has increased its market demand. However, its resource recycling rate is low and environmentally dependent. Furthermore, its natural sources are endangered, further increasing prices. Commercial culture can address resource constraints of it.Understanding the effects of environmental factors on the production of its active components would improve the technology for cultivation and germplasm conservation. Here, we studied the effects of light intensities on the flavonoid production and revealed the molecular mechanism using RNA-seq analysis. Plants were exposed to five levels of light intensity through the periods of germination to flowering, the flavonoid contents were measured using HPLC. Quantification of epimedin A, epimedin B, epimedin C, and icariin showed that the flavonoid contents varied with different light intensity levels. And the largest amount of epimedin C was produced at light intensity level 4 (I4. Next, the leaves under the treatment of three light intensity levels ("L", "M" and "H" with the largest differences in the flavonoid content, were subjected to RNA-seq analysis. Transcriptome reconstruction identified 43,657 unigenes. All unigene sequences were annotated by searching against the Nr, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG databases. In total, 4008, 5260, and 3591 significant differentially expressed genes (DEGs were identified between the groups L vs. M, M vs. H and L vs. H. Particularly, twenty-one full-length genes involved in flavonoid biosynthesis were identified. The expression levels of the flavonol synthase, chalcone synthase genes were strongly associated with light-induced flavonoid abundance with the highest expression levels found in the H group. Furthermore, 65 transcription factors

  14. The co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels

    Science.gov (United States)

    Getto, Elizabeth Margaret

    The objective of this study was to understand the co-evolution of microstructure features in self-ion irradiated HT9 at very high damage levels. HT9 (heat 84425) was pre-implanted with 10 atom parts per million helium and then irradiated with 5 MeV Fe++ in the temperature range of 440-480°C to 188 dpa. A damage dependence study from 75 to 650 dpa was performed at the peak swelling temperature of 460°C. The swelling, dislocation and precipitate evolution was determined using Analytic Electron Microscopes in both Conventional Transmission electron microscopy (CTEM) and Scanning Transmission Electron Microscopy (STEM) modes. Void swelling reached a nominally linear rate of 0.03%/dpa from 188 to 650 dpa at 460°C. G phase precipitates were observed by 75 dpa and grew linearly up to 650 dpa. M 2X was observed by 250 dpa and peaked in volume fraction at 450 dpa. Dislocation loop evolution was observed up to 650 dpa including a step change in diameter between 375 and 450 dpa; which correlated with nucleation and growth of M2X. The experimental results were interpreted using a rate theory model, the Radiation Induced Microstructure Evolution (RIME), in the damage range from 188 to 650 dpa. A simple system of voids and dislocations was modeled in which the dislocations measured from experiment were used as input, or the dislocations were allowed to evolve dynamically, resulting in swelling that was overestimated by 63% relative to that observed experimentally. G phase had limited effect on the void or dislocation behavior. The behavior of M2X within the microstructure was characterized as a direct effect as a coherent sink, and as an indirect effect in consuming carbon from the matrix, which had the largest impact on both void and dislocation behavior. A slowly monotonically increasing swelling rate was observed both experimentally and computationally, with swelling rates of ˜0.025%/dpa and ˜0.036%/dpa before and after 450 dpa. The agreement in void behavior between

  15. Understanding the molecular-level chemistry of water plasmas and the effects of surface modification and deposition on a selection of oxide substrates

    Science.gov (United States)

    Trevino, Kristina J.

    2011-12-01

    This dissertation first examines electrical discharges used to study wastewater samples for contaminant detection and abatement. Two different water samples contaminated with differing concentrations of either methanol (MeOH) or methyl tert-butyl ether (MTBE) were used to follow breakdown mechanisms. Emission from CO* was used to monitor the contaminant and for molecular breakdown confirmation through actinometric OES as it can only arise from the carbon-based contaminant in either system. Detection was achieved at concentrations as low as 0.01 ppm, and molecular decomposition was seen at a variety of plasma parameters. This dissertation also explores the vibrational (thetaV), rotational (thetaR) and translational (thetaT) temperatures for a range of diatomic species in different plasma systems. For the majority of the plasma species studied, thetaV are much higher than thetaR and thetaT. This suggests that more energy is partitioned into the vibrational degrees of freedom in our plasmas. The thetaR reported are significantly lower in all the plasma systems studied and this is a result of radical equilibration to the plasma gas temperature. thetaT values show two characteristics; (1) they are less than the thetaV and higher than the theta R and (2) show varying trends with plasma parameters. Radical energetics were examined through comparison of thetaR, thetaT, and thetaV, yielding significant insight on the partitioning of internal and kinetic energies in plasmas. Correlations between energy partitioning results and corresponding radical surface scattering coefficients obtained using our imaging of radicals interacting with surfaces (IRIS) technique are also presented. Another aspect of plasma process chemistry, namely surface modification via plasma treatment, was investigated through characterization of metal oxides (SiOxNy, nat-SiO2, and dep-SiO2) following their exposure to a range of plasma discharges. Here, emphasis was placed on the surface wettability

  16. Context-Aware Mobile Service Adaptation via a Co-Evolution eXtended Classifier System in Mobile Network Environments

    OpenAIRE

    Shangguang Wang; Zibin Zheng; Zhengping Wu; Qibo Sun; Hua Zou; Fangchun Yang

    2014-01-01

    With the popularity of mobile services, an effective context-aware mobile service adaptation is becoming more and more important for operators. In this paper, we propose a Co-evolution eXtended Classifier System (CXCS) to perform context-aware mobile service adaptation. Our key idea is to learn user context, match adaptation rule, and provide the best suitable mobile services for users. Different from previous adaptation schemes, our proposed CXCS can produce a new user's initial classifier p...

  17. Streamflow recession patterns can help unravel the role of climate and humans in landscape co-evolution

    OpenAIRE

    P. W. Bogaart; Y. van der Velde; S. W. Lyon; S. C. Dekker

    2016-01-01

    Traditionally, long-term predictions of river discharges and their extremes include constant relationships between landscape properties and model parameters. However, due to the co-evolution of many landscape properties more sophisticated methods are necessary to quantify future landscape–hydrological model relationships. As a first step towards such an approach we use the Brutsaert and Nieber (1977) analysis method to characterize streamflow recession behaviour of  ≈  200 S...

  18. Stream flow recession patterns can help unravel the role of climate and humans in landscape co-evolution

    OpenAIRE

    P. W. Bogaart; Y. van der Velde; S. W. Lyon; S. C. Dekker

    2015-01-01

    Traditionally, long term predictions of river discharges and their extremes include constant relationships between landscape properties and model parameters. However, due to co-evolution of many of landscape properties more sophisticated methods to quantify future landscape-hydrological model relationships are likely necessary. As a first step towards such an approach we use the Brutsaert and Nieber (1977) analysis method to characterize streamflow recession ...

  19. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

    Science.gov (United States)

    Cabrol, Nathalie A.

    2018-01-01

    Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration.

  20. Coexistence via coevolution driven by reduced allelochemical effects and increased tolerance to competition between invasive and native plants.

    Science.gov (United States)

    Huang, Fangfang; Lankau, Richard; Peng, Shaolin

    2018-04-01

    Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history. Alliaria petiolata and P. pumila tended to develop greater tolerance to competition over invasion history. Their coexistence was promoted more by increases in stabilizing relative to equalizing processes. These changes likely stem in part from reductions in allelopathic traits in the invader and evolution of tolerance in the native. These results suggested that some native species can evolve tolerance against the competitive effects of strong invaders, which likely promoted their persistence in invaded communities. However, the potential for coevolutionary rescue of competing populations is likely to vary across native species, and evolutionary processes should not be expected to compensate for the ecological consequences of exotic invasions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  1. A conceptual socio-hydrological model of the co-evolution of humans and water: case study of the Tarim River basin, western China

    Science.gov (United States)

    Liu, D.; Tian, F.; Lin, M.; Sivapalan, M.

    2015-02-01

    The complex interactions and feedbacks between humans and water are critically important issues but remain poorly understood in the newly proposed discipline of socio-hydrology (Sivapalan et al., 2012). An exploratory model with the appropriate level of simplification can be valuable for improving our understanding of the co-evolution and self-organization of socio-hydrological systems driven by interactions and feedbacks operating at different scales. In this study, a simplified conceptual socio-hydrological model based on logistic growth curves is developed for the Tarim River basin in western China and is used to illustrate the explanatory power of such a co-evolutionary model. The study area is the main stream of the Tarim River, which is divided into two modeling units. The socio-hydrological system is composed of four sub-systems, i.e., the hydrological, ecological, economic, and social sub-systems. In each modeling unit, the hydrological equation focusing on water balance is coupled to the other three evolutionary equations to represent the dynamics of the social sub-system (denoted by population), the economic sub-system (denoted by irrigated crop area ratio), and the ecological sub-system (denoted by natural vegetation cover), each of which is expressed in terms of a logistic growth curve. Four feedback loops are identified to represent the complex interactions among different sub-systems and different spatial units, of which two are inner loops occurring within each separate unit and the other two are outer loops linking the two modeling units. The feedback mechanisms are incorporated into the constitutive relations for model parameters, i.e., the colonization and mortality rates in the logistic growth curves that are jointly determined by the state variables of all sub-systems. The co-evolution of the Tarim socio-hydrological system is then analyzed with this conceptual model to gain insights into the overall system dynamics and its sensitivity to the

  2. Cooperative Coevolution with Formula-Based Variable Grouping for Large-Scale Global Optimization.

    Science.gov (United States)

    Wang, Yuping; Liu, Haiyan; Wei, Fei; Zong, Tingting; Li, Xiaodong

    2017-08-09

    For a large-scale global optimization (LSGO) problem, divide-and-conquer is usually considered an effective strategy to decompose the problem into smaller subproblems, each of which can then be solved individually. Among these decomposition methods, variable grouping is shown to be promising in recent years. Existing variable grouping methods usually assume the problem to be black-box (i.e., assuming that an analytical model of the objective function is unknown), and they attempt to learn appropriate variable grouping that would allow for a better decomposition of the problem. In such cases, these variable grouping methods do not make a direct use of the formula of the objective function. However, it can be argued that many real-world problems are white-box problems, that is, the formulas of objective functions are often known a priori. These formulas of the objective functions provide rich information which can then be used to design an effective variable group method. In this article, a formula-based grouping strategy (FBG) for white-box problems is first proposed. It groups variables directly via the formula of an objective function which usually consists of a finite number of operations (i.e., four arithmetic operations "[Formula: see text]", "[Formula: see text]", "[Formula: see text]", "[Formula: see text]" and composite operations of basic elementary functions). In FBG, the operations are classified into two classes: one resulting in nonseparable variables, and the other resulting in separable variables. In FBG, variables can be automatically grouped into a suitable number of non-interacting subcomponents, with variables in each subcomponent being interdependent. FBG can easily be applied to any white-box problem and can be integrated into a cooperative coevolution framework. Based on FBG, a novel cooperative coevolution algorithm with formula-based variable grouping (so-called CCF) is proposed in this article for decomposing a large-scale white-box problem

  3. Towards the understanding of the molecular weight dependence of essential work of fracture in semi-crystalline polymers: A study on poly(ε-caprolactone

    Directory of Open Access Journals (Sweden)

    F. Tuba

    2014-11-01

    Full Text Available The plane-stress ductile fracture of poly(#-caprolactone (PCL has been investigated as a function of molecular weight and related crystalline structure. Because of the interacting effects in semi-crystalline polymers a separate study of a given structural parameter is rather challenging. Nevertheless, this polymer seems to be a good model material to study the effect of molecular weight on the essential work of fracture, as the interactions between the separate parameters, at room temperature, are negligible. The molecular characteristics of PCL were determined by size exclusion chromatography. To confirm the entangled molecular structure of studied polymers rheological measurements were performed. The crystalline morphology has been characterized by differential scanning calorimetry and wide angle X-ray diffraction. Quasi-static tensile tests and essential work of fracture tests were performed to study the mechanical behavior. Based on the experimental observations an empirical model has been proposed to outline the molecular weight and crystallinity dependence of the essential work of fracture in this semi-crystalline polymer.

  4. A black-hole mass measurement from molecular gas kinematics in NGC4526.

    Science.gov (United States)

    Davis, Timothy A; Bureau, Martin; Cappellari, Michele; Sarzi, Marc; Blitz, Leo

    2013-02-21

    The masses of the supermassive black holes found in galaxy bulges are correlated with a multitude of galaxy properties, leading to suggestions that galaxies and black holes may evolve together. The number of reliably measured black-hole masses is small, and the number of methods for measuring them is limited, holding back attempts to understand this co-evolution. Directly measuring black-hole masses is currently possible with stellar kinematics (in early-type galaxies), ionized-gas kinematics (in some spiral and early-type galaxies) and in rare objects that have central maser emission. Here we report that by modelling the effect of a black hole on the kinematics of molecular gas it is possible to fit interferometric observations of CO emission and thereby accurately estimate black-hole masses. We study the dynamics of the gas in the early-type galaxy NGC 4526, and obtain a best fit that requires the presence of a central dark object of 4.5(+4.2)(-3.1) × 10(8) solar masses (3σ confidence limit). With the next-generation millimetre-wavelength interferometers these observations could be reproduced in galaxies out to 75 megaparsecs in less than 5 hours of observing time. The use of molecular gas as a kinematic tracer should thus allow one to estimate black-hole masses in hundreds of galaxies in the local Universe, many more than are accessible with current techniques.

  5. Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

    Science.gov (United States)

    Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

    2017-05-01

    In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

  6. Life cycles, molecular phylogeny and historical biogeography of the ‘pygmaeus’ microphallids (Digenea: Microphallidae): widespread parasites of marine and coastal birds in the Holarctic

    Czech Academy of Sciences Publication Activity Database

    Galaktionov, K.V.; Blasco-Costa, Maria Isabel; Olson, P. D.

    2012-01-01

    Roč. 139, č. 10 (2012), s. 1346-1360 ISSN 0031-1820 Institutional support: RVO:60077344 Keywords : marine parasites * trematode * Microphallus * parasite speciation * parasite transmission * host-parasite co-evolution * host switching * host-parasite assemblages Subject RIV: EH - Ecology, Behaviour; EB - Genetics ; Molecular Biology (BC-A) Impact factor: 2.355, year: 2012

  7. Coevolution of policy, market and technical price risks in the EU ETS

    International Nuclear Information System (INIS)

    Blyth, William; Bunn, Derek

    2011-01-01

    Within the EU, there have been calls for governments to provide greater certainty over carbon prices, even though it is evident that their price risk is not entirely due to policy uncertainty. We develop a stochastic simulation model of price formation in the EU ETS to analyse the coevolution of policy, market and technology risks under different initiatives. The current situation of a weak (20%) overall abatement target motivates various technology-support interventions, elevating policy uncertainty as the major source of carbon price risk. In contrast, taking a firm decision to move to a more stringent 30% cap would leave the EU-ETS price formation driven much more by market forces than by policy risks. This leads to considerations of how much risk mitigation by governments would be appropriate, and how much should be taken as business risk by the market participants. - Highlights: → Methodology is developed to track EU-ETS risk factors and their interactions. → Policy risks are found to be the most significant when carbon prices are low. → Robust carbon signals in a cap-and-trade require stringent targets. → Multiple policies create downward price pressure, increasing policy risk exposure. → Fuel prices also are important, whilst technology risk plays a small part until later.

  8. Coevolution within a transcriptional network by compensatory trans and cis mutations

    KAUST Repository

    Kuo, D.

    2010-10-26

    Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “coevolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners.

  9. Plant-parasite coevolution: bridging the gap between genetics and ecology.

    Science.gov (United States)

    Brown, James K M; Tellier, Aurélien

    2011-01-01

    We review current ideas about coevolution of plants and parasites, particularly processes that generate genetic diversity. Frequencies of host resistance and parasite virulence alleles that interact in gene-for-gene (GFG) relationships coevolve in the familiar boom-and-bust cycle, in which resistance is selected when virulence is rare, and virulence is selected when resistance is common. The cycle can result in stable polymorphism when diverse ecological and epidemiological factors cause negative direct frequency-dependent selection (ndFDS) on host resistance, parasite virulence, or both, such that the benefit of a trait to fitness declines as its frequency increases. Polymorphism can also be stabilized by overdominance, when heterozygous hosts have greater resistance than homozygotes to diverse pathogens. Genetic diversity can also persist in the form of statistical polymorphism, sustained by random processes acting on gene frequencies and population size. Stable polymorphism allows alleles to be long-lived and genetic variation to be detectable in natural populations. In agriculture, many of the factors promoting stability in host-parasite interactions have been lost, leading to arms races of host defenses and parasite effectors. Copyright © 2011 by Annual Reviews. All rights reserved.

  10. Coevolution of bed surface patchiness and channel morphology: 2. Numerical experiments

    Science.gov (United States)

    Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

    2015-01-01

    In gravel bed rivers, bed topography and the bed surface grain size distribution evolve simultaneously, but it is not clear how feedbacks between topography and grain sorting affect channel morphology. In this, the second of a pair of papers examining interactions between bed topography and bed surface sorting in gravel bed rivers, we use a two-dimensional morphodynamic model to perform numerical experiments designed to explore the coevolution of both free and forced bars and bed surface patches. Model runs were carried out on a computational grid simulating a 200 m long, 2.75 m wide, straight, rectangular channel, with an initially flat bed at a slope of 0.0137. Over five numerical experiments, we varied (a) whether an obstruction was present, (b) whether the sediment was a gravel mixture or a single size, and (c) whether the bed surface grain size feeds back on the hydraulic roughness field. Experiments with channel obstructions developed a train of alternate bars that became stationary and were connected to the obstruction. Freely migrating alternate bars formed in the experiments without channel obstructions. Simulations incorporating roughness feedbacks between the bed surface and flow field produced flatter, broader, and longer bars than simulations using constant roughness or uniform sediment. Our findings suggest that patches are not simply a by-product of bed topography, but they interact with the evolving bed and influence morphologic evolution.

  11. Coevolution between human's anticancer activities and functional foods from crop origin center in the world.

    Science.gov (United States)

    Zeng, Ya-Wen; Du, Juan; Pu, Xiao-Ying; Yang, Jia-Zhen; Yang, Tao; Yang, Shu-Ming; Yang, Xiao-Meng

    2015-01-01

    Cancer is the leading cause of death around the world. Anticancer activities from many functional food sources have been reported in years, but correlation between cancer prevalence and types of food with anticancer activities from crop origin center in the world as well as food source with human migration are unclear. Hunger from food shortage is the cause of early human evolution from Africa to Asia and later into Eurasia. The richest functional foods are found in crop origin centers, housing about 70% in the world populations. Crop origin centers have lower cancer incidence and mortality in the world, especially Central Asia, Middle East, Southwest China, India and Ethiopia. Asia and Africa with the richest anticancer crops is not only the most important evolution base of humans and origin center of anticancer functional crop, but also is the lowest mortality and incidence of cancers in the world. Cancer prevention of early human migrations was associated with functional foods from crop origin centers, especially Asia with four centers and one subcenter of crop origin, accounting for 58% of the world population. These results reveal that coevolution between human's anticancer activities associated with functional foods for crop origin centers, especially in Asia and Africa.

  12. Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks

    Directory of Open Access Journals (Sweden)

    Na Lin

    2017-03-01

    Full Text Available In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS2Os, which extend the single population particle swarm optimization (PSO algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS2O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS2O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm’s performance. Then PS2O is used for solving the radio frequency identification (RFID network planning (RNP problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

  13. Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

    Science.gov (United States)

    Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

    2017-03-01

    In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

  14. Insect host-parasite coevolution in the light of experimental evolution.

    Science.gov (United States)

    Kerstes, Niels A G; Martin, Oliver Y

    2014-08-01

    The many ways parasites can impact their host species have been the focus of intense study using a range of approaches. A particularly promising but under-used method in this context is experimental evolution, because it allows targeted manipulation of known populations exposed to contrasting conditions. The strong potential of applying this method to the study of insect hosts and their associated parasites is demonstrated by the few available long-term experiments where insects have been exposed to parasites. In this review, we summarize these studies, which have delivered valuable insights into the evolution of resistance in response to parasite pressure, the underlying mechanisms, as well as correlated genetic responses. We further assess findings from relevant artificial selection studies in the interrelated contexts of immunity, life history, and reproduction. In addition, we discuss a number of well-studied Tribolium castaneum-Nosema whitei coevolution experiments in more detail and provide suggestions for research. Specifically, we suggest that future experiments should also be performed using nonmodel hosts and should incorporate contrasting experimental conditions, such as population sizes or environments. Finally, we expect that adding a third partner, for example, a second parasite or symbiont, to a host-parasite system could strongly impact (co)evolutionary dynamics. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  15. Sexually antagonistic coevolution for sexual harassment can act as a barrier to further invasions by parthenogenesis.

    Science.gov (United States)

    Kawatsu, Kazutaka

    2013-02-01

    The assumption of a twofold cost of sex not only complicates the maintenance of sex but also sets conditions for sexual conflict: in organisms with the twofold cost, males often sexually harass females. Sexual harassment is detrimental to female fitness and thus might help maintain sexual populations if male harassment inflicts a harsher cost on parthenogens than on sexual females (asymmetric harassment cost). However, the generality of this concept is now considered doubtful because selective harassment of parthenogens results in loss of mating opportunities for males. Using three mathematical models, I show here that sexual harassment still can impose the asymmetric cost on parthenogens. First, I apply the Lotka-Volterra model to show the degree of asymmetric harassment cost that permits sex to be maintained stably in the population. Second, using adaptive dynamics, I examine whether sexually antagonistic coevolution for sexual harassment, which occurs only in sexual populations, can promote the asymmetric harassment cost. Finally, an individual-based model, which assumes a spatial structure unlike that in the other two, demonstrates that the asymmetric evolution of harassment cost prevents further invasions of parthenogens from different patches into sexual lineages; these mechanisms may account for allopatric distributions of sexual and parthenogenetic lineages as well as the maintenance of sex.

  16. Plant water use efficiency shapes co-evolution of stomata size and density over geologic time

    Science.gov (United States)

    Assouline, S.; Or, D.

    2010-12-01

    The appearance of stomata and formation of impervious leaf cuticle are key elements in terrestrial plant evolution allowing plants to control gaseous diffusion and regulate water loss during simultaneous carbon dioxide uptake. An important plant gaseous diffusion adaptation was achieved by co-evolution of stomata density (D) and maximum aperture size (S), whose product α=S.D defines the evaporating fraction of the leaf surface and determines gaseous conductance. The plant leaf fossil record reveals significant variations in D and S over the 400 Myrs of the Phanerozoic eon, whose impact on gas-exchange capacity and on plant evolution are not fully understood. Characteristics of evaporation suppression from perforated diffusion barriers deduced from plant fossil record delineate the evolution of α as atmospheric CO2 declined from 4000 ppm to present day values. Surprisingly, despite non monotonous variations in α during plant evolution, plant water use efficiency (WUE) has improved systematically during the decrease in atmospheric CO2 over the Phanerozoic, at variance with conventional predictions. The new WUE trend is based on physical relations between α and evaporation suppression by perforated diffusion barriers, providing new insights on the dominance of water related regulatory function and on consequences of future CO2 enriched atmosphere on plant function and hydrologic cycle such as continental runoff scenarios.

  17. Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

    Directory of Open Access Journals (Sweden)

    Andrea N. Loes

    2018-02-01

    Full Text Available Toll-like receptor 4 (TLR4 induces inflammation in response to both pathogen- and host-derived molecules. Lipopolysaccharide (LPS recognition by TLR4 has been shown to occur across the amniotes, but endogenous signaling through TLR4 has not been validated outside of placental mammals. To determine whether endogenous danger signaling is also shared across amniotes, we studied the evolution of TLR4-activation by the calgranulin proteins (S100A8, S100A9, and S100A12, a clade of host molecules that potently activate TLR4 in placental mammals. We performed phylogenetic and syntenic analysis and found MRP-126—a gene in birds and reptiles—is likely orthologous to the mammalian calgranulins. We then used an ex vivo TLR4 activation assay to establish that calgranulin pro-inflammatory activity is not specific to placental mammals, but is also exhibited by representative marsupial and sauropsid species. This activity is strongly dependent on the cofactors CD14 and MD-2 for all species studied, suggesting a conserved mode of activation across the amniotes. Ortholog complementation experiments between the calgranulins, TLR4, CD14, and MD-2 revealed extensive lineage specific-coevolution and multi-way interactions between components that are necessary for the activation of NF-κB signaling by calgranulins and LPS. Our work demonstrates that calgranulin activation of TLR4 evolved at least ~320 million years ago and has been conserved in the amniote innate immune system.

  18. Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus

    Directory of Open Access Journals (Sweden)

    Himanshu Manchanda

    2016-08-01

    Full Text Available Severe influenza associated with strong symptoms and lung inflammation can be caused by intra-host evolution of quasispecies with aspartic acid or glycine in hemagglutinin position 222 (HA-222D/G; H1 numbering. To gain insights into the dynamics of host response to this coevolution and to identify key mechanisms contributing to copathogenesis, the lung transcriptional response of BALB/c mice infected with an A(H1N1pdm09 isolate consisting HA-222D/G quasispecies was analyzed from day 1 to 12 post infection (p.i. At day 2 p.i. 968 differentially expressed genes (DEGs were detected. The DEG number declined to 359 at day 4 and reached 1001 at day 7 p.i. prior to recovery. Interestingly, a biphasic expression profile was shown for the majority of these genes. Cytokine assays confirmed these results on protein level exemplarily for two key inflammatory cytokines, interferon gamma and interleukin 6. Using a reverse engineering strategy, a regulatory network was inferred to hypothetically explain the biphasic pattern for selected DEGs. Known regulatory interactions were extracted by Pathway Studio 9.0 and integrated during network inference. The hypothetic gene regulatory network revealed a positive feedback loop of Ifng, Stat1, and Tlr3 gene signaling that was triggered by the HA-G222 variant and correlated with a clinical symptom score indicating disease severity.

  19. Co-evolution of MHC class I and variable NK cell receptors in placental mammals

    Science.gov (United States)

    Guethlein, Lisbeth A.; Norman, Paul J.; Hilton, Hugo G.; Parham, Peter

    2015-01-01

    Summary Shaping natural killer (NK) cell functions in human immunity and reproduction are diverse killer-cell immunoglobulin-like receptors (KIRs) that recognize polymorphic MHC class I determinants. A survey of placental mammals suggests KIRs serve as variable NK cell receptors only in certain primates and artiodactyls. Divergence of functional and variable KIRs in primates and artiodactyls predates placental reproduction. Among artiodactyls, cattle but not pigs have diverse KIRs. Catarrhine (humans, apes, and Old World monkeys) and platyrrhine (New World monkeys) primates, but not prosimians, have diverse KIRs. Platyrrhine and catarrhine systems of KIR and MHC class I are highly diverged, but within the catarrhines a stepwise co-evolution of MHC class I and KIRs is discerned. In Old World monkeys, diversification focuses on MHC-A and MHC-B and their cognate lineage II KIR. With evolution of C1-bearing MHC-C from MHC-B, as informed by orangutan, the focus changes to MHC-C and its cognate lineage III KIR. Evolution of C2 from C1 and fixation of MHC-C, drove further elaboration of MHC-C-specific KIRs, as exemplified by chimpanzee. In humans, the evolutionary trajectory changes again. Emerging from reorganization of the KIR locus and selective attenuation of KIR avidity for MHC class I are the functionally distinctive KIR A and KIR B haplotypes. PMID:26284483

  20. Coevolution of adaptive technology, maladaptive culture and population size in a producer-scrounger game.

    Science.gov (United States)

    Lehmann, Laurent; Feldman, Marcus W

    2009-11-07

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a 'producer-scrounger' game, which can also usefully be interpreted as an 'individual-social' learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction.

  1. Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks.

    Directory of Open Access Journals (Sweden)

    Jeewoen Shin

    2015-10-01

    Full Text Available Robustness, defined as tolerance to perturbations such as mutations and environmental fluctuations, is pervasive in biological systems. However, robustness often coexists with its counterpart, evolvability--the ability of perturbations to generate new phenotypes. Previous models of gene regulatory network evolution have shown that robustness evolves under stabilizing selection, but it is unclear how robustness and evolvability will emerge in common coevolutionary scenarios. We consider a two-species model of coevolution involving one host and one parasite population. By using two interacting species, key model parameters that determine the fitness landscapes become emergent properties of the model, avoiding the need to impose these parameters externally. In our study, parasites are modeled on species such as cuckoos where mimicry of the host phenotype confers high fitness to the parasite but lower fitness to the host. Here, frequent phenotype changes are favored as each population continually adapts to the other population. Sensitivity evolves at the network level such that point mutations can induce large phenotype changes. Crucially, the sensitive points of the network are broadly distributed throughout the network and continually relocate. Each time sensitive points in the network are mutated, new ones appear to take their place. We have therefore named this phenomenon "whack-a-mole" sensitivity, after a popular fun park game. We predict that this type of sensitivity will evolve under conditions of strong directional selection, an observation that helps interpret existing experimental evidence, for example, during the emergence of bacterial antibiotic resistance.

  2. The Ecological Dynamics of Natural Selection: Traits and the Coevolution of Community Structure.

    Science.gov (United States)

    McPeek, Mark A

    2017-05-01

    Natural selection has both genetic and ecological dynamics. The fitnesses of individuals change with their ecological context, and so the form and strength of selective agents change with abiotic factors and the phenotypes and abundances of interacting species. I use standard models of consumer-resource interactions to explore the ecological dynamics of natural selection and how various trait types influence these dynamics and the resulting structure of a community of coevolving species. Evolutionary optima favored by natural selection depend critically on the abundances of interacting species, and the traits of species can undergo dynamic cycling in limited areas of parameter space. The ecological dynamics of natural selection can also drive shifts from one adaptive peak to another, and these ecologically driven adaptive peak shifts are fundamental to the dynamics of niche differentiation. Moreover, this ecological differentiation is fostered in more productive and more benign environments where species interactions are stronger and where the selection gradients generated by species interactions are stronger. Finally, community structure resulting from coevolution depends fundamentally on the types of traits that underlie species interactions. The ecological dynamics of the process cannot be simplified, neglected, or ignored if we are to build a predictive theory of natural selection.

  3. Co-evolution of strategies and update rules in the prisoner's dilemma game on complex networks

    International Nuclear Information System (INIS)

    Cardillo, Alessio; Gomez-Gardenes, Jesus; Vilone, Daniele; Sanchez, Angel

    2010-01-01

    In this paper, we study a weak prisoner's dilemma (PD) game in which both strategies and update rules are subjected to evolutionary pressure. Interactions among agents are specified by complex topologies, and we consider both homogeneous and heterogeneous situations. We consider deterministic and stochastic update rules for the strategies, which in turn may consider single links or the full context when selecting agents to copy from. Our results indicate that the co-evolutionary process preserves heterogeneous networks as a suitable framework for the emergence of cooperation. Furthermore, on those networks the update rule leading to a larger fraction, which we call replicator dynamics, is selected during co-evolution. On homogeneous networks, we observe that even if the replicator dynamics again turns out to be the selected update rule, the cooperation level is greater than on a fixed update rule framework. We conclude that for a variety of topologies, the fact that the dynamics co-evolves with the strategies leads, in general, to more cooperation in the weak PD game.

  4. Coevolution between flight morphology, vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

    Science.gov (United States)

    Graça, M B; Pequeno, P A C L; Franklin, E; Morais, J W

    2017-10-01

    Occurrence patterns are partly shaped by the affinity of species with habitat conditions. For winged organisms, flight-related attributes are vital for ecological performance. However, due to the different reproductive roles of each sex, we expect divergence in flight energy budget, and consequently different selection responses between sexes. We used tropical frugivorous butterflies as models to investigate coevolution between flight morphology, sex dimorphism and vertical stratification. We studied 94 species of Amazonian fruit-feeding butterflies sampled in seven sites across 3341 ha. We used wing-thorax ratio as a proxy for flight capacity and hierarchical Bayesian modelling to estimate stratum preference. We detected a strong phylogenetic signal in wing-thorax ratio in both sexes. Stouter fast-flying species preferred the canopy, whereas more slender slow-flying species preferred the understorey. However, this relationship was stronger in females than in males, suggesting that female phenotype associates more intimately with habitat conditions. Within species, males were stouter than females and sexual dimorphism was sharper in understorey species. Because trait-habitat relationships were independent from phylogeny, the matching between flight morphology and stratum preference is more likely to reflect adaptive radiation than shared ancestry. This study sheds light on the impact of flight and sexual dimorphism on the evolution and ecological adaptation of flying organisms. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  5. Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age.

    Science.gov (United States)

    Schaarschmidt, Joerg; Monastyrskyy, Bohdan; Kryshtafovych, Andriy; Bonvin, Alexandre M J J

    2018-03-01

    Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology-based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single-domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures. © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc.

  6. Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals

    Science.gov (United States)

    Reilly, Anthony M.; Tkatchenko, Alexandre

    2013-07-01

    The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013), 10.1021/jz400226x], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.

  7. Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs

    Science.gov (United States)

    Zaheer-ul-Haq; Khan, Waqasuddin

    2011-01-01

    Class II major histocompatibility complex (MHC II) molecules as expressed by antigen-presenting cells are heterodimeric cell-surface glycoprotein receptors that are fundamental in initiating and propagating an immune response by presenting tumor-associated antigenic peptides to CD4+/TH cells. The loading efficiency of such peptides can be improved by small organic compounds (MHC Loading Enhancers—MLEs), that convert the non-receptive peptide conformation of MHC II to a peptide-receptive conformation. In a reversible reaction, these compounds open up the binding site of MHC II molecules by specific interactions with a yet undefined pocket. Here, we performed molecular docking and molecular dynamics simulation studies of adamantyl compounds on the predicted cavity around the P1 pocket of 2 allelic variants of HLA-DRs. The purpose was to investigate the suitability of adamantyl compounds as MLEs at the dimorphic β86 position. Docking studies revealed that besides numerous molecular interactions formed by the adamantyl compounds, Asnβ82, Tyrβ83, and Thrβ90 are the crucial amino acid residues that are characterized as the "sensors" of peptide loading. Molecular dynamics simulation studies exposed the dynamical structural changes that HLA-DRs adopted as a response to binding of 3-(1-adamantyl)-5-hydrazidocarbonyl-1H-pyrazole (AdCaPy). The conformations of AdCaPy complexed with the Glyβ86 HLA-DR allelic variant are well correlated with the stabilized form of peptide-loaded HLA-DRs, further confirming the role of AdCaPy as a MLE. Hydrogen bonding interaction analysis clearly demonstrated that after making suitable contacts with AdCaPy, HLA-DR changes its local conformation. However, AdCaPy complexed with HLA-DR having Valβ86 at the dimorphic position did not accommodate AdCaPy as MLE due to steric hindrance caused by the valine.

  8. Understanding the Polar Character Trend in a Series of Diels-Alder Reactions Using Molecular Quantum Similarity and Chemical Reactivity Descriptors

    Directory of Open Access Journals (Sweden)

    Alejandro Morales-Bayuelo

    2014-01-01

    Full Text Available In molecular similarity there is a premise “similar molecules tend to behave similarly”; however in the actual quantum similarity field there is no clear methodology to describe the similarity in chemical reactivity, and with this end an analysis of charge-transfer (CT processes in a series of Diels-Alder (DA reactions between cyclopentadiene (Cp and cyano substitutions on ethylene has been studied. The CT analysis is performed in the reagent assuming a grand canonical ensemble and the considerations for an electrophilic system using B3LYP/6-31G(d and M06-2X/6-311 + G(d,p methods. An analysis for CT was performed in agreement with the experimental results with a good statistical correlation (R2=0.9118 relating the polar character to the bond force constants in DA reactions. The quantum distortion analysis on the transition states (TS was performed using molecular quantum similarity indexes of overlap and coulomb showing good correlation (R2=0.8330 between the rate constants and quantum similarity indexes. In this sense, an electronic reorganization based on molecular polarization in terms of CT is proposed; therefore, new interpretations on the electronic systematization of the DA reactions are presented, taking into account that today such electronic systematization is an open problem in organic physical chemistry. Additionally, one way to quantify the similarity in chemical reactivity was shown, taking into account the dependence of the molecular alignment on properties when their position changes; in this sense a possible way to quantify the similarity of the CT in systematic form on these DA cycloadditions was shown.

  9. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

    Science.gov (United States)

    Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

    2016-12-01

    Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the K m changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Species-specific genes under selection characterize the co-evolution of slavemaker and host lifestyles.

    Science.gov (United States)

    Feldmeyer, B; Elsner, D; Alleman, A; Foitzik, S

    2017-12-04

    The transition to a parasitic lifestyle entails comprehensive changes to the selective regime. In parasites, genes encoding for traits that facilitate host detection, exploitation and transmission should be under selection. Slavemaking ants are social parasites that exploit the altruistic behaviour of their hosts by stealing heterospecific host brood during raids, which afterwards serve as slaves in slavemaker nests. Here we search for evidence of selection in the transcriptomes of three slavemaker species and three closely related hosts. We expected selection on genes underlying recognition and raiding or defense behaviour. Analyses of selective forces in species with a slavemaker or host lifestyle allowed investigation into whether or not repeated instances of slavemaker evolution share the same genetic basis. To investigate the genetic basis of host-slavemaker co-evolution, we created orthologous clusters from transcriptome sequences of six Temnothorax ant species - three slavemakers and three hosts - to identify genes with signatures of selection. We further tested for functional enrichment in selected genes from slavemakers and hosts respectively and investigated which pathways the according genes belong to. Our phylogenetic analysis, based on more than 5000 ortholog sequences, revealed sister species status for two slavemakers as well as two hosts, contradicting a previous phylogeny based on mtDNA. We identified 309 genes with signs of positive selection on branches leading to slavemakers and 161 leading to hosts. Among these were genes potentially involved in cuticular hydrocarbon synthesis, thus species recognition, and circadian clock functionality possibly explaining the different activity patterns of slavemakers and hosts. There was little overlap of genes with signatures of positive selection among species, which are involved in numerous different functions and different pathways. We identified different genes, functions and pathways under positive

  11. Sexual coevolution of spermatophore envelopes and female genital traits in butterflies: Evidence of male coercion?

    Directory of Open Access Journals (Sweden)

    Víctor Sánchez

    2014-01-01

    Full Text Available Signa are sclerotized structures located on the inner wall of the corpus bursa of female Lepidoptera whose main function is tearing open spermatophores. The sexually antagonistic coevolution (SAC hypothesis proposes that the thickness of spermatophore envelopes has driven the evolution of the females signa; this idea is based in the fact that in many lepidopterans female sexual receptivity is at least partially controlled by the volume of ejaculate remaining in the corpus bursa. According to the SAC hypothesis, males evolved thick spermatophore envelopes to delay the post-mating recovery of female sexual receptivity thus reducing sperm competition; in response, females evolved signa for breaking spermatophore envelopes faster, gaining access to the resources contained in them and reducing their intermating intervals; the evolution of signa, in turn, favored the evolution of even thicker spermatophore envelopes, and so on. We tested two predictions of the SAC hypothesis with comparative data on the thickness of spermatophore envelopes of eleven species of Heliconiinae butterflies. The first prediction is that the spermatophore envelopes of polyandrous species with signa will be thicker than those of monandrous species without signa. In agreement with this prediction, we found that the spermatophore envelopes of a polyandrous Heliconius species with signa are thicker than those of two monandrous Heliconius species without signa. The second prediction is that in some species with signa males could enforce monandry in females by evolving “very thick” spermatophore envelopes, in these species we predict that their spermatophore envelopes will be thicker than those of their closer polyandrous relatives with signa. In agreement with this prediction, we found that in two out of three comparisons, spermatophore envelopes of monandrous species with signa have thicker spermatophore envelopes than their closer polyandrous relatives with signa. Thus, our

  12. Phase-specific Geochemistry of Ni: a Tracer of Geosphere-Biosphere Co-evolution?

    Science.gov (United States)

    Ciscato, E. R.; Vance, D.; Bontognali, T. R. R.; Poulton, S.

    2016-12-01

    Metalloproteome analyses and culturing studies have suggested that trace metals, such as Cu, Fe, Mo, Ni, and Zn, were selectively utilized by different organisms and specific metabolisms throughout the evolution of the biosphere. Methanogens have a particular requirement for Ni and culturing studies have shown that they fractionate Ni isotopes upon uptake. It is not clear, however, whether a resulting Ni isotopic signal can be preserved in the geological record. We have developed a new approach that enables us to analyze phase-specific authigenic trace metal enrichments, and their respective isotopic signatures, in (predominantly organic-rich) sediments from the geological record. An acid digestion step followed by high-pressure ashing allows us to separate an `organic matter + Pyrite' phase from an `HF-extractable' phase. We have applied this approach to investigate the distribution of Ni isotopes in a variety of modern sediments, including organic-rich sediments from upwelling margins and a hypersaline lagoonal setting where methanogenesis is likely to be an active process. Preliminary results on geological record samples show a δ60Ni for the `HF-extractable' phases that agrees with the average continental crust, whereas the `organic matter + Pyrite' phases are heavier and shifted in the direction of modern seawater. By combining this data with our δ60Ni dataset from modern sediments, we investigate the dynamics of Ni cycling in environments with different O2 and H2S availabilities both in the modern and throughout the past 3.2 billion years. Our phase-specific δ60Ni record is of instrumental importance in determining whether a biologically induced fractionation imparted by methanogens is indeed observable, and if it can be used as a biosignature for tracing the predominance of methanogenic pathways throughout the co-evolution of the geosphere and biosphere.

  13. Toward the understanding of the molecular basis for the inhibition of COX-1 and COX-2 by phenolic compounds present in Uruguayan propolis and grape pomace.

    Science.gov (United States)

    Paulino, Margot; Alvareda, Elena; Iribarne, Federico; Miranda, Pablo; Espinosa, Victoria; Aguilera, Sara; Pardo, Helena

    2016-12-01

    Propolis and grape pomace have significant amounts of phenols which can take part in anti-inflammatory mechanisms. As the cyclooxygenases 1 and 2 (COX-1 and COX-2) are involved in said mechanisms, the possibility for a selective inhibition of COX-2 was analyzed in vitro and in silico. Propolis and grape pomace from Uruguayan species were collected, extracted in hydroalcoholic mixture and analyzed. Based on phenols previously identified, and taking as reference the crystallographic structures of COX-1 and COX-2 in complex with the commercial drug Celecoxib, a molecular docking procedure was devised to adjust 123 phenolic molecular models at the enzyme-binding sites. The most important results of this work are that the extracts have an overall inhibition activity very similar in COX-1 and COX-2, i.e. they do not possess selective inhibition activity for COX-2. Nevertheless, 10 compounds of the phenolic database turned out to be more selective and 94 phenols resulted with similar selectivity than Celecoxib, an outcome that accounts for the overall experimental inhibition measures. Binding site environment observations showed increased polarity in COX-2 as compared with COX-1, suggesting that polarity is the key for selectivity. Accordingly, the screening of molecular contacts pointed to the residues: Arg106, Gln178, Leu338, Ser339, Tyr341, Tyr371, Arg499, Ala502, Val509, and Ser516, which would explain, at the atomic level, the anti-inflammatory effect of the phenolic compounds. Among them, Gln178 and Arg499 appear to be essential for the selective inhibition of COX-2.

  14. Early human communication helps in understanding language evolution.

    Science.gov (United States)

    Lenti Boero, Daniela

    2014-12-01

    Building a theory on extant species, as Ackermann et al. do, is a useful contribution to the field of language evolution. Here, I add another living model that might be of interest: human language ontogeny in the first year of life. A better knowledge of this phase might help in understanding two more topics among the "several building blocks of a comprehensive theory of the evolution of spoken language" indicated in their conclusion by Ackermann et al., that is, the foundation of the co-evolution of linguistic motor skills with the auditory skills underlying speech perception, and the possible phylogenetic interactions of protospeech production with referential capabilities.

  15. Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

    Science.gov (United States)

    Springer, Michael T.

    2014-01-01

    Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

  16. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria.

    Science.gov (United States)

    Bull, Carolee T; Koike, Steven T

    2015-01-01

    Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.

  17. The Co-evolution of Language and the Brain: A Review of Two Contrastive Views (Pinker & Deacon)

    DEFF Research Database (Denmark)

    Christensen, Ken Ramshøj

    2001-01-01

    This article is a review of two contrastive views on the co-evolution of language and the brain – The Language Instinct by Steven Pinker (1994) and The Symbolic Species by Terrence Deacon (1997). As language is a trait unique to mankind it can not be equated with nonlinguistic communication – hum...... on the evolutionary advantage of the ability to establish and maintain social alliances and contracts and to outsmart social cheaters but they disagree on what this cheating involves. Pinker defines cheaters as social parasites, while Deacon defines them adulterers....

  18. Socio-hydrologic Perspectives of the Co-evolution of Humans and Water in the Tarim River Basin, Western China

    Science.gov (United States)

    Liu, Ye; Tian, Fuqiang; Hu, Heping; Liu, Dengfeng; Sivapalan, Murugesu

    2013-04-01

    Socio-hydrology studies the co-evolution of coupled human-water systems, which is of great importance for long-term sustainable water resource management in basins suffering from serious eco-environmental degradation. Process socio-hydrology can benefit from the exploring the patterns of historical co-evolution of coupled human-water systems as a way to discovering the organizing principles that may underpin their co-evolution. As a self-organized entity, the human-water system in a river basin would evolve into certain steady states over a sufficiently long time but then could also experience sudden shifts due to internal or external disturbances that exceed system thresholds. In this study, we discuss three steady states (also called stages in the social sciences, including natural, human exploitation and recovery stages) and transitions between these during the past 1500 years in the Tarim River Basin of Western China, which a rich history of civilization including its place in the famous Silk Road that connected China to Europe. Specifically, during the natural stage with a sound environment that existed before the 19th century, shifts in the ecohydrological regime were mainly caused by environmental changes such river channel migration and climate change. During the human exploitation stages in the 5th and again in the 19th-20th centuries, however, humans gradually became the main drivers for system evolution, during which the basin experienced rapid population growth, fast socio-economic development and intense human activities. By the 1970s, after 200 years of colonization, the Tarim River Basin evolved into a new regime with vulnerable ecosystem and water system, and suffered from serious water shortages and desertification. Human society then began to take a critical look into the effects of their activities and reappraise the impact of human development on the ecohydrological system, which eventually led the basin into a treatment and recovery stage

  19. Calling all Campy--how routine investigation and molecular characterization impacts the understanding of campylobacteriosis epidemiology--Alaska, United States, 2004-2013.

    Science.gov (United States)

    Castrodale, L J; Provo, G M; Xavier, C M; McLaughlin, J B

    2016-01-01

    Unlike most jurisdictions in the United States, Alaska performs pulsed-field gel electrophoresis (PFGE) characterization of all Campylobacter sp. isolates at the state public health laboratory--a practice that started in 2002. Moreover, in order to ensure early detection and response to campylobacteriosis outbreaks, the Alaska Section of Epidemiology has investigated all incident Campylobacter sp. case reports since 2004. This report summarizes the public health impact of routine incident case investigations and molecular characterization of all Campylobacter sp. isolates. In sum, we found that these efforts have contributed to better characterization of the epidemiology of campylobacteriosis in Alaska, and facilitated more rapid outbreak detection, more public health investigations, and earlier public health interventions.

  20. Comparative modeling and molecular docking analysis of white, brown and soft rot fungal laccases using lignin model compounds for understanding the structural and functional properties of laccases.

    Science.gov (United States)

    Kameshwar, Ayyappa Kumar Sista; Barber, Richard; Qin, Wensheng

    2018-01-01

    Extrinsic catalytic properties of laccase enable it to oxidize a wide range of aromatic (phenolic and non-phenolic) compounds which makes it commercially an important enzyme. In this study, we have extensively compared and analyzed the physico-chemical, structural and functional properties of white, brown and soft rot fungal laccases using standard protein analysis software. We have computationally predicted the three-dimensional comparative models of these laccases and later performed the molecular docking studies using the lignin model compounds. We also report a customizable rapid and reliable protein modelling and docking pipeline for developing structurally and functionally stable protein structures. We have observed that soft rot fungal laccases exhibited comparatively higher structural variation (higher random coil) when compared to brown and white rot fungal laccases. White and brown rot fungal laccase sequences exhibited higher similarity for conserved domains of Trametes versicolor laccase, whereas soft rot fungal laccases shared higher similarity towards conserved domains of Melanocarpus albomyces laccase. Results obtained from molecular docking studies showed that aminoacids PRO, PHE, LEU, LYS and GLN were commonly found to interact with the ligands. We have also observed that white and brown rot fungal laccases showed similar docking patterns (topologically monomer, dimer and trimer bind at same pocket location and tetramer binds at another pocket location) when compared to soft rot fungal laccases. Finally, the binding efficiencies of white and brown rot fungal laccases with lignin model compounds were higher compared to the soft rot fungi. These findings can be further applied in developing genetically efficient laccases which can be applied in growing biofuel and bioremediation industries. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Understanding the molecular basis of stability in Kunitz (STI) family of inhibitors in terms of a conserved core tryptophan residue: A theoretical investigation.

    Science.gov (United States)

    Datta Sharma, Ravi; Goswami, Nabajyoti; Ghosh, Debasree; Majumder, Sudip

    2017-08-01

    β-trefoil is one of the superfolds among proteins. Important classes of proteins like Interleukins (ILs), FibroblastGrowth Factors (FGFs), Kunitz (STI) family of inhibitors etc. belong to this fold. Kunitz (STI) family of inhibitors of proteins possess a highly conserved and structurally important Trytophan 91 (W91) residue, which stitches the top layer of the barrel with the lid. In this article we have investigated the molecular insights of the involvement of this W91 residue in the stability and folding pathway of Kunitz (STI) family. Winged bean Chymotrypsin inhibitor (WCI), a member of Kunitz (STI) family was chosen as a model system for carrying out the work. Molecular dynamics (MD) simulations were run with a set of total six proteins, including wild type WCI (WT) & five mutants namely W91F, W91M, W91A, W91H and W91I. Among all of them the coordinates of four proteins were taken from their crystal structures deposited in the Protein Data Bank (PDB), where as the coordinates for the rest two was generated using in-silico modelling. Our results suggest that truly this W91 residue plays a determining role in stability and folding pathway of Kunitz (STI) family. The mutants are less stable and more susceptible to quicker unfolding at higher temperatures compared to the wild type WCI. These effects are most pronounced for the smallest mutants namely W91H and W91A, indicating more is the cavity created by mutation at W91 position more the proteins becomes unstable. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. The bitter barricading of prostaglandin biosynthesis pathway: understanding the molecular mechanism of selective cyclooxygenase-2 inhibition by amarogentin, a secoiridoid glycoside from Swertia chirayita.

    Directory of Open Access Journals (Sweden)

    Shantanu Shukla

    Full Text Available Swertia chirayita, a medicinal herb inhabiting the challenging terrains and high altitudes of the Himalayas, is a rich source of essential phytochemical isolates. Amarogentin, a bitter secoiridoid glycoside from S. chirayita, shows varied activity in several patho-physiological conditions, predominantly in leishmaniasis and carcinogenesis. Experimental analysis has revealed that amarogentin downregulates the cyclooxygenase-2 (COX-2 activity and helps to curtail skin carcinogenesis in mouse models; however, there exists no account on selective inhibition of the inducible cyclooxygenase (COX isoform by amarogentin. Hence the computer-aided drug discovery methods were used to unravel the COX-2 inhibitory mechanism of amarogentin and to check its selectivity for the inducible isoform over the constitutive one. The generated theoretical models of both isoforms were subjected to molecular docking analysis with amarogentin and twenty-one other Food and Drug Authority (FDA approved lead molecules. The post-docking binding energy profile of amarogentin was comparable to the binding energy profiles of the FDA approved selective COX-2 inhibitors. Subsequent molecular dynamics simulation analysis delineated the difference in the stability of both complexes, with amarogentin-COX-2 complex being more stable after 40ns simulation. The total binding free energy calculated by MMGBSA for the amarogentin-COX-2 complex was -52.35 KCal/mol against a binding free energy of -8.57 KCal/mol for amarogentin-COX-1 complex, suggesting a possible selective inhibition of the COX-2 protein by the natural inhibitor. Amarogentin achieves this potential selectivity by small, yet significant, structural differences inherent to the binding cavities of the two isoforms. Hypothetically, it might block the entry of the natural substrates in the hydrophobic binding channel of the COX-2, inhibiting the cyclooxygenation step. To sum up briefly, this work highlights the mechanism of the

  3. Selective binding of pyrene in subdomain IB of human serum albumin: Combining energy transfer spectroscopy and molecular modelling to understand protein binding flexibility

    Science.gov (United States)

    Ling, Irene; Taha, Mohamed; Al-Sharji, Nada A.; Abou-Zied, Osama K.

    2018-04-01

    The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory. The estimated FRET apparent distance between pyrene and Trp214 was 27 Å, which was closely reproduced by the docking analysis (29 Å) and MD simulation (32 Å). The highest affinity site for pyrene was found to be in subdomain IB from the docking results. The calculated equilibrium structure of the complex using MD simulation shows that the ligand is largely stabilized by hydrophobic interaction with Phe165, Phe127, and the nonpolar moieties of Tyr138 and Tyr161. The fluorescence vibronic peak ratio I1/I3 of bound pyrene inside HSA indicates the presence of polar effect in the local environment of pyrene which is less than that of free pyrene in buffer. This was clarified by the MD simulation results in which an average of 5.7 water molecules were found within 0.5 nm of pyrene in the binding site. Comparing the fluorescence signals and lifetimes of pyrene inside HSA to that free in buffer, the high tendency of pyrene to form dimer was almost completely suppressed inside HSA, indicating a high selectivity of the binding pocket toward pyrene monomer. The current results emphasize the ability of HSA, as a major carrier of several drugs and ligands in blood, to bind hydrophobic molecules in cavities other than subdomain IIA which is known to bind most hydrophobic drugs. This ability stems from the nature of the amino acids forming the binding

  4. Emergent dynamics of fairness in the spatial coevolution of proposer and responder species in the ultimatum game.

    Directory of Open Access Journals (Sweden)

    Reiji Suzuki

    Full Text Available While spatially local interactions are ubiquitous between coevolving species sharing recourses (e.g., plant-insect interactions, their effects on such coevolution processes of strategies involving the share of a resource are still not clearly understood. We construct a two-dimensional spatial model of the coevolution of the proposer and responder species in the ultimatum game (UG, in which a pair of proposer and responder individuals at each site plays the UG. We investigate the effects of the locality of interactions and the intensity of selection on the emergence of fairness between these species. We show that the lower intensity of selection favors fair strategies in general, and there are no significant differences in the evolution of fairness between the cases with local and global interactions when the intensity of selection is low. However, as the intensity of selection becomes higher, the spatially local interactions contribute to the evolution of fairer strategies more than the global interactions, even though fair strategies become more difficult to evolve. This positive effect of spatial interactions is expected to be due to the mutual benefit of fairness for both proposer and responder species in future generations, which brings about a dynamic evolution process of fairness.

  5. The Main Sequence of Star Forming Galaxies and AGNs at High-Z: Evidence for in situ Coevolution

    Science.gov (United States)

    Mancuso, Claudia; Lapi, Andrea; Massardi, Marcella; Danese, Luigi

    2017-11-01

    We provide a novel, unifying physical interpretation on the origin, the average shape, the scatter and the cosmic evolution for the main sequence of star forming galaxies and AGNs at high redshift (z>1). We achieve this goal in a model independent way, starting from redshift-dependent SFR functions based on the latest UV/ far-IR data from HST/Herschel and related statistics of strong gravitationally lensed sources (see for details Fig. 1 in Mancuso, Lapi et al. 2016a, ApJ 823,128). We also used deterministic evolutionary tracks for the history of star formation and black hole accretion, inspired by the in situ co-evolution scenario (see Fig. 2), and gauged on a wealth of multiwavelength observations including the observed Eddington ratio distribution. We validated our ingredients against many observables (see Mancuso, Lapi et al. 2016A, ApJ 823,128). The resulting Main Sequences are in excellent agreement with current observational data. We also provided a new interpretation for off-main sequence galaxies and AGNs in terms of the in situ coevolution scenario.

  6. Coevolution and hierarchical interactions of Tomato mosaic virus and the resistance gene Tm-1.

    Directory of Open Access Journals (Sweden)

    Kazuhiro Ishibashi

    Full Text Available During antagonistic coevolution between viruses and their hosts, viruses have a major advantage by evolving more rapidly. Nevertheless, viruses and their hosts coexist and have coevolved, although the processes remain largely unknown. We previously identified Tm-1 that confers resistance to Tomato mosaic virus (ToMV, and revealed that it encodes a protein that binds ToMV replication proteins and inhibits RNA replication. Tm-1 was introgressed from a wild tomato species Solanum habrochaites into the cultivated tomato species Solanum lycopersicum. In this study, we analyzed Tm-1 alleles in S. habrochaites. Although most part of this gene was under purifying selection, a cluster of nonsynonymous substitutions in a small region important for inhibitory activity was identified, suggesting that the region is under positive selection. We then examined the resistance of S. habrochaites plants to ToMV. Approximately 60% of 149 individuals from 24 accessions were resistant to ToMV, while the others accumulated detectable levels of coat protein after inoculation. Unexpectedly, many S. habrochaites plants were observed in which even multiplication of the Tm-1-resistance-breaking ToMV mutant LT1 was inhibited. An amino acid change in the positively selected region of the Tm-1 protein was responsible for the inhibition of LT1 multiplication. This amino acid change allowed Tm-1 to bind LT1 replication proteins without losing the ability to bind replication proteins of wild-type ToMV. The antiviral spectra and biochemical properties suggest that Tm-1 has evolved by changing the strengths of its inhibitory activity rather than diversifying the recognition spectra. In the LT1-resistant S. habrochaites plants inoculated with LT1, mutant viruses emerged whose multiplication was not inhibited by the Tm-1 allele that confers resistance to LT1. However, the resistance-breaking mutants were less competitive than the parental strains in the absence of Tm-1. Based on

  7. Understanding the adsorptive interactions of arsenate-iron nanoparticles with curved fullerene-like sheets in activated carbon using a quantum mechanics/molecular mechanics computational approach.

    Science.gov (United States)

    Ha, Nguyen Ngoc; Cam, Le Minh; Ha, Nguyen Thi Thu; Goh, Bee-Min; Saunders, Martin; Jiang, Zhong-Tao; Altarawneh, Mohammednoor; Dlugogorski, Bogdan Z; El-Harbawi, Mohanad; Yin, Chun-Yang

    2017-06-07

    The prevalence of global arsenic groundwater contamination has driven widespread research on developing effective treatment systems including adsorption using various sorbents. The uptake of arsenic-based contaminants onto established sorbents such as activated carbon (AC) can be effectively enhanced via immobilization/impregnation of iron-based elements on the porous AC surface. Recent suggestions that AC pores structurally consist of an eclectic mix of curved fullerene-like sheets may affect the arsenic adsorption dynamics within the AC pores and is further complicated by the presence of nano-sized iron-based elements. We have therefore, attempted to shed light on the adsorptive interactions of arsenate-iron nanoparticles with curved fullerene-like sheets by using hybridized quantum mechanics/molecular mechanics (QMMM) calculations and microscopy characterization. It is found that, subsequent to optimization, chemisorption between HAsO 4 2- and the AC carbon sheet (endothermic process) is virtually non-existent - this observation is supported by experimental results. Conversely, the incorporation of iron nanoparticles (FeNPs) into the AC carbon sheet greatly facilitates chemisorption of HAsO 4 2- . Our calculation implies that iron carbide is formed at the junction between the iron and the AC interface and this tightly chemosorbed layer prevents detachment of the FeNPs on the AC surface. Other aspects including electronic structure/properties, carbon arrangement defects and rate of adsorptive interaction, which are determined using the Climbing-Image NEB method, are also discussed.

  8. Controlled experiments of hillslope co-evolution at the Biosphere 2 Landscape Evolution Observatory: toward prediction of coupled hydrological, biogeochemical, and ecological change

    Science.gov (United States)

    Volkmann, T. H. M.; Sengupta, A.; Pangle, L.; Abramson, N.; Barron-Gafford, G.; Breshears, D. D.; Bugaj, A.; Chorover, J.; Dontsova, K.; Durcik, M.; Ferre, T. P. A.; Harman, C. J.; Hunt, E.; Huxman, T. E.; Kim, M.; Maier, R. M.; Matos, K.; Alves Meira Neto, A.; Meredith, L. K.; Monson, R. K.; Niu, G. Y.; Pelletier, J. D.; Rasmussen, C.; Ruiz, J.; Saleska, S. R.; Schaap, M. G.; Sibayan, M.; Tuller, M.; Van Haren, J. L. M.; Wang, Y.; Zeng, X.; Troch, P. A.

    2017-12-01

    Understanding the process interactions and feedbacks among water, microbes, plants, and porous geological media is crucial for improving predictions of the response of Earth's critical zone to future climatic conditions. However, the integrated co-evolution of landscapes under change is notoriously difficult to investigate. Laboratory studies are typically limited in spatial and temporal scale, while field studies lack observational density and control. To bridge the gap between controlled lab and uncontrolled field studies, the University of Arizona - Biosphere 2 built a macrocosm experiment of unprecedented scale: the Landscape Evolution Observatory (LEO). LEO consists of three replicated, 330-m2 hillslope landscapes inside a 5000-m2 environmentally controlled facility. The engineered landscapes contain 1-m depth of basaltic tephra ground to homogenous loamy sand that will undergo physical, chemical, and mineralogical changes over many years. Each landscape contains a dense sensor network capable of resolving water, carbon, and energy cycling processes at sub-meter to whole-landscape scale. Embedded sampling devices allow for quantification of biogeochemical processes, and facilitate the use of chemical tracers applied with the artificial rainfall. LEO is now fully operational and intensive forcing experiments have been launched. While operating the massive infrastructure poses significant challenges, LEO has demonstrated the capacity of tracking multi-scale matter and energy fluxes at a level of detail impossible in field experiments. Initial sensor, sampler, and restricted soil coring data are already providing insights into the tight linkages between water flow, weathering, and (micro-) biological community development during incipient landscape evolution. Over the years to come, these interacting processes are anticipated to drive the model systems to increasingly complex states, potentially perturbed by changes in climatic forcing. By intensively monitoring

  9. Understanding the Electronic Structure of 4d Metal Complexes: From Molecular Spinors to L-Edge Spectra of a di-Ru Catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Alperovich, Igor; Smolentsev, Grigory; Moonshiram, Dooshaye; Jurss, Jonah W.; Concepcion, Javier J.; Meyer, Thomas J.; Soldatov, Alexander; Pushkar, Yulia (UNC); (Purdue); (SFU-Russia); (Lund)

    2015-09-17

    L{sub 2,3}-edge X-ray absorption spectroscopy (XAS) has demonstrated unique capabilities for the analysis of the electronic structure of di-Ru complexes such as the blue dimer cis,cis-[Ru{sub 2}{sup III}O(H{sub 2}O){sub 2}(bpy){sub 4}]{sup 4+} water oxidation catalyst. Spectra of the blue dimer and the monomeric [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex show considerably different splitting of the Ru L{sub 2,3} absorption edge, which reflects changes in the relative energies of the Ru 4d orbitals caused by hybridization with a bridging ligand and spin-orbit coupling effects. To aid the interpretation of spectroscopic data, we developed a new approach, which computes L{sub 2,3}-edges XAS spectra as dipole transitions between molecular spinors of 4d transition metal complexes. This allows for careful inclusion of the spin-orbit coupling effects and the hybridization of the Ru 4d and ligand orbitals. The obtained theoretical Ru L{sub 2,3}-edge spectra are in close agreement with experiment. Critically, existing single-electron methods (FEFF, FDMNES) broadly used to simulate XAS could not reproduce the experimental Ru L-edge spectra for the [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex nor for the blue dimer, while charge transfer multiplet (CTM) calculations were not applicable due to the complexity and low symmetry of the blue dimer water oxidation catalyst. We demonstrated that L-edge spectroscopy is informative for analysis of bridging metal complexes. The developed computational approach enhances L-edge spectroscopy as a tool for analysis of the electronic structures of complexes, materials, catalysts, and reactive intermediates with 4d transition metals.

  10. Histidine adsorption on TiO2 nanoparticles: an integrated spectroscopic, thermodynamic, and molecular-based approach toward understanding nano-bio interactions.

    Science.gov (United States)

    Mudunkotuwa, Imali A; Grassian, Vicki H

    2014-07-29

    Nanoparticles in biological media form dynamic entities as a result of competitive adsorption of proteins on nanoparticle surfaces called protein coronas. The protein affinity toward nanoparticle surfaces potentially depends on the constituent amino acid side chains which are on the protein exterior and thus exposed to the solution and available for interaction. Therefore, studying the adsorption of individual amino acids on nanoparticle surfaces can provide valuable insights into the overall evolution of nanoparticles in solution and the protein corona that forms. In the current study, the surface adsorption of l-histidine on TiO2 nanoparticles with a diameter of 5 nm at pH 7.4 (physiological pH) is studied from both macroscopic and molecular perspectives. Quantitative adsorption measurements of l-histidine on 5 nm TiO2 particles yield maximum adsorption coverage of 6.2 ± 0.3 × 10(13) molecules cm(-2) at 293 K and pH 7.4. These quantitative adsorption measurements also yield values for the equilibrium constant and free energy of adsorption of K = 4.3 ± 0.5 × 10(2) L mol(-1) and ΔG = -14.8 ± 0.3 kJ mol(-1), respectively. Detailed analysis of the adsorption between histidine and 5 nm TiO2 nanoparticle surfaces with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy indicates both the imidazole side chain and the amine group interacting with the nanoparticle surface and the adsorption to be reversible. The adsorption results in no change in surface charge and therefore does not change nanoparticle-nanoparticle interactions and thus aggregation behavior of these 5 nm TiO2 nanoparticles in aqueous solution.

  11. Single nucleotide polymorphism-based molecular typing of M. leprae from multicase families of leprosy patients and their surroundings to understand the transmission of leprosy.

    Science.gov (United States)

    Turankar, R P; Lavania, M; Chaitanya, V S; Sengupta, U; Darlong, J; Darlong, F; Siva Sai, K S R; Jadhav, R S

    2014-03-01

    The exact mode of transmission of leprosy is not clearly understood; however, many studies have demonstrated active transmission of leprosy around a source case. Families of five active leprosy cases and their household contacts were chosen from a high endemic area in Purulia. Fifty-two soil samples were also collected from different areas of their houses. DNA was extracted from slit-skin smears (SSS) and soil samples and the Mycobacterium leprae-specific RLEP (129 bp) region was amplified using PCR. Molecular typing of M. leprae was performed for all RLEP PCR-positive samples by single nucleotide polymorphism (SNP) typing and confirmation by DNA sequencing. SSS of these five patients and six out of the total 28 contacts were PCR positive for RLEP whereas 17 soil samples out of 52 showed the presence of M. leprae DNA. SNP typing of M. leprae from all RLEP PCR-positive subjects (patients and smear-positive contacts) and 10 soil samples showed the SNP type 1 genotype. M. leprae DNA from the five leprosy patients and the six contacts was further subtyped and the D subtype was noted in all patients and contacts, except for one contact where the C subtype was identified. Typing followed by subtyping of M. leprae clearly revealed that either the contacts were infected by the patients or both patients and contacts had the same source of infection. It also revealed that the type of M. leprae in the soil in the inhabited areas where patients resided was also of the same type as that found in patients. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  12. Understanding the role of single molecular ZnS precursors in the synthesis of In(Zn)P/ZnS nanocrystals.

    Science.gov (United States)

    Xi, Lifei; Cho, Deok-Yong; Duchamp, Martial; Boothroyd, Chris B; Lek, Jun Yan; Besmehn, Astrid; Waser, Rainer; Lam, Yeng Ming; Kardynal, Beata

    2014-10-22

    Environmentally friendly nanocrystals (NCs) such as InP are in demand for various applications, such as biomedical labeling, solar cells, sensors, and light-emitting diodes (LEDs). To fulfill their potential applications, the synthesis of such high-quality "green" InP NCs required further improvement so as to achieve better stability, higher brightness NCs, and also to have a more robust synthesis route. The present study addresses our efforts on the synthesis of high-quality In(Zn)P/ZnS core-shell NCs using an air- and moisture-stable ZnS single molecular precursor (SMP) and In(Zn)P cores. The SMP method has recently emerged as a promising route for the surface overcoating of NCs due to its simplicity, high reproducibility, low reaction temperature, and flexibility in controlling the reaction. The synthesis involved heating the In(Zn)P core solution and Zn(S2CNR2) (where R = methyl, ethyl, butyl, or benzyl and referred to as ZDMT, ZDET, ZDBT, or ZDBzT, respectively) in oleylamine (OLA) to 90-250 °C for 0.5-2.5 h. In this work, we systematically studied the influence of different SMP end groups, the complex formation and stability between the SMP and oleylamine (OLA), the reaction temperature, and the amount of SMP on the synthesis of high-quality In(Zn)P/ZnS NCs. We found that thiocarbamate end groups are an important factor contributing to the low-temperature growth of high-quality In(Zn)P/ZnS NCs, as the end groups affect the polarity of the molecules and result in a different steric arrangement. We found that use of SMP with bulky end groups (ZDBzT) results in nanocrystals with higher photoluminescence quantum yield (PL QY) and better dispersibility than those synthesized with SMPs with the shorter alkyl chain groups (ZDMT, ZDET, or ZDBT). At the optimal conditions, the PL QY of red emission In(Zn)P/ZnS NCs is 55 ± 4%, which is one of the highest values reported. On the basis of structural (XAS, XPS, XRD, TEM) and optical characterization, we propose a

  13. Studying the co-evolution of production and test code in open source and industrial developer test processes through repository mining

    NARCIS (Netherlands)

    Zaidman, A.; Van Rompaey, B.; Van Deursen, A.; Demeyer, S.

    2010-01-01

    Many software production processes advocate rigorous development testing alongside functional code writing, which implies that both test code and production code should co-evolve. To gain insight in the nature of this co-evolution, this paper proposes three views (realized by a tool called TeMo)

  14. Comparing the co-evolution of production and test code in open source and industrial developer test processes through repository mining

    NARCIS (Netherlands)

    Van Rompaey, B.; Zaidman, A.E.; Van Deursen, A.; Demeyer, S.

    2008-01-01

    This paper represents an extension to our previous work: Mining software repositories to study coevolution of production & test code. Proceedings of the International Conference on Software Testing, Verification, and Validation (ICST), IEEE Computer Society, 2008; doi:10.1109/ICST.2008.47

  15. Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the Apterostigma pilosum group ant-fungus mutualism

    Science.gov (United States)

    Bryn T.M. Dentinger; D.Jean Lodge; Andrew B. Munkacsi; Dennis E. Desjardin; David J. McLaughlin

    2009-01-01

    The ~50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus ...

  16. Molecular pathways

    DEFF Research Database (Denmark)

    Cox, Thomas R; Erler, Janine Terra

    2014-01-01

    that 45% of deaths in the developed world are linked to fibrotic disease. Fibrosis and cancer are known to be inextricably linked; however, we are only just beginning to understand the common and overlapping molecular pathways between the two. Here, we discuss what is known about the intersection...... of fibrosis and cancer, with a focus on cancer metastasis, and highlight some of the exciting new potential clinical targets that are emerging from analysis of the molecular pathways associated with these two devastating diseases. Clin Cancer Res; 20(14); 3637-43. ©2014 AACR....

  17. Morphological and transcriptional response of an anhydrobiotic insect to ionizing radiation and desiccation: steps forward in understanding molecular background of extreme radioresistance in higher eukaryotes

    Science.gov (United States)

    Gusev, Oleg; Novikova, Nataliya; Sychev, Vladimir; Okuda, Takashi; Kikawada, Takahiro; Sakashita, Tetsuya; Mukae, Kyosuke

    2012-07-01

    Life in extreme or drastically changing environments in many cases leads to evolutionary evolvement of mechanisms of cross-resistance to different abiotic stresses, often never actually faced by the organism in its natural habitat. Larvae of the sleeping chironomidPolypedilum vanderplanki (Diptera) are able to resist complete desiccation and in the dry form survive under excess of various abiotic stresses, including exposure to space environment. One of the most intriguing features of the anhydrobiotic larvae is resistance to extremely high doses of different types of ionizing radiation. To understand the cross-tolerance mechanism, we have analyzed the structural changes in the nuclear DNA using transmission electron microscopy and DNA comet assays in relation to anhydrobiosis and radiation. We find that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. The DNA fragmentation level and the recovery of DNA integrity in the rehydrated after anhydrobiosis larvae were similar to those of hydrated larvae irradiated with 70 Gy of high-linear energy transfer (LET) ions (4He+). In comparison, low-LET radiation (gamma rays) of the same dose causes less initial damage to the larvae, and recovery of DNA repair is complete within 24 h. Genome-wide analysis of mRNA expression in the larvae revealed that a large group of genes (including antioxidants, anhydrobiosis-specific biomolecules and protein-reparation enzymes) showed a similar patterns of activity in response to both desiccation and ionizing radiation. We conclude that t one of the factors explaining the relationship between the resistance to ionizing radiation and the ability to undergo anhydrobiosis in the sleeping chironomid would be an adaptation to desiccation-inflicted proteins and nuclear DNA damage.

  18. Molecular subgroups of medulloblastoma

    OpenAIRE

    Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

    2012-01-01

    Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understand...

  19. Understanding Carbohydrates

    Science.gov (United States)

    ... Size: A A A Listen En Español Understanding Carbohydrates How much and what type of carbohydrate foods ... glucose levels in your target range. Explore: Understanding Carbohydrates Glycemic Index and Diabetes Learn about the glycemic ...

  20. Co-evolution of intelligent socio-technical systems modelling and applications in large scale emergency and transport domains

    CERN Document Server

    2013-01-01

    As the interconnectivity between humans through technical devices is becoming ubiquitous, the next step is already in the making: ambient intelligence, i.e. smart (technical) environments, which will eventually play the same active role in communication as the human players, leading to a co-evolution in all domains where real-time communication is essential. This topical volume, based on the findings of the Socionical European research project, gives equal attention to two highly relevant domains of applications: transport, specifically traffic, dynamics from the viewpoint of a socio-technical interaction and evacuation scenarios for large-scale emergency situations. Care was taken to investigate as much as possible the limits of scalability and to combine the modeling using complex systems science approaches with relevant data analysis.

  1. Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution.

    Science.gov (United States)

    Butler, R J; Barrett, P M; Kenrick, P; Penn, M G

    2009-03-01

    Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to

  2. Sexual Conflict over the Maintenance of Sex: Effects of Sexually Antagonistic Coevolution for Reproductive Isolation of Parthenogenesis

    Science.gov (United States)

    Kawatsu, Kazutaka

    2013-01-01

    Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction. PMID:23469150

  3. Sexual conflict over the maintenance of sex: effects of sexually antagonistic coevolution for reproductive isolation of parthenogenesis.

    Science.gov (United States)

    Kawatsu, Kazutaka

    2013-01-01

    Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.

  4. Sexual conflict over the maintenance of sex: effects of sexually antagonistic coevolution for reproductive isolation of parthenogenesis.

    Directory of Open Access Journals (Sweden)

    Kazutaka Kawatsu

    Full Text Available Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.

  5. Genetic and forma specialis diversity in Blumeria graminis of cereals and its implications for host-pathogen co-evolution.

    Science.gov (United States)

    Wyand, Rebecca A; Brown, James K M

    2003-05-01

    SUMMARY The grass powdery mildew fungus, Blumeria graminis is classified into eight formae speciales (ff.spp.) based on strict host specialization. However, evidence suggests that host ranges extend to more than one genus and are particularly diverse among samples from the Middle East, the proposed centre of origin and diversification of crop plants. This study investigated whether geographical origin, host species or both determine the genetic variation in B. graminis that is found in cereals, sampled from Europe, Asia and North America, and whether there is any evidence for co-evolution between pathogen and host. Phylogenetic analysis of nucleotide sequence variation within the ribosomal DNA Internal Transcribed Spacer (ITS) regions and the beta-tubulin (tub2) gene gives rise to two dendrograms with different topologies. In both trees, isolates of B. graminis from cultivated cereals are grouped according to their principal host genus. This grouping was supported by amplified fragment length polymorphism (AFLP) analysis and cross-infectivity tests. However, there was no evidence of co-evolution. There was far greater divergence between ff.spp. in tub2 sequences than ITS regions and a faster rate of mutation of tub2, especially in the third base position of exons. It is proposed that variation in the rDNA-ITS regions is constrained either by their functional role in the processing of rDNA precursor molecules or by concerted evolution, hence limiting their use in phylogenetic studies. AFLP data suggests an overall lack of correlation between geographical and genetic distances. This may be related to the long distance dispersal exhibited by B. graminis.

  6. The Evolution of a Female Genital Trait Widely Distributed in the Lepidoptera: Comparative Evidence for an Effect of Sexual Coevolution

    Science.gov (United States)

    Sánchez, Víctor; Hernández-Baños, Blanca Estela; Cordero, Carlos

    2011-01-01

    Background Sexual coevolution is considered responsible for the evolution of many male genital traits, but its effect on female genital morphology is poorly understood. In many lepidopterans, females become temporarily unreceptive after mating and the length of this refractory period is inversely related to the amount of spermatophore remaining in their genital tracts. Sperm competition can select for males that delay female remating by transferring spermatophores with thick spermatophore envelopes that take more time to be broken. These envelopes could select for signa, sclerotized sharp structures located within the female genital tract, that are used for breaking spermatophores. Thus, this hypothesis predicts that thick spermatophore envelopes and signa evolve in polyandrous species, and that these adaptations are lost when monandry evolves subsequently. Here we test the expected associations between female mating pattern and presence/absence of signa, and review the scant information available on the thickness of spermatophore envelopes. Methodology/Principal Findings We made a literature review and found information on female mating pattern (monandry/polyandry), presence/absence of signa and phylogenetic position for 37 taxa. We built a phylogenetic supertree for these taxa, mapped both traits on it, and tested for the predicted association by using Pagel's test for correlated evolution. We found that, as predicted by our hypothesis, monandry evolved eight times and in five of them signa were lost; preliminary evidence suggests that at least in two of the three exceptions males imposed monandry on females by means of specially thick spermatophore envelopes. Previously published data on six genera of Papilionidae is in agreement with the predicted associations between mating pattern and the characteristics of spermatophore envelopes and signa. Conclusions/Significance Our results support the hypothesis that signa are a product of sexually antagonistic

  7. The evolution of a female genital trait widely distributed in the Lepidoptera: comparative evidence for an effect of sexual coevolution.

    Directory of Open Access Journals (Sweden)

    Víctor Sánchez

    Full Text Available BACKGROUND: Sexual coevolution is considered responsible for the evolution of many male genital traits, but its effect on female genital morphology is poorly understood. In many lepidopterans, females become temporarily unreceptive after mating and the length of this refractory period is inversely related to the amount of spermatophore remaining in their genital tracts. Sperm competition can select for males that delay female remating by transferring spermatophores with thick spermatophore envelopes that take more time to be broken. These envelopes could select for signa, sclerotized sharp structures located within the female genital tract, that are used for breaking spermatophores. Thus, this hypothesis predicts that thick spermatophore envelopes and signa evolve in polyandrous species, and that these adaptations are lost when monandry evolves subsequently. Here we test the expected associations between female mating pattern and presence/absence of signa, and review the scant information available on the thickness of spermatophore envelopes. METHODOLOGY/PRINCIPAL FINDINGS: We made a literature review and found information on female mating pattern (monandry/polyandry, presence/absence of signa and phylogenetic position for 37 taxa. We built a phylogenetic supertree for these taxa, mapped both traits on it, and tested for the predicted association by using Pagel's test for correlated evolution. We found that, as predicted by our hypothesis, monandry evolved eight times and in five of them signa were lost; preliminary evidence suggests that at least in two of the three exceptions males imposed monandry on females by means of specially thick spermatophore envelopes. Previously published data on six genera of Papilionidae is in agreement with the predicted associations between mating pattern and the characteristics of spermatophore envelopes and signa. CONCLUSIONS/SIGNIFICANCE: Our results support the hypothesis that signa are a product of sexually

  8. Phenotype selection reveals coevolution of muscle glycogen and protein and PTEN as a gate keeper for the accretion of muscle mass in adult female mice.

    Science.gov (United States)

    Sawitzky, Mandy; Zeissler, Anja; Langhammer, Martina; Bielohuby, Maximilian; Stock, Peggy; Hammon, Harald M; Görs, Solvig; Metges, Cornelia C; Stoehr, Barbara J M; Bidlingmaier, Martin; Fromm-Dornieden, Carolin; Baumgartner, Bernhard G; Christ, Bruno; Brenig, Bertram; Binder, Gerhard; Metzger, Friedrich; Renne, Ulla; Hoeflich, Andreas

    2012-01-01

    We have investigated molecular mechanisms for muscle mass accretion in a non-inbred mouse model (DU6P mice) characterized by extreme muscle mass. This extreme muscle mass was developed during 138 generations of phenotype selection for high protein content. Due to the repeated trait selection a complex setting of different mechanisms was expected to be enriched during the selection experiment. In muscle from 29-week female DU6P mice we have identified robust increases of protein kinase B activation (AKT, Ser-473, up to 2-fold) if compared to 11- and 54-week DU6P mice or controls. While a number of accepted effectors of AKT activation, including IGF-I, IGF-II, insulin/IGF-receptor, myostatin or integrin-linked kinase (ILK), were not correlated with this increase, phosphatase and tensin homologue deleted on chromosome 10 (PTEN) was down-regulated in 29-week female DU6P mice. In addition, higher levels of PTEN phosphorylation were found identifying a second mechanism of PTEN inhibition. Inhibition of PTEN and activation of AKT correlated with specific activation of p70S6 kinase and ribosomal protein S6, reduced phosphorylation of eukaryotic initiation factor 2α (eIF2α) and higher rates of protein synthesis in 29-week female DU6P mice. On the other hand, AKT activation also translated into specific inactivation of glycogen synthase kinase 3ß (GSK3ß) and an increase of muscular glycogen. In muscles from 29-week female DU6P mice a significant increase of protein/DNA was identified, which was not due to a reduction of protein breakdown or to specific increases of translation initiation. Instead our data support the conclusion that a higher rate of protein translation is contributing to the higher muscle mass in mid-aged female DU6P mice. Our results further reveal coevolution of high protein and high glycogen content during the selection experiment and identify PTEN as gate keeper for muscle mass in mid-aged female DU6P mice.

  9. Towards understanding molecular modes of probiotic action

    NARCIS (Netherlands)

    Marco, M.L.; Pavan, S.; Kleerebezem, M.

    2006-01-01

    The possibility that certain microorganisms might be beneficial to human health is highlighted by the numerous consumer products containing probiotic bacteria. Probiotics are typically administered in food that, following entry into the gastro-intestinal tract, results in measurable health-promoting

  10. A Molecular Framework for Understanding DCIS

    Science.gov (United States)

    2017-10-01

    WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER The Chancellor, Masters and Scholars of the...410 whole genome libraries and dissected material from 115 freshly frozen patient biopsies. The tissue included for RNA and DNA analysis DCIS, IDC...using (and other kits on the market ) was only compatible with sequencing machines after the DNA had been sheared (resulting in removal of end

  11. A Molecular Framework for Understanding DCIS

    Science.gov (United States)

    2016-10-01

    many lesions per patient) compared to whole genome sequencing. We plan to use the ExomeCNV algorithm [8] to call copy number aberrations in breast...samples as this algorithm was designed for tumor-normal comparison data. We plan to identify variants using the GATK toolkit, which shows the...regression to dissect the genetic basis of gene expression. PPI networks in BioGRID and other online functional databases (e.g. Gene Ontology (GO

  12. Understanding classification

    NARCIS (Netherlands)

    Subianto, M.

    2009-01-01

    In practical data analysis, the understandability of models plays an important role in their acceptance. In the data mining literature, however, understandability plays is hardly ever mentioned. If it is mentioned, it is interpreted as meaning that the models have to be simple. In this thesis we

  13. Embodied understanding.

    Science.gov (United States)

    Johnson, Mark

    2015-01-01

    Western culture has inherited a view of understanding as an intellectual cognitive operation of grasping of concepts and their relations. However, cognitive science research has shown that this received intellectualist conception is substantially out of touch with how humans actually make and experience meaning. The view emerging from the mind sciences recognizes that understanding is profoundly embodied, insofar as our conceptualization and reasoning recruit sensory, motor, and affective patterns and processes to structure our understanding of, and engagement with, our world. A psychologically realistic account of understanding must begin with the patterns of ongoing interaction between an organism and its physical and cultural environments and must include both our emotional responses to changes in our body and environment, and also the actions by which we continuously transform our experience. Consequently, embodied understanding is not merely a conceptual/propositional activity of thought, but rather constitutes our most basic way of being in, and engaging with, our surroundings in a deep visceral manner.

  14. The dominantly expressed class I molecule of the chicken MHC is explained by coevolution with the polymorphic peptide transporter (TAP) genes

    DEFF Research Database (Denmark)

    Walker, Brian A; Hunt, Lawrence G; Sowa, Anna K

    2011-01-01

    is expressed at a high level, which can result in strong MHC associations with resistance to particular infectious pathogens. However, the basis for having a single dominantly expressed class I molecule has been unclear. Here we report TAP1 and TAP2 sequences from 16 chicken lines, and show that both genes......In most mammals, the MHC class I molecules are polymorphic and determine the specificity of peptide presentation, whereas the transporter associated with antigen presentation (TAP) heterodimers are functionally monomorphic. In chickens, there are two classical class I genes but only one...... dominantly expressed class I molecule. These results show that coevolution between class I and TAP genes can explain the presence of a single dominantly expressed class I molecule in common chicken MHC haplotypes. Moreover, such coevolution in the primordial MHC may have been responsible for the appearance...

  15. The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

    Science.gov (United States)

    Di Giulio, Massimo

    2017-11-07

    The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal

  16. Understanding semantics

    DEFF Research Database (Denmark)

    Thrane, Torben

    1997-01-01

    Understanding natural language is a cognitive, information-driven process. Discussing some of the consequences of this fact, the paper offers a novel look at the semantic effect of lexical nouns and the identification of reference types....

  17. Understanding Alzheimer's

    Science.gov (United States)

    ... Navigation Bar Home Current Issue Past Issues Understanding Alzheimer's Past Issues / Fall 2007 Table of Contents For ... and brain scans. No treatment so far stops Alzheimer's. However, for some in the disease's early and ...

  18. Understanding homelessness

    OpenAIRE

    Somerville, Peter

    2013-01-01

    This paper reviews the literature on understanding homelessness. It criticizes approaches that ignore, distort or diminish the humanity of homeless people, or else, add little to our understanding of that humanity. In particular, it rejects what it calls “epidemiological” approaches, which deny the possibility of agency for homeless people, insofar as those approaches view the situation of those people largely as a “social fact”, to be explained in terms of causal variables or “risk factors” ...

  19. An effect of 16S rRNA intercistronic variability on coevolutionary analysis in symbiotic bacteria: Molecular phylogeny of Arsenophonus triatominarum

    Czech Academy of Sciences Publication Activity Database

    Šorfová, Pavlína; Škeříková, Andrea; Hypša, Václav

    2008-01-01

    Roč. 31, č. 2 (2008), s. 88-100 ISSN 0723-2020 R&D Projects: GA ČR GA206/04/0520; GA AV ČR IAA601410708 Institutional research plan: CEZ:AV0Z60220518 Keywords : intragenomic heterogeneity * 16S rRNA * coevolution * insect symbionts * molecular phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 2.582, year: 2008

  20. Molecular cloning of ion channels in Felis catus that are related to periodic paralyses in man: a contribution to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis.

    Science.gov (United States)

    Zapata, Marlyn; Kunii, Ilda S; Paninka, Rolf M; Simões, Denise M N; Castillo, Víctor A; Reche, Archivaldo; Maciel, Rui M B; Dias da Silva, Magnus R

    2014-07-25

    Neck ventroflexion in cats has different causes; however, the most common is the hypokalemia associated with flaccid paralysis secondary to chronic renal failure. In humans, the most common causes of acute flaccid paralysis are hypokalemia precipitated by thyrotoxicosis and familial forms linked to mutations in sodium, potassium, and calcium channel genes. Here, we describe the sequencing and analysis of skeletal muscle ion channels in Felis catus that could be related to periodic paralyses in humans, contributing to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis. We studied genomic DNA from eleven cats, including five animals that were hyperthyroid with hypokalemia, although only one presented with muscle weakness, and six healthy control domestic cats. We identified the ion channel ortholog genes KCNJ2, KCNJ12, KCNJ14, CACNA1S and SCN4A in the Felis catus genome, together with several polymorphic variants. Upon comparative alignment with other genomes, we found that Felis catus provides evidence for a high genomic conservation of ion channel sequences. Although we hypothesized that neck ventroflexion in cats could be associated with a thyrotoxic or familial periodic paralysis channel mutation, we did not identify any previously detected human channel mutation in the hyperthyroid cat presenting hypokalemia. However, based on the small number of affected cats in this study, we cannot yet rule out this molecular mechanism. Notwithstanding, hyperthyroidism should still be considered as a differential diagnosis in hypokalemic feline paralysis. © 2014. Published by The Company of Biologists Ltd.

  1. Molecular cloning of ion channels in Felis catus that are related to periodic paralyses in man: a contribution to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis

    Directory of Open Access Journals (Sweden)

    Marlyn Zapata

    2014-07-01

    Full Text Available Neck ventroflexion in cats has different causes; however, the most common is the hypokalemia associated with flaccid paralysis secondary to chronic renal failure. In humans, the most common causes of acute flaccid paralysis are hypokalemia precipitated by thyrotoxicosis and familial forms linked to mutations in sodium, potassium, and calcium channel genes. Here, we describe the sequencing and analysis of skeletal muscle ion channels in Felis catus that could be related to periodic paralyses in humans, contributing to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis. We studied genomic DNA from eleven cats, including five animals that were hyperthyroid with hypokalemia, although only one presented with muscle weakness, and six healthy control domestic cats. We identified the ion channel ortholog genes KCNJ2, KCNJ12, KCNJ14, CACNA1S and SCN4A in the Felis catus genome, together with several polymorphic variants. Upon comparative alignment with other genomes, we found that Felis catus provides evidence for a high genomic conservation of ion channel sequences. Although we hypothesized that neck ventroflexion in cats could be associated with a thyrotoxic or familial periodic paralysis channel mutation, we did not identify any previously detected human channel mutation in the hyperthyroid cat presenting hypokalemia. However, based on the small number of affected cats in this study, we cannot yet rule out this molecular mechanism. Notwithstanding, hyperthyroidism should still be considered as a differential diagnosis in hypokalemic feline paralysis.

  2. Cyclic incrementality in competitive coevolution: Evolvability through pseudo-Baldwinian switching-genes

    NARCIS (Netherlands)

    Janssen, R.; Nolfi, S.; Haselager, W.F.G.; Sprinkhuizen-Kuyper, I.G.

    2016-01-01

    Coevolving systems are notoriously difficult to understand. This is largely due to the Red Queen effect that dictates heterospecific fitness interdependence. In simulation studies of coevolving systems, master tournaments are often used to obtain more informed fitness measures by testing evolved

  3. Understanding Maple

    CERN Document Server

    Thompson, Ian

    2016-01-01

    Maple is a powerful symbolic computation system that is widely used in universities around the world. This short introduction gives readers an insight into the rules that control how the system works, and how to understand, fix, and avoid common problems. Topics covered include algebra, calculus, linear algebra, graphics, programming, and procedures. Each chapter contains numerous illustrative examples, using mathematics that does not extend beyond first-year undergraduate material. Maple worksheets containing these examples are available for download from the author's personal website. The book is suitable for new users, but where advanced topics are central to understanding Maple they are tackled head-on. Many concepts which are absent from introductory books and manuals are described in detail. With this book, students, teachers and researchers will gain a solid understanding of Maple and how to use it to solve complex mathematical problems in a simple and efficient way.

  4. Understanding physics

    CERN Document Server

    Mansfield, Michael

    2011-01-01

    Understanding Physics - Second edition is a comprehensive, yet compact, introductory physics textbook aimed at physics undergraduates and also at engineers and other scientists taking a general physics course. Written with today's students in mind, this text covers the core material required by an introductory course in a clear and refreshing way. A second colour is used throughout to enhance learning and understanding. Each topic is introduced from first principles so that the text is suitable for students without a prior background in physics. At the same time the book is designed to enable

  5. Human TCR-MHC coevolution after divergence from mice includes increased nontemplate-encoded CDR3 diversity.

    Science.gov (United States)

    Chen, Xiaojing; Poncette, Lucia; Blankenstein, Thomas

    2017-11-06

    For thymic selection and responses to pathogens, T cells interact through their αβ T cell receptor (TCR) with peptide-major histocompatibility complex (MHC) molecules on antigen-presenting cells. How the diverse TCRs interact with a multitude of MHC molecules is unresolved. It is also unclear how humans generate larger TCR repertoires than mice do. We compared the TCR repertoire of CD4 T cells selected from a single mouse or human MHC class II (MHC II) in mice containing the human TCR gene loci. Human MHC II yielded greater thymic output and a more diverse TCR repertoire. The complementarity determining region 3 (CDR3) length adjusted for different inherent V-segment affinities to MHC II. Humans evolved with greater nontemplate-encoded CDR3 diversity than did mice. Our data, which demonstrate human TCR-MHC coevolution after divergence from rodents, explain the greater T cell diversity in humans and suggest a mechanism for ensuring that any V-J gene combination can be selected by a single MHC II. © 2017 Chen et al.

  6. Co-Evolution and Bio-Social Construction: The Kichwa Agroforestry Systems (Chakras in the Ecuadorian Amazonia

    Directory of Open Access Journals (Sweden)

    Daniel Coq-Huelva

    2017-10-01

    Full Text Available Polycultured agrarian systems in Ecuadorian Amazonia (also called chakras or swollen gardens are characterised by a market-oriented crop for the generation of monetary income, for example, cocoa, other agricultural products (e.g., banana and cassava, and livestock for family farm consumption. Moreover, a chakra is an outstanding example of agroforestry production, in which ecological, social and economic elements co-evolve from a set of close and strong connections. In this context, the conservation and transformation of their biological subsystems can be understood as the result of complex interactions between anthropogenic and non-anthropogenic factors. In turn, such interactions are essential to provide food and monetary income to the indigenous community. Relevant agency capabilities exist that could cause an agroforestry system to take a different path of co-evolution, that is, towards greater or lesser sustainability associated with different levels of complexity. In conclusion, chakras have key ecological features that can mitigate the impact of human population growth in Amazonia. Additionally, chakras have their own processes of social self-regulation which enhance the possibilities of adaptation of Kichwa communities to changing environmental conditions, being essential elements in local food sovereignty, equitable gender relations and the respect of ancestral wisdom.

  7. Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism

    Directory of Open Access Journals (Sweden)

    De Craene Johan-Owen

    2012-07-01

    Full Text Available Abstract Background Membrane trafficking involves the complex regulation of proteins and lipids intracellular localization and is required for metabolic uptake, cell growth and development. Different trafficking pathways passing through the endosomes are coordinated by the ENTH/ANTH/VHS adaptor protein superfamily. The endosomes are crucial for eukaryotes since the acquisition of the endomembrane system was a central process in eukaryogenesis. Results Our in silico analysis of this ENTH/ANTH/VHS superfamily, consisting of proteins gathered from 84 complete genomes representative of the different eukaryotic taxa, revealed that genomic distribution of this superfamily allows to discriminate Fungi and Metazoa from Plantae and Protists. Next, in a four way genome wide comparison, we showed that this discriminative feature is observed not only for other membrane trafficking effectors, but also for proteins involved in metabolism and in cytokinesis, suggesting that metabolism, cytokinesis and intracellular trafficking pathways co-evolved. Moreover, some of the proteins identified were implicated in multiple functions, in either trafficking and metabolism or trafficking and cytokinesis, suggesting that membrane trafficking is central to this co-evolution process. Conclusions Our study suggests that membrane trafficking and compartmentalization were not only key features for the emergence of eukaryotic cells but also drove the separation of the eukaryotes in the different taxa.

  8. Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators.

    Science.gov (United States)

    Kotov, Alexey A; Taylor, Derek J

    2011-05-19

    The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera) remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at fossils from a Mesozoic Mongolian site, in hopes of gaining insights into the timescale of the evolution of Daphnia. We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA) that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae). Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older) or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae) with the subgenus Daphnia is much older than previously known -- since the Mesozoic.

  9. Mesozoic fossils (>145 Mya suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators

    Directory of Open Access Journals (Sweden)

    Taylor Derek J

    2011-05-01

    Full Text Available Abstract Background The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at Daphnia. Results We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae. Conclusions Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae with the subgenus Daphnia is much older than previously known -- since the Mesozoic.

  10. Replicated population divergence caused by localized coevolution? A test of three hypotheses in the red crossbill-lodgepole pine system.

    Science.gov (United States)

    Edelaar, P; Benkman, C W

    2006-09-01

    Several lines of evidence support the hypothesis that local populations of red crossbills (Loxia curvirostra complex) enter into a predator-prey arms race with lodgepole pine (Pinus contorta latifolia) in the absence of competing pine squirrels (Tamiasciurus hudsonicus). Nevertheless, the alternative hypotheses that neutral evolution or factors other than squirrels have caused crossbill population differentiation have not been thoroughly tested. We compared crossbill and pine cone morphology between island populations where squirrels are absent or present, and mainland sites where squirrels are present, in order to distinguish among these hypotheses. All comparisons supported an effect of squirrel absence, not island status, on crossbill and cone morphology. Hence our results provide further evidence that strong localized coevolutionary interactions in a geographic mosaic have driven adaptive population differentiation. In addition, vocal differentiation of crossbills was related to the absence of squirrels, but not to island status. As morphological and vocal differentiation is correlated with reproductive isolation in crossbills, the geographic mosaic of coevolution also seems to promote ecological speciation.

  11. The antibiotic viomycin as a model peptide for the origin of the co-evolution of RNA and proteins

    Science.gov (United States)

    Wank, Herbert; Clodi, Elisabeth; Wallis, Mary G.; Schroeder, Renée

    1999-08-01

    Viomycin is an RNA-binding peptide antibiotic which inhibits prokaryotic protein synthesis and group I intron self-splicing. This antibiotic enhances the activity of the ribozyme derived from the Neurospora crassa VS RNA, and at sub-inhibitory concentrations it induces the formation of group I intron oligomers. Here, we address the question whether viomycin exerts specificity in the promotion of RNA-RNA interactions. In an in vitro selection experiment we tested the ability of viomycin to specifically select molecules out of an RNA pool. Group I intron RNA was incubated with a pool of random sequence RNA, or with a pool of RNA molecules which had previously been enriched for viomycin-binding RNAs. Viomycin was added in order to select viomycin-binding RNAs and to guide their interaction with the intron RNA resulting in recombinant molecules. Viomycin was indeed capable of specifically selecting RNA molecules which contain viomycin-binding sites promoting recombination. These results suggest that small peptides are able to play the role of selector molecules in a putative `RNA World' launching the co-evolution of RNA and proteins into an `RNA-protein World'.

  12. Quasi-biweekly oscillations of the South Asian monsoon and its co-evolution in the upper and lower troposphere

    Science.gov (United States)

    Ortega, Sebastián; Webster, Peter J.; Toma, Violeta; Chang, Hai-Ru

    2017-11-01

    The Upper Tropospheric Quasi-Biweekly Oscillation (UQBW) of the South Asian monsoon is studied using the potential vorticity field on the 370 K isentrope. The UQBW is shown to be a common occurrence in the upper troposphere during the monsoon, and its typical evolution is described. We suggest that the UQBW is a phenomenon of both the middle and tropical latitudes, owing its existence to the presence of the planetary-scale upper-tropospheric monsoon anticyclone. The UQBW is first identified as Rossby waves originating in the northern flank of the monsoon anticyclone. These Rossby waves break when reaching the Pacific Ocean, and their associated cyclonic PV anomalies move southward to the east of Asia and then westward across the Indian Ocean and Africa advected by the monsoon anticyclone. A strong correlation, or co-evolution, between the UQBW and quasi-biweekly oscillations in the lower troposphere (QBW) is also found. In particular, analysis of vertically-integrated horizontal moisture transport, 850 hPa geopotential, and outgoing long-wave radiation show that the UQBW is usually observed at the same time as, and co-evolves with, the lower tropospheric QBW over South Asia. We discuss the nature of the UQBW, and its possible physical link with the QBW.

  13. Gene-Culture Coevolution and Sex Ratios: II. Sex-Chromosomal Distorters and Cultural Preferences for Offspring Sex

    Science.gov (United States)

    Kumm; Feldman

    1997-08-01

    Cultural preferences for the sex of offspring may produce behavior, such as female infanticide, sex-selective abortion and sex-selective parental investment, which alter the sex ratio in a population. Empirical evidence suggests that some genetic sex-ratio distorters are located on the sex chromosomes. Interactions between cultural preferences and sex-linked sex-ratio distorters are examined. Criteria for the spread of cultural preferences and sex-chromosomal distorter alleles are derived analytically, and the coevolution of preferences and distorters is examined through numerical iteration. Evolutionary equilibria and trajectories of gene-culture interactions involving sex-chromosomal distorter alleles may produce severely male- or female-biased primary sex ratios and adult sex ratios in populations. Adult sex ratios, primary sex ratios, allele frequencies and the prevalence of cultural preferences in the population are sensitive to initial conditions and cultural transmission parameters. During the coevolutionary process phenoallelic association is observed in many cases and is associated with unusual dynamics. Copyright 1997 Academic Press

  14. Understanding Energy

    Science.gov (United States)

    Menon, Deepika; Shelby, Blake; Mattingly, Christine

    2016-01-01

    "Energy" is a term often used in everyday language. Even young children associate energy with the food they eat, feeling tired after playing soccer, or when asked to turn the lights off to save light energy. However, they may not have the scientific conceptual understanding of energy at this age. Teaching energy and matter could be…

  15. Principles of molecular oncology

    National Research Council Canada - National Science Library

    Bronchud, Miguel H; Thomas, E. Donnall; Weatherall, D. J; Crowther, D. G

    2004-01-01

    ...-threatening diseases. Many new molecularly targeted diagnostics and therapeutics described in this text, developed based on the rapid growth in our understanding of the molecular basis of cancer, already substantially improve survival of patients with previously lethal malignancies, and also improve quality of life because of fewer toxicities. Clearly re...

  16. Principles of molecular oncology

    National Research Council Canada - National Science Library

    Bronchud, Miguel H

    2008-01-01

    ...-threatening diseases. Many new molecularly targeted diagnostics and therapeutics described in this text, developed based on the rapid growth in our understanding of the molecular basis of cancer, already substantially improve survival of patients with previously lethal malignancies, and also improve quality of life because of fewer toxicities. Clearly re...

  17. Coevolution of URAT1 and Uricase during Primate Evolution: Implications for Serum Urate Homeostasis and Gout.

    Science.gov (United States)

    Tan, Philip K; Farrar, Jennifer E; Gaucher, Eric A; Miner, Jeffrey N

    2016-09-01

    Uric acid is the highly insoluble end-product of purine metabolism in humans. Serum levels exceeding the solubility threshold can trigger formation of urate crystals resulting in gouty arthritis. Uric acid is primarily excreted through the kidneys with 90% reabsorbed back into the bloodstream through the uric acid transporter URAT1. This reabsorption process is essential for the high serum uric acid levels found in humans. We discovered that URAT1 proteins from humans and baboons have higher affinity for uric acid compared with transporters from rats and mice. This difference in transport kinetics of URAT1 orthologs, along with inability of modern apes to oxidize uric acid due to loss of the uricase enzyme, prompted us to ask whether these events occurred concomitantly during primate evolution. Ancestral URAT1 sequences were computationally inferred and ancient transporters were resurrected and assayed, revealing that affinity for uric acid was increased during the evolution of primates. This molecular fine-tuning occurred between the origins of simians and their diversification into New- and Old-World monkey and ape lineages. Remarkably, it was driven in large-part by only a few amino acid replacements within the transporter. This alteration in primate URAT1 coincided with changes in uricase that greatly diminished the enzymatic activity and took place 27-77 Ma. These results suggest that the modifications to URAT1 transporters were potentially adaptive and that maintaining more constant, high levels of serum uric acid may have provided an advantage to our primate ancestors. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Understanding translation

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Gottlieb, Henrik; Klitgård, Ida

    Understanding Translation is designed as a textbook for courses on the theory and practice of translation in general and of particular types of translation - such as interpreting, screen translation and literary translation. The aim of the book is to help you gain an in-depth understanding...... of the phenomenon of translation and to provide you with a conceptual framework for the analysis of various aspects of professional translation. Intended readers are students of translation and languages, but the book will also be relevant for others who are interested in the theory and practice of translation...... - translators, language teachers, translation users and literary, TV and film critics, for instance. Discussions focus on translation between Danish and English....

  19. Understanding Resilience

    Directory of Open Access Journals (Sweden)

    Gang eWu

    2013-02-01

    Full Text Available Resilience is the ability to adapt successfully in the face of stress and adversity. Stressful life events, trauma and chronic adversity can have a substantial impact on brain function and structure, and can result in the development of PTSD, depression and other psychiatric disorders. However, most individuals do not develop such illnesses after experiencing stressful life events, and are thus thought to be resilient. Resilience as successful adaptation relies on effective responses to environmental challenges and ultimate resistance to the deleterious effects of stress, therefore a greater understanding of the factors that promote such effects is of great relevance. This review focuses on recent findings regarding genetic, epigenetic, developmental, psychosocial and neurochemical factors that are considered essential contributors to the development of resilience. Neural circuits and pathways involved in mediating resilience are also discussed. The growing understanding of resilience factors will hopefully lead to the development of new pharmacological and psychological interventions for enhancing resilience and mitigating the untoward consequences.

  20. Understand electronics

    CERN Document Server

    Bishop, Owen

    2013-01-01

    Understand Electronics provides a readable introduction to the exciting world of electronics for the student or enthusiast with little previous knowledge. The subject is treated with the minimum of mathematics and the book is extensively illustrated.This is an essential guide for the newcomer to electronics, and replaces the author's best-selling Beginner's Guide to Electronics.The step-by-step approach makes this book ideal for introductory courses such as the Intermediate GNVQ.

  1. Understanding users

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav Viggo

    2014-01-01

    Segmentation of users can help libraries in the process of understanding user similarities and differences. Segmentation can also form the basis for selecting segments of target users and for developing tailored services for specific target segments. Several approaches and techniques have been...... segmentation project using computer-generated clusters. Compared to traditional marketing texts, this article also tries to identify user segments or images or metaphors by the library profession itself....

  2. Understanding unemployment

    OpenAIRE

    Guillaume Rocheteau

    2006-01-01

    Modern economists have built models of the labor market, which isolate the market’s key drivers and describe the way these interact to produce particular levels of unemployment. One of the most popular models used by macroeconomists today is the search-matching model of equilibrium unemployment. We explain this model, and show how it can be applied to understand the way various policies, such as unemployment benefits, taxes, or technological changes, can affect the unemployment rate.

  3. Understanding Technology?

    Directory of Open Access Journals (Sweden)

    Erik Bendtsen

    2016-11-01

    Full Text Available We are facing radical changes in our ways of living in the nearest future. Not necessarily of our own choice, but because tchnological development is moving so fast, that it will have still greater impact on many aspects of our lives. We have seen the beginnings of that change within the latest 35 years or so, but according to newest research that change will speed up immensely in the nearest years to come. The impact of that change or these changes will affect our working life immensely as a consequence of automation. How these changes are brought about and which are their consequences in a broad sense is being attempted to be understood and guessed by researchers. No one knows for sure, but specific patterns are visible. This paper will not try to guess, what will come, but will rather try to understand the deepest ”nature” of technology in order to understand the driving factors in this development: the genesis of technology in a broad sense in order to contibute to the understanding of the basis for the expected development.

  4. Studies towards the understanding of the effects of ionizing radiations at the molecular scale (20-150 keV H{sup +}/H + He Collisions; dissociative electron attachment to water)

    Energy Technology Data Exchange (ETDEWEB)

    Coupier, B

    2005-11-15

    This work comes within the scope of recent studies towards a better understanding of the effect of ionizing radiation at the molecular scale on biological systems. It is composed of two parts. The first one presents a new set of coincidence measurements of cross sections for the impact of protons or hydrogen atoms on helium in the energy range 20-150 keV of interest for the radiation biology. It is an archetypical system of interest for the theoreticians and there exists only a few studies on the impact of hydrogen atoms on helium. This study with helium was also motivated for the sake of performing a general test of functioning of the apparatus before investigating more complicated systems. Similar studies were then performed by replacing helium with water and biological molecules of relevance (Uracil, Thymine...) as target. This constitutes a study of direct effects of fast ionizing radiations on molecules of biological interest. The second part of the thesis deals with another type of ionizing radiations which can be seen as indirect effects of the first fast ionizing radiations studied in the first part. Low energy electrons emission in the energy range 1 to 16 eV follows the bombardment of the matter by swift protons/hydrogen atoms; these electrons have in turn an ionizing influence on the environment. A review of the dissociative electron attachment to water was undertaken motivated by the existing discrepancies between old studies on the same subject. A special attention was given to the problem of high energy kinetic ion discrimination in the trochoidal monochromator used for this work. (author)

  5. Co-evolution of Microbial Community and Groundwater Geochemistry in the Piedmont of Jianghan Plain, China

    Science.gov (United States)

    Ma, J.; Liu, H.; Tong, L.; Wang, Y.; Liu, S.; Zhao, L.

    2017-12-01

    It was crucial to understand the reference status of the microbial community in different groundwater systems. However, despite its high economic and ecological value, non-saline groundwater had received less attention. The objective of this study was to link the geochemical feature to microbial characteristics of two adjacent pristine non-saline confined aquifers from the piedmont of Jianghan plain, China. A field-scale analysis was performed along groundwater flow field to identify the groundwater evolution process. Microbial community was identified with high-throughput 16S rRNA genes pyrosequencing method. Results showed that no significant hydraulic connection existed between the two adjacent aquifers, which had distinctly different groundwater evolution processes. The main geochemical evolutionary process of the 1st confined aquifer was carbonate rock dissolution and iron-manganese mineral reduction dissolution, while the 2nd confined aquifer was carbonate rock dissolution and sulfate reduction. Although it was still non-saline groundwater, increasing salinity still significantly affected the structural characteristics of microbial communities in the 1st confined aquifer. Different from the 1st confined aquifer, sulfate and redox were the main driving factors on the microbial community structure in the 2nd confined aquifer, and gradually shaped it to a sulfate reduction zone, a methane oxidation zone and a methane production zone from the upstream to the downstream. The microbial community structure was intimately associated with geochemical evolution, thus it should be further considered in view of a better understanding of groundwater ecology and sustainable management strategies.

  6. Sandbox rheometry: Co-evolution of stress and strain in Riedel- and Critical Wedge-experiments

    Science.gov (United States)

    Ritter, Malte C.; Santimano, Tasca; Rosenau, Matthias; Leever, Karen; Oncken, Onno

    2018-01-01

    Analogue sandbox experiments have been used for a long time to understand tectonic processes, because they facilitate detailed measurements of deformation at a spatio-temporal resolution unachievable from natural data. Despite this long history, force measurements to further characterise the mechanical evolution in analogue sandbox experiments have only emerged recently. Combined continuous measurements of forces and deformation in such experiments, an approach here referred to as "sandbox rheometry", are a new tool that may help to better understand work budgets and force balances for tectonic systems and to derive constitutive laws for regional scale deformation. In this article we present an experimental device that facilitates precise measurements of boundary forces and surface deformation at high temporal and spatial resolution. We demonstrate its capabilities in two classical experiments: one of strike-slip deformation (the Riedel set-up) and one of compressional accretionary deformation (the Critical Wedge set-up). In these we are able to directly observe a correlation between strain weakening and strain localisation that had previously only been inferred, namely the coincidence of the maximum localisation rate with the onset of weakening. Additionally, we observe in the compressional experiment a hysteresis of localisation with respect to the mechanical evolution that reflects the internal structural complexity of an accretionary wedge.

  7. Understanding uncertainty

    CERN Document Server

    Lindley, Dennis V

    2013-01-01

    Praise for the First Edition ""...a reference for everyone who is interested in knowing and handling uncertainty.""-Journal of Applied Statistics The critically acclaimed First Edition of Understanding Uncertainty provided a study of uncertainty addressed to scholars in all fields, showing that uncertainty could be measured by probability, and that probability obeyed three basic rules that enabled uncertainty to be handled sensibly in everyday life. These ideas were extended to embrace the scientific method and to show how decisions, containing an uncertain element, could be rationally made.

  8. Understanding analysis

    CERN Document Server

    Abbott, Stephen

    2015-01-01

    This lively introductory text exposes the student to the rewards of a rigorous study of functions of a real variable. In each chapter, informal discussions of questions that give analysis its inherent fascination are followed by precise, but not overly formal, developments of the techniques needed to make sense of them. By focusing on the unifying themes of approximation and the resolution of paradoxes that arise in the transition from the finite to the infinite, the text turns what could be a daunting cascade of definitions and theorems into a coherent and engaging progression of ideas. Acutely aware of the need for rigor, the student is much better prepared to understand what constitutes a proper mathematical proof and how to write one. Fifteen years of classroom experience with the first edition of Understanding Analysis have solidified and refined the central narrative of the second edition. Roughly 150 new exercises join a selection of the best exercises from the first edition, and three more project-sty...

  9. Understanding ayurveda.

    Science.gov (United States)

    Gadgil, Vaidya Dilip

    2010-01-01

    Ayurveda needs to achieve its full potential both in India and globally. This requires imparting to its students full appreciation of Ayurveda's power and strength, particularly proper understanding of the advantages of applying it to treat chronic and acute diseases. To this end, we explain the necessity of learning Sanskrit as a medium of study, and the advantages of learning the Texts in the traditional way, rather than relying on translations with all the loss of meaning and precision, which that entails. We emphasize the use of Triskandhakosha as a means to fully understand Ayurveda fundamental concepts and technical terms, so that all their shades of meaning are fully understood, and all their usages given in different places in the texts. Only by such methods can full appreciation of Ayurvedic wisdom be achieved, and the full depth and power of its knowledge be applied. Only then will its true status among systems of medicine come to be appreciated, either in India or more widely in the world as a whole.

  10. Understanding Ayurveda

    Directory of Open Access Journals (Sweden)

    Vaidya Dilip Gadgil

    2010-01-01

    Full Text Available Ayurveda needs to achieve its full potential both in India and globally. This requires imparting to its students full appreciation of Ayurveda′s power and strength, particularly proper understanding of the advantages of applying it to treat chronic and acute diseases. To this end, we explain the necessity of learning Sanskrit as a medium of study, and the advantages of learning the Texts in the traditional way, rather than relying on translations with all the loss of meaning and precision, which that entails. We emphasize the use of Triskandhakosha as a means to fully understand Ayurveda fundamental concepts and technical terms, so that all their shades of meaning are fully understood, and all their usages given in different places in the texts. Only by such methods can full appreciation of Ayurvedic wisdom be achieved, and the full depth and power of its knowledge be applied. Only then will its true status among systems of medicine come to be appreciated, either in India or more widely in the world as a whole.

  11. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

    Directory of Open Access Journals (Sweden)

    John F Heidelberg

    Full Text Available CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B' as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

  12. Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors.

    Science.gov (United States)

    Guevara, Elaine E; Veilleux, Carrie C; Saltonstall, Kristin; Caccone, Adalgisa; Mundy, Nicholas I; Bradley, Brenda J

    2016-09-01

    We explored whether variation in the sweet taste receptor protein T1R3 in primates could contribute to differences in sweet taste repertoire among species, potentially reflecting coevolution with local plants. Specifically, we examined which primates are likely to be sweet "tasters" of brazzein, a protein found in the fruit of the African plant Pentadiplandra brazzeana that tastes intensely sweet to humans, but provides little energy. Sweet proteins like brazzein are thought to mimic the taste of sugars to entice seed dispersers. We examined the evolution of T1R3 and assessed whether primates are likely "deceived" by such biochemical mimicry. Using published and new sequence data for TAS1R3, we characterized 57 primates and other mammals at the two amino acid sites necessary to taste brazzein to determine which species are tasters. We further used dN/dS-based methods to look for statistical evidence of accelerated evolution in this protein across primate lineages. The taster genotype is shared across most catarrhines, suggesting that most African primates can be "tricked" into eating and dispersing P. brazzeana's seeds for little caloric gain. Western gorillas (Gorilla gorilla), however, exhibit derived mutations at the two brazzein-critical positions, and although fruit is a substantial portion of the western gorilla diet, they have not been observed to eat P. brazzeana. Our analyses of protein evolution found no signature of positive selection on TAS1R3 along the gorilla lineage. We propose that the gorilla-specific mutations at the TAS1R3 locus encoding T1R3 could be a counter-adaptation to the false sweet signal of brazzein. © 2016 Wiley Periodicals, Inc.

  13. The E-MOSAICS project: simulating the formation and co-evolution of galaxies and their star cluster populations

    Science.gov (United States)

    Pfeffer, Joel; Kruijssen, J. M. Diederik; Crain, Robert A.; Bastian, Nate

    2018-04-01

    We introduce the MOdelling Star cluster population Assembly In Cosmological Simulations within EAGLE (E-MOSAICS) project. E-MOSAICS incorporates models describing the formation, evolution, and disruption of star clusters into the EAGLE galaxy formation simulations, enabling the examination of the co-evolution of star clusters and their host galaxies in a fully cosmological context. A fraction of the star formation rate of dense gas is assumed to yield a cluster population; this fraction and the population's initial properties are governed by the physical properties of the natal gas. The subsequent evolution and disruption of the entire cluster population are followed accounting for two-body relaxation, stellar evolution, and gravitational shocks induced by the local tidal field. This introductory paper presents a detailed description of the model and initial results from a suite of 10 simulations of ˜L⋆ galaxies with disc-like morphologies at z = 0. The simulations broadly reproduce key observed characteristics of young star clusters and globular clusters (GCs), without invoking separate formation mechanisms for each population. The simulated GCs are the surviving population of massive clusters formed at early epochs (z ≳ 1-2), when the characteristic pressures and surface densities of star-forming gas were significantly higher than observed in local galaxies. We examine the influence of the star formation and assembly histories of galaxies on their cluster populations, finding that (at similar present-day mass) earlier-forming galaxies foster a more massive and disruption-resilient cluster population, while galaxies with late mergers are capable of forming massive clusters even at late cosmic epochs. We find that the phenomenological treatment of interstellar gas in EAGLE precludes the accurate modelling of cluster disruption in low-density environments, but infer that simulations incorporating an explicitly modelled cold interstellar gas phase will overcome

  14. Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

    Science.gov (United States)

    Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Antunes, Agostinho

    2015-10-06

    The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

  15. Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

    Directory of Open Access Journals (Sweden)

    Engelen Stefan

    2012-02-01

    Full Text Available Abstract Background Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.

  16. Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth.

    Science.gov (United States)

    Grosch, Eugene G; Hazen, Robert M

    2015-10-01

    Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

  17. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease

    International Nuclear Information System (INIS)

    Yedidi, Ravikiran S.; Muhuhi, Joseck M.; Liu, Zhigang; Bencze, Krisztina Z.; Koupparis, Kyriacos; O’Connor, Carrie E.; Kovari, Iulia A.; Spaller, Mark R.; Kovari, Ladislau C.

    2013-01-01

    Highlights: •Inhibitors against MDR HIV-1 protease were designed, synthesized and evaluated. •Lead peptide (6a) showed potent inhibition (IC 50 : 4.4 nM) of MDR HIV-1 protease. •(6a) Showed favorable binding isotherms against NL4-3 and MDR proteases. •(6a) Induced perturbations in the 15 N-HSQC spectrum of MDR HIV-1 protease. •Molecular modeling suggested that (6a) may induce total flap closure inMDR protease. -- Abstract: Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: (1TW7)), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC 50 : 4.4 nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6aagainst both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of 15 N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV

  18. Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

    Science.gov (United States)

    Mullon, Charles; Lehmann, Laurent

    2017-08-01

    Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is

  19. Understanding physics

    CERN Document Server

    Cassidy, David; Rutherford, James

    2002-01-01

    Understanding Physics provides a thorough grounding in contemporary physics while placing physics into its social and historical context Based in large part on the highly respected Project Physics Course developed by two of the authors, it also integrates the results of recent pedagogical research The text thus - teaches about the basic phenomena in the physical world and the concepts developed to explain them - shows that science is a rational human endeavor with a long and continuing tradition, involving many different cultures and people - develops facility in critical thinking, reasoned argumentation, evaluation of evidence, mathematical modeling, and ethical values The treatment emphasizes not only what we know but also how we know it, why we believe it, and what effects that knowledge has - Why do we believe the Earth and planets revolve around the Sun? - Why do we believe that matter is made of atoms? - How do relativity theory and quantum mechanics alter our conception of Nature and in what ways do th...

  20. Modelling the morphodynamics and co-evolution of coast and estuarine environments

    Science.gov (United States)

    Morris, Chloe; Coulthard, Tom; Parsons, Daniel R.; Manson, Susan; Barkwith, Andrew

    2017-04-01

    The morphodynamics of coast and estuarine environments are known to be sensitive to environmental change and sea-level rise. However, whilst these systems have received considerable individual research attention, how they interact and co-evolve is relatively understudied. These systems are intrinsically linked and it is therefore advantageous to study them holistically in order to build a more comprehensive understanding of their behaviour and to inform sustainable management over the long term. Complex environments such as these are often studied using numerical modelling techniques. Inherent from the limited research in this area, existing models are currently not capable of simulating dynamic coast-estuarine interactions. A new model is being developed through coupling the one-line Coastline Evolution Model (CEM) with CAESAR-Lisflood (C-L), a hydrodynamic Landscape Evolution Model. It is intended that the eventual model be used to advance the understanding of these systems and how they may evolve over the mid to long term in response to climate change. In the UK, the Holderness Coast, Humber Estuary and Spurn Point system offers a diverse and complex case study for this research. Holderness is one of the fastest eroding coastlines in Europe and research suggests that the large volumes of material removed from its cliffs are responsible for the formation of the Spurn Point feature and for the Holocene infilling of the Humber Estuary. Marine, fluvial and coastal processes are continually reshaping this system and over the next century, it is predicted that climate change could lead to increased erosion along the coast and supply of material to the Humber Estuary and Spurn Point. How this manifests will be hugely influential to the future morphology of these systems and the existence of Spurn Point. Progress to date includes a new version of the CEM that has been prepared for integration into C-L and includes an improved graphical user interface and more complex

  1. Coevolution of dependency distance, hierarchical structure and word order. Comment on "Dependency distance: a new perspective on syntactic patterns in natural languages" by Haitao Liu et al.

    Science.gov (United States)

    Jing, Yingqi

    2017-07-01

    Exploring the relationships between structural rules and their linearization constraints have been a central issue in formal syntax and linguistic typology [1]. Liu et al. give a historical overview of the investigation of dependency distance minimization (DDM) in various fields, and specify its potential connections with the graphic patterns of syntactic structure and the linear ordering of words and constituents in real sentences [2]. This comment focuses on discussing the relations between dependency distance (DD), hierarchical structure and word order, and advocates further study on the coevolution of these traits in language histories.

  2. Co-evolution of the brand effect and competitiveness in evolving networks

    International Nuclear Information System (INIS)

    Guo Jin-Li

    2014-01-01

    The principle that ‘the brand effect is attractive’ underlies the preferential attachment. Here we show that the brand effect is just one dimension of attractiveness. Another dimension is competitiveness. We firstly introduce a general framework that allows us to investigate the competitive aspect of real networks, instead of simply preferring popular nodes. Our model accurately describes the evolution of social and technological networks. The phenomenon that more competitive nodes become richer can help us to understand the evolution of many competitive systems in nature and society. In general, the paper provides an explicit analytical expression of degree distributions of the network. In particular, the model yields a nontrivial time evolution of nodes' properties and the scale-free behavior with exponents depending on the microscopic parameters characterizing the competition rules. Secondly, through theoretical analyses and numerical simulations, we reveal that our model has not only the universality for the homogeneous weighted network, but also the character for the heterogeneous weighted network. Thirdly, we also develop a model based on the profit-driven mechanism. It can better describe the observed phenomenon in enterprise cooperation networks. We show that the standard preferential attachment, the growing random graph, the initial attractiveness model, the fitness model, and weighted networks can all be seen as degenerate cases of our model. (general)

  3. Coevolution in communication senders and receivers: vocal behavior and auditory processing in multiple songbird species.

    Science.gov (United States)

    Woolley, Sarah M N; Moore, Jordan M

    2011-04-01

    Communication is a strong selective pressure on brain evolution because the exchange of information between individuals is crucial for fitness-related behaviors, such as mating. Given the importance of communication, the brains of signal senders and receivers are likely to be functionally coordinated. We study vocal behavior and auditory processing in multiple species of estrildid finches with the goal of understanding how species identity and early experience interact to shape the neural systems that subserve communication. Male finches learn to produce species-specific songs, and both sexes learn to recognize songs. Our studies indicate that closely related species exhibit different auditory coding properties in the midbrain and forebrain and that early life experience of vocalizations contributes to these differences. Moreover, birds that naturally sing tonal songs can learn broadband songs from heterospecific tutors, providing an opportunity to examine the interplay between species identity and early experience in the development of vocal behavior and auditory tuning. © 2011 New York Academy of Sciences.

  4. Co-evolution of the brand effect and competitiveness in evolving networks

    Science.gov (United States)

    Guo, Jin-Li

    2014-07-01

    The principle that ‘the brand effect is attractive’ underlies the preferential attachment. Here we show that the brand effect is just one dimension of attractiveness. Another dimension is competitiveness. We firstly introduce a general framework that allows us to investigate the competitive aspect of real networks, instead of simply preferring popular nodes. Our model accurately describes the evolution of social and technological networks. The phenomenon that more competitive nodes become richer can help us to understand the evolution of many competitive systems in nature and society. In general, the paper provides an explicit analytical expression of degree distributions of the network. In particular, the model yields a nontrivial time evolution of nodes' properties and the scale-free behavior with exponents depending on the microscopic parameters characterizing the competition rules. Secondly, through theoretical analyses and numerical simulations, we reveal that our model has not only the universality for the homogeneous weighted network, but also the character for the heterogeneous weighted network. Thirdly, we also develop a model based on the profit-driven mechanism. It can better describe the observed phenomenon in enterprise cooperation networks. We show that the standard preferential attachment, the growing random graph, the initial attractiveness model, the fitness model, and weighted networks can all be seen as degenerate cases of our model.

  5. Uniformitarianism and its Discontents: Microbial Evolution and Co-evolution of Life and Earth

    Science.gov (United States)

    Wing, B. A.

    2016-12-01

    For the first ≈4 billion years of Earth history, life was microscopic. There are ≈5x1030 bacteria and archaea on Earth today. Mean turnover times of natural microbial populations are days to millennia (10-2 to 103 years). Assuming that a similar-sized microbial biosphere has been maintained since ≈4 billion years ago, the number of microbes that have ever lived on Earth is awesome: >1037 to 1042. In broad brush, these numbers represent the individual microbial evolution experiments run by Nature. They are many, many orders of magnitude greater than the number of stars in the universe. Despite this numerical hurdle, the geological record is read with the assumption that microbes in the geological past were doing exactly what microbes do today. In this presentation, I will discuss evolutionary impacts on a critical microbial phentypic trait - sulfur isotope fractionation - that has played a critical role in our interpretations of the the evolution of the Earth system. The discussion will range from microbial evolution experiments to models of metabolic evolution, with an eye toward understanding the evolutionary weaknesses and strengths in our uniformiatrian world view.

  6. Interpreting Sustainability through Co-Evolution: Evidence from Religious Accommodations in Rome

    Directory of Open Access Journals (Sweden)

    Paola M. A. Paniccia

    2017-12-01

    Full Text Available In recent decades, concepts such as sustainability, innovation, and competitiveness have become fundamental for the development of tourist destinations, and thus, particularly, for the generation of value co-creation processes. To understand the role of tourism firms in these processes, more theoretical and empirical research is required. This paper addresses this need by examining the increasing role played by religious accommodations, adopting a co-evolutionary approach to sustainability and the resulting value co-creation processes. The study focuses on the dynamics of the relationship between this new hospitality model, territories, and tourists, through the analysis of six case studies localized in the historic centre of Rome (Italy. Findings show that religious accommodations can be considered as a new sustainability-oriented hospitality model that, by creating effective multi-level co-evolutionary adaptations with its territory and tourists, positively affects sustainable development as well as the generation of value co-creation processes. The paper contributes significantly both to sustainability literature and to the study of new hospitality models. Thus, theoretical and managerial implications emerge, together with suggestions for future research.

  7. Spatially variable coevolution between a haemosporidian parasite and the MHC of a widely distributed passerine.

    Science.gov (United States)

    Jones, Matthew R; Cheviron, Zachary A; Carling, Matthew D

    2015-03-01

    The environment shapes host-parasite interactions, but how environmental variation affects the diversity and composition of parasite-defense genes of hosts is unresolved. In vertebrates, the highly variable major histocompatibility complex (MHC) gene family plays an essential role in the adaptive immune system by recognizing pathogen infection and initiating the cellular immune response. Investigating MHC-parasite associations across heterogeneous landscapes may elucidate the role of spatially fluctuating selection in the maintenance of high levels of genetic variation at the MHC. We studied patterns of association between an avian haemosporidian blood parasite and the MHC of rufous-collared sparrows (Zonotrichia capensis) that inhabit environments with widely varying haemosporidian infection prevalence in the Peruvian Andes. MHC diversity peaked in populations with high infection prevalence, although intra-individual MHC diversity was not associated with infection status. MHC nucleotide and protein sequences associated with infection absence tended to be rare, consistent with negative frequency-dependent selection. We found an MHC variant associated with a ∽26% decrease in infection probability at middle elevations (1501-3100 m) where prevalence was highest. Several other variants were associated with a significant increase in infection probability in low haemosporidian prevalence environments, which can be interpreted as susceptibility or quantitative resistance. Our study highlights important challenges in understanding MHC evolution in natural systems, but may point to a role of negative frequency-dependent selection and fluctuating spatial selection in the evolution of Z. capensisMHC.

  8. Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?

    Directory of Open Access Journals (Sweden)

    María Carmen Cenit

    2015-08-01

    Full Text Available It is widely recognized that the intestinal microbiota plays a role in the initiation and perpetuation of intestinal inflammation in numerous chronic conditions. Most studies report intestinal dysbiosis in celiac disease (CD patients, untreated and treated with a gluten-free diet (GFD, compared to healthy controls. CD patients with gastrointestinal symptoms are also known to have a different microbiota compared to patients with dermatitis herpetiformis and controls, suggesting that the microbiota is involved in disease manifestation. Furthermore, a dysbiotic microbiota seems to be associated with persistent gastrointestinal symptoms in treated CD patients, suggesting its pathogenic implication in these particular cases. GFD per se influences gut microbiota composition, and thus constitutes an inevitable confounding factor in studies conducted in CD patients. To improve our understanding of whether intestinal dysbiosis is the cause or consequence of disease, prospective studies in healthy infants at family risk of CD are underway. These studies have revealed that the CD host genotype selects for the early colonizers of the infant’s gut, which together with environmental factors (e.g., breast-feeding, antibiotics, etc. could influence the development of oral tolerance to gluten. Indeed, some CD genes and/or their altered expression play a role in bacterial colonization and sensing. In turn, intestinal dysbiosis could promote an abnormal response to gluten or other environmental CD-promoting factors (e.g., infections in predisposed individuals. Here, we review the current knowledge of host-microbe interactions and how host genetics/epigenetics and environmental factors shape gut microbiota and may influence disease risk. We also summarize the current knowledge about the potential mechanisms of action of the intestinal microbiota and specific components that affect CD pathogenesis.

  9. Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?

    Science.gov (United States)

    Cenit, María Carmen; Olivares, Marta; Codoñer-Franch, Pilar; Sanz, Yolanda

    2015-08-17

    It is widely recognized that the intestinal microbiota plays a role in the initiation and perpetuation of intestinal inflammation in numerous chronic conditions. Most studies report intestinal dysbiosis in celiac disease (CD) patients, untreated and treated with a gluten-free diet (GFD), compared to healthy controls. CD patients with gastrointestinal symptoms are also known to have a different microbiota compared to patients with dermatitis herpetiformis and controls, suggesting that the microbiota is involved in disease manifestation. Furthermore, a dysbiotic microbiota seems to be associated with persistent gastrointestinal symptoms in treated CD patients, suggesting its pathogenic implication in these particular cases. GFD per se influences gut microbiota composition, and thus constitutes an inevitable confounding factor in studies conducted in CD patients. To improve our understanding of whether intestinal dysbiosis is the cause or consequence of disease, prospective studies in healthy infants at family risk of CD are underway. These studies have revealed that the CD host genotype selects for the early colonizers of the infant's gut, which together with environmental factors (e.g., breast-feeding, antibiotics, etc.) could influence the development of oral tolerance to gluten. Indeed, some CD genes and/or their altered expression play a role in bacterial colonization and sensing. In turn, intestinal dysbiosis could promote an abnormal response to gluten or other environmental CD-promoting factors (e.g., infections) in predisposed individuals. Here, we review the current knowledge of host-microbe interactions and how host genetics/epigenetics and environmental factors shape gut microbiota and may influence disease risk. We also summarize the current knowledge about the potential mechanisms of action of the intestinal microbiota and specific components that affect CD pathogenesis.

  10. Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?

    Science.gov (United States)

    Cenit, María Carmen; Olivares, Marta; Codoñer-Franch, Pilar; Sanz, Yolanda

    2015-01-01

    It is widely recognized that the intestinal microbiota plays a role in the initiation and perpetuation of intestinal inflammation in numerous chronic conditions. Most studies report intestinal dysbiosis in celiac disease (CD) patients, untreated and treated with a gluten-free diet (GFD), compared to healthy controls. CD patients with gastrointestinal symptoms are also known to have a different microbiota compared to patients with dermatitis herpetiformis and controls, suggesting that the microbiota is involved in disease manifestation. Furthermore, a dysbiotic microbiota seems to be associated with persistent gastrointestinal symptoms in treated CD patients, suggesting its pathogenic implication in these particular cases. GFD per se influences gut microbiota composition, and thus constitutes an inevitable confounding factor in studies conducted in CD patients. To improve our understanding of whether intestinal dysbiosis is the cause or consequence of disease, prospective studies in healthy infants at family risk of CD are underway. These studies have revealed that the CD host genotype selects for the early colonizers of the infant’s gut, which together with environmental factors (e.g., breast-feeding, antibiotics, etc.) could influence the development of oral tolerance to gluten. Indeed, some CD genes and/or their altered expression play a role in bacterial colonization and sensing. In turn, intestinal dysbiosis could promote an abnormal response to gluten or other environmental CD-promoting factors (e.g., infections) in predisposed individuals. Here, we review the current knowledge of host-microbe interactions and how host genetics/epigenetics and environmental factors shape gut microbiota and may influence disease risk. We also summarize the current knowledge about the potential mechanisms of action of the intestinal microbiota and specific components that affect CD pathogenesis. PMID:26287240

  11. Molecular spintronics.

    Science.gov (United States)

    Sanvito, Stefano

    2011-06-01

    The electron spin made its debut in the device world only two decades ago but today our ability of detecting the spin state of a moving electron underpins the entire magnetic data storage industry. This technological revolution has been driven by a constant improvement in our understanding on how spins can be injected, manipulated and detected in the solid state, a field which is collectively named Spintronics. Recently a number of pioneering experiments and theoretical works suggest that organic materials can offer similar and perhaps superior performances in making spin-devices than the more conventional inorganic metals and semiconductors. Furthermore they can pave the way for radically new device concepts. This is Molecular Spintronics, a blossoming research area aimed at exploring how the unique properties of the organic world can marry the requirements of spin-devices. Importantly, after a first phase, where most of the research was focussed on exporting the concepts of inorganic spintronics to organic materials, the field has moved to a more mature age, where the exploitation of the unique properties of molecules has begun to emerge. Molecular spintronics now collects a diverse and interdisciplinary community ranging from device physicists to synthetic chemists to surface scientists. In this critical review, I will survey this fascinating, rapidly evolving, field with a particular eye on new directions and opportunities. The main differences and challenges with respect to standard spintronics will be discussed and so will be the potential cross-fertilization with other fields (177 references).

  12. Understanding PISA

    Directory of Open Access Journals (Sweden)

    Stephen DOWNES

    2005-04-01

    Full Text Available Understanding PISA Stephen DOWNESMoncton, CANADA ABSTRACT The headline was dramatic enough to cause a ripple in the reading public. "Students who use computers a lot at school have worse maths and reading performance," noted the BBC news article, citing a 2004 study by Ludger Woessmann and Thomas Fuchs (Fuchs and Woessman, 2004. It was not long before the blogosphere took notice. Taking the theme and running with it, Alice and Bill ask, "Computers Make School Kids Dumber?" They theorize, "If you track the admitted decline of education, you'll probably notice that it follows along with the increase of technology in the classroom." In a similar vein, James Bartholomew asks, "Do you think that the government will turn down the volume of its boasting about how it has spent billions introducing computers in schools (while keeping down the pay of teachers so much that there are shortages? Do you think it will stop sending governors of state schools glossy pamphlets about insisting that computers are used in their schools as much as possible?" In this study, therefore, PISA looks well beyond educational attainment, and also includes school demographics, such as whether it is a public or private school, has large or small classes, or has access or not to technological resources. Finally, it does measure student information-their family background, access to books and computers and parental support as well. The PISA survey departs from previous surveys in disregarding the stated curricula of the schools being measured. Therefore, the conclusion is not surprising, nor even wrong for him to consider independently of any parental or teacher support, considered without reference to the software running on it, considered without reference to student attitudes and interests, does not positively impact an education. Finally, he focus on missing the reporting of results

  13. The role of insulin C-peptide in the coevolution analyses of the insulin signaling pathway: a hint for its functions.

    Directory of Open Access Journals (Sweden)

    Shuai Wang

    Full Text Available As the linker between the A chain and B chain of proinsulin, C-peptide displays high variability in length and amino acid composition, and has been considered as an inert byproduct of insulin synthesis and processing for many years. Recent studies have suggested that C-peptide can act as a bioactive hormone, exerting various biological effects on the pathophysiology and treatment of diabetes. In this study, we analyzed the coevolution of insulin molecules among vertebrates, aiming at exploring the evolutionary characteristics of insulin molecule, especially the C-peptide. We also calculated the correlations of evolutionary rates between the insulin and the insulin receptor (IR sequences as well as the domain-domain pairs of the ligand and receptor by the mirrortree method. The results revealed distinctive features of C-peptide in insulin intramolecular coevolution and correlated residue substitutions, which partly supported the idea that C-peptide can act as a bioactive hormone, with significant sequence features, as well as a linker assisting the formation of mature insulin during synthesis. Interestingly, the evolution of C-peptide exerted the highest correlation with that of the insulin receptor and its ligand binding domain (LBD, implying a potential relationship with the insulin signaling pathway.

  14. Climate-vegetation-soil interactions and long-term hydrologic partitioning: signatures of catchment co-evolution

    Directory of Open Access Journals (Sweden)

    P. A. Troch

    2013-06-01

    subsurface storage release time scales produce significantly more E/P. Vegetation in these catchments have longer access to this additional groundwater source and thus are less prone to water stress. Further analysis reveals that climates that give rise to more (less E/P are associated with catchments that have vegetation with less (more efficient water use parameters. In particular, the climates with tendency to produce more E/P have catchments that have lower % root fraction and less light use efficiency. Our results suggest that their exists strong interactions between climate, vegetation and soil properties that lead to specific hydrologic partitioning at the catchment scale. This co-evolution of catchment vegetation and soils with climate needs to be further explored to improve our capabilities to predict hydrologic partitioning in ungauged basins.

  15. Combined 3D-QSAR and molecular docking study on 7,8-dialkyl-1,3-diaminopyrrolo-[3,2-f] Quinazoline series compounds to understand the binding mechanism of DHFR inhibitors

    Science.gov (United States)

    Aouidate, Adnane; Ghaleb, Adib; Ghamali, Mounir; Chtita, Samir; Choukrad, M'barek; Sbai, Abdelouahid; Bouachrine, Mohammed; Lakhlifi, Tahar

    2017-07-01

    A series of nineteen DHFR inhibitors was studied based on the combination of two computational techniques namely, three-dimensional quantitative structure activity relationship (3D-QSAR) and molecular docking. The comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were developed using 19 molecules having pIC50 ranging from 9.244 to 5.839. The best CoMFA and CoMSIA models show conventional determination coefficients R2 of 0.96 and 0.93 as well as the Leave One Out cross-validation determination coefficients Q2 of 0.64 and 0.72, respectively. The predictive ability of those models was evaluated by the external validation using a test set of five compounds with predicted determination coefficients R2test of 0.92 and 0.94, respectively. The binding mode between this kind of compounds and the DHFR enzyme in addition to the key amino acid residues were explored by molecular docking simulation. Contour maps and molecular docking identified that the R1 and R2 natures at the pyrazole moiety are the important features for the optimization of the binding affinity to the DHFR receptor. According to the good concordance between the CoMFA/CoMSIA contour maps and docking results, the obtained information was explored to design novel molecules.

  16. Multimodality cardiovascular molecular imaging technology.

    Science.gov (United States)

    O'Donnell, Matthew; McVeigh, Elliot R; Strauss, H William; Tanaka, Atsushi; Bouma, Brett E; Tearney, Guillermo J; Guttman, Michael A; Garcia, Ernest V

    2010-05-01

    Cardiovascular molecular imaging is a new discipline that integrates scientific advances in both functional imaging and molecular probes to improve our understanding of the molecular basis of the cardiovascular system. These advances are driven by in vivo imaging of molecular processes in animals, usually small animals, and are rapidly moving toward clinical applications. Molecular imaging has the potential to revolutionize the diagnosis and treatment of cardiovascular disease. The 2 key components of all molecular imaging systems are the molecular contrast agents and the imaging system providing spatial and temporal localization of these agents within the body. They must deliver images with the appropriate sensitivity and specificity to drive clinical applications. As work in molecular contrast agents matures and highly sensitive and specific probes are developed, these systems will provide the imaging technologies required for translation into clinical tools. This is the promise of molecular medicine.

  17. Baculovirus Molecular Evolution via Gene Turnover and Recurrent Positive Selection of Key Genes.

    Science.gov (United States)

    Hill, Tom; Unckless, Robert L

    2017-11-15

    Hosts and viruses are locked in an evolutionary arms race. Hosts are constantly evolving to suppress virulence and replication, while viruses, which are reliant on host machinery for survival and reproduction, develop counterstrategies to escape this immune defense. Viruses must also adapt to novel conditions while establishing themselves in a host species. Both processes provide strong selection for viral adaptation. Understanding adaptive evolution in insect viruses can help us to better understand adaptive evolution in general and is important due to the use of these viruses as biocontrol agents and for protecting ecologically or economically important species from outbreaks. Here we examine the molecular evolution of baculoviruses and nudiviruses, a group of insect-infecting viruses with key roles in biocontrol. We looked for signatures of selection between genomes of baculoviruses infecting a range of species and within a population of baculoviruses. Both analyses found only a few strong signatures of positive selection, primarily in replication- and transcription-associated genes and several structural protein genes. In both analyses, we detected a conserved complex of genes, including the helicase gene, showing consistently high levels of adaptive evolution, suggesting that they may be key in antagonistic coevolution to escape host suppression. These genes are integral to the baculovirus life cycle and may be good focal genes for developing baculoviruses as effective biocontrol agents or for targeting baculoviruses infecting ecologically relevant species. Recombination and complex genomes make evolution in these double-stranded DNA viruses more efficient than that in smaller RNA viruses with error-prone replication, as seen via signatures of selection in specific genes within a population of baculoviruses. IMPORTANCE Most viral evolutionary studies focus on RNA viruses. While these viruses cause many human and animal diseases, such studies leave us with a

  18. Theoretical molecular biophysics

    CERN Document Server

    Scherer, Philipp O J

    2017-01-01

    This book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to b...

  19. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  20. Global Operations Coevolution

    DEFF Research Database (Denmark)

    Slepniov, Dmitrij; Wæhrens, Brian Vejrum; Gubi, Ebbe

    2013-01-01

    Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial e...... of analysis and involving temporal adaptations. In terms of managerial implications, the study provides managers with lessons for designing a robust system of globally dispersed operations.......Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial...... equipment firm and describes how its operations configuration has been changing over time. The chapter identifies the key determinants of this change and uncovers some of its hidden effects. The chapter closes with propositions for how to respond to these effects through the development of a distinct...

  1. Co-Evolution.

    Science.gov (United States)

    McGhee, Robert

    2002-01-01

    Discusses the role of techniques of DNA analysis in assessing the genetic relationships between various species. Focuses on wolf-dog evolution using DNA evidence and historical data about human/wolf-dog relationships. (DDR)

  2. Socio-hydrologic perspectives of the co-evolution of humans and water in the Tarim River basin, Western China: the Taiji-Tire model

    Science.gov (United States)

    Liu, Y.; Tian, F.; Hu, H.; Sivapalan, M.

    2014-04-01

    This paper presents a historical socio-hydrological analysis of the Tarim River basin (TRB), Xinjiang Uyghur Autonomous Region, in Western China, from the time of the opening of the Silk Road to the present. The analysis is aimed at exploring the historical co-evolution of coupled human-water systems and at identifying common patterns or organizing principles underpinning socio-hydrological systems (SHS). As a self-organized entity, the evolution of the human-water system in the Tarim Basin reached stable states for long periods of time, but then was punctuated by sudden shifts due to internal or external disturbances. In this study, we discuss three stable periods (i.e., natural, human exploitation, and degradation and recovery) and the transitions in between during the past 2000 years. During the "natural" stage that existed pre-18th century, with small-scale human society and sound environment, evolution of the SHS was mainly driven by natural environmental changes such as river channel migration and climate change. During the human exploitation stage, especially in the 19th and 20th centuries, it experienced rapid population growth, massive land reclamation and fast socio-economic development, and humans became the principal players of system evolution. By the 1970s, the Tarim Basin had evolved into a new regime with a vulnerable eco-hydrological system seemingly populated beyond its carrying capacity, and a human society that began to suffer from serious water shortages, land salinization and desertification. With intensified deterioration of river health and increased recognition of unsustainability of traditional development patterns, human intervention and recovery measures have since been adopted. As a result, the basin has shown a reverse regime shift towards some healing of the environmental damage. Based on our analysis within TRB and a common theory of social development, four general types of SHSs are defined according to their characteristic spatio

  3. Molecular hematology

    National Research Council Canada - National Science Library

    Provan, Drew; Gribben, John

    2010-01-01

    ... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...

  4. Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

    Directory of Open Access Journals (Sweden)

    David Juan

    2016-02-01

    Full Text Available Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs.

  5. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Nonequilibrium molecular dynamics

    Directory of Open Access Journals (Sweden)

    Wm.G.Hoover

    2005-01-01

    Full Text Available Nonequilibrium Molecular Dynamics is a powerful simulation tool. Like its equilibrium cousin, nonequilibrium molecular dynamics is based on time-reversible equations of motion. But unlike conventional mechanics, nonequilibrium molecular dynamics provides a consistent microscopic basis for the irreversible macroscopic Second Law of Thermodynamics. We recall here how fast computers led to the development of nonequilibrium molecular dynamics from the statistical mechanics of the 1950s. Computer-based theories facilitated revolutionary breakthroughs in understanding during the 1970s and 1980s. The new idea key to the nonequilibrium development was the replacement of the external thermodynamic environment by internal control variables. The new variables can control temperature, or pressure, or energy, or stress, or heat flux. These thermostat, barostat, ergostat, ... variables can control and maintain nonequilibrium states. We illustrate the methods with a simple example well-suited to student exploration, a thermostatted harmonic oscillator exposed to a temperature gradient.

  7. Mesoporous molecular sieve catalysts

    DEFF Research Database (Denmark)

    Højholt, Karen Thrane

    This thesis deals with a very specific class of molecular sieves known as zeolites. Zeolites are a class of crystalline aluminosilicates characterised by pores or cavities of molecular dimensions as part of their crystal structure. In this work zeolites were modified for the use and understanding...... of different catalytic applications. Primarily the zeolites were modified regarding the porosity and the introduction of metals to the framework. The obtained materials were used as solid acid catalysts, as an inert matrix for stabilising metal nanoparticles and as an anchoring material for molecular metal....... Furthermore, preliminary work was done using mesoporous ZSM-5 zeolites as support material for anchoring molecular CoMo6 species for the application as potential bi-functional catalyst in simultaneous hydrodesulfurisation (HDS) and hydrocracking. HDS activity tests revealed that the anchoring improved...

  8. EAACI Molecular Allergology User's Guide

    NARCIS (Netherlands)

    Matricardi, P. M.; Kleine-Tebbe, J.; Hoffmann, H. J.; Valenta, R.; Hilger, C.; Hofmaier, S.; Aalberse, R. C.; Agache, I.; Asero, R.; Ballmer-Weber, B.; Barber, D.; Beyer, K.; Biedermann, T.; Bilò, M. B.; Blank, S.; Bohle, B.; Bosshard, P. P.; Breiteneder, H.; Brough, H. A.; Caraballo, L.; Caubet, J. C.; Crameri, R.; Davies, J. M.; Douladiris, N.; Ebisawa, M.; EIgenmann, P. A.; Fernandez-Rivas, M.; Ferreira, F.; Gadermaier, G.; Glatz, M.; Hamilton, R. G.; Hawranek, T.; Hellings, P.; Hoffmann-Sommergruber, K.; Jakob, T.; Jappe, U.; Jutel, M.; Kamath, S. D.; Knol, E. F.; Korosec, P.; Kuehn, A.; Lack, G.; Lopata, A. L.; Mäkelä, M.; Morisset, M.; Niederberger, V.; Nowak-Węgrzyn, A. H.; Papadopoulos, N. G.; Pastorello, E. A.; Pauli, G.; Platts-Mills, T.; Posa, D.; Poulsen, L. K.; Raulf, M.; Sastre, J.; Scala, E.; Schmid, J. M.; Schmid-Grendelmeier, P.; van Hage, M.; van Ree, R.; Vieths, S.; Weber, R.; Wickman, M.; Muraro, A.; Ollert, M.

    2016-01-01

    The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology

  9. Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug-Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies.

    Science.gov (United States)

    Yao, Jianzhuang; Wang, Xia; Luo, Haixia; Gu, Pengfei

    2017-11-16

    Shikimate kinase (SK) is the fifth bacterial enzyme involved in the shikimate pathway for biosynthesis of life-indispensable components, such as aromatic amino acids. The absence of the shikimate pathway in humans makes SK an attractive target for the rational design of drugs aimed at pathogenesis bacteria, such as Mycobacterium tuberculosis and Helicobacter pylori. However, an effective inhibitor of SK (e.g., a transition-state analogue) is still not available on the market due, at least in part, to a lack of knowledge on the catalytic mechanism and the nature of the rate-limiting transition state. Herein, quantum mechanical/molecular mechanical (QM/MM) reaction coordinate, molecular dynamics (MD), and free-energy simulations have been performed to answer these questions. The results presented herein demonstrate that the phosphoryl-transfer process, which is the rate-limiting step of SK-catalyzed phosphorylation of shikimic acid (SKM), is a concerted one-step reaction proceeding through a loose transition state. The computational results agree well with those of experimental studies, specifically NMR results, X-ray crystal structure observation, and activation free-energy barrier. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Molecular Biology and Prevention of Endometrial Cancer

    National Research Council Canada - National Science Library

    Maxwell, George

    2003-01-01

    To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive therapy. Methods: 1...

  11. Molecular Biology and Prevention of Endometrial Cancer

    National Research Council Canada - National Science Library

    Maxwell, George L

    2004-01-01

    To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive therapy. Methods: 1...

  12. Molecular Biology and Prevention of Endometrial Cancer

    National Research Council Canada - National Scien