WorldWideScience

Sample records for evolutionary systems biology

  1. A Philosophical Perspective on Evolutionary Systems Biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S; Siegal, Mark L

    2015-03-01

    Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.

  2. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  3. A framework for evolutionary systems biology.

    Science.gov (United States)

    Loewe, Laurence

    2009-02-24

    Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.

  4. A framework for evolutionary systems biology

    Directory of Open Access Journals (Sweden)

    Loewe Laurence

    2009-02-01

    Full Text Available Abstract Background Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Results Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. Conclusion EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.

  5. Robust design of biological circuits: evolutionary systems biology approach.

    Science.gov (United States)

    Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

    2011-01-01

    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

  6. Evolutionary bioscience as regulatory systems biology.

    Science.gov (United States)

    Davidson, Eric H

    2011-09-01

    At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved. Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, causal explanation of evolutionary change in developmental process must be considered at a system level. Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. From experimental systems to evolutionary biology: an impossible journey?

    Science.gov (United States)

    Morange, Michel

    2013-01-01

    The historical approach to the sciences has undergone a sea change during recent decades. Maybe the major contribution of Hans-Jörg Rheinberger to this movement was his demonstration of the importance of experimental systems, and of their transformations, in the development of the sciences. To describe these transformations, Hans-Jörg borrows metaphors from evolutionary biology. I want to argue that evolutionary biologists can find in these recent historical studies plenty of models and concepts to address unresolved issues in their discipline. At a time when transdisciplinarity is highly praised, it is useful to provide a precise description of the obstacles that have so far prevented this exchange.

  8. Evolutionary systems biology: what it is and why it matters.

    Science.gov (United States)

    Soyer, Orkun S; O'Malley, Maureen A

    2013-08-01

    Evolutionary systems biology (ESB) is a rapidly growing integrative approach that has the core aim of generating mechanistic and evolutionary understanding of genotype-phenotype relationships at multiple levels. ESB's more specific objectives include extending knowledge gained from model organisms to non-model organisms, predicting the effects of mutations, and defining the core network structures and dynamics that have evolved to cause particular intracellular and intercellular responses. By combining mathematical, molecular, and cellular approaches to evolution, ESB adds new insights and methods to the modern evolutionary synthesis, and offers ways in which to enhance its explanatory and predictive capacities. This combination of prediction and explanation marks ESB out as a research manifesto that goes further than its two contributing fields. Here, we summarize ESB via an analysis of characteristic research examples and exploratory questions, while also making a case for why these integrative efforts are worth pursuing. © 2013 WILEY Periodicals, Inc.

  9. Driving developmental and evolutionary change: A systems biology view.

    Science.gov (United States)

    Bard, Jonathan

    2013-04-01

    Embryonic development is underpinned by ∼50 core processes that drive morphogenesis, growth, patterning and differentiation, and each is the functional output of a complex molecular network. Processes are thus the natural and parsimonious link between genotype and phenotype and the obvious focus for any discussion of biological change. Here, the implications of this approach are explored. One is that many features of developmental change can be modeled as mathematical graphs, or sets of connected triplets of the general form . In these, the verbs (edges) are the outputs of the processes that drive change and the nouns (nodes) are the time-dependent states of biological entities (from molecules to tissues). Such graphs help unpick the multi-level complexity of developmental phenomena and may help suggest new experiments. Another comes from analyzing the effect of mutation that lead to tinkering with the dynamic properties of these processes and to congenital abnormalities; if these changes are both inherited and advantageous, they become evolutionary modifications. In this context, protein networks often represents what classical evolutionary genetics sees as genes, and the realization that traits reflect the output processes of complex networks, particularly for growth, patterning and pigmentation, rather than anything simpler clarifies some problems that the evolutionary synthesis of the 1950s has found hard to solve. In the wider context, most processes are used many times in development and cooperate to produce tissue modules (bones, branching duct systems, muscles etc.). Their underlying generative networks can thus be thought of as genomic modules or subroutines. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Use of genome-scale metabolic models in evolutionary systems biology.

    NARCIS (Netherlands)

    Papp, B.; Szappanos, B.; Notebaart, R.A.

    2011-01-01

    One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for

  11. Use of genome-scale metabolic models in evolutionary systems biology.

    Science.gov (United States)

    Papp, Balázs; Szappanos, Balázs; Notebaart, Richard A

    2011-01-01

    One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.

  12. Marine mammals: evolutionary biology

    National Research Council Canada - National Science Library

    Berta, Annalisa; Sumich, James L; Kovacs, Kit M

    2015-01-01

    The third edition of Marine Mammals: Evolutionary Biology provides a comprehensive and current assessment of the diversity, evolution, and biology of marine mammals, while highlighting the latest tools and techniques for their study...

  13. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 11. Evolutionary Biology Today - The Domain of Evolutionary Biology. Amitabh Joshi. Series Article Volume 7 Issue 11 November 2002 pp 8-17. Fulltext. Click here to view fulltext PDF. Permanent link:

  14. Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems.

    Science.gov (United States)

    Szekely, Pablo; Sheftel, Hila; Mayo, Avi; Alon, Uri

    2013-01-01

    Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical. For example, regulatory systems that are designed to repair damage must be effective in reducing damage, but economical in not making too many repair proteins because making excessive proteins carries a fitness cost to the cell, called protein burden. In order to see how biological systems compromise between the two tasks of effectiveness and economy, we applied an approach from economics and engineering called Pareto optimality. This approach allows calculating the best-compromise systems that optimally combine the two tasks. We used a simple and general model for regulation, known as integral feedback, and showed that best-compromise systems have particular combinations of biochemical parameters that control the response rate and basal level. We find that the optimal systems fall on a curve in parameter space. Due to this feature, even if one is able to measure only a small fraction of the system's parameters, one can infer the rest. We applied this approach to estimate parameters in three biological systems: response to heat shock and response to DNA damage in bacteria, and calcium homeostasis in mammals.

  15. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary ' genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history, evolution, the evolutionary genetics of biological clocks, the evolution of ecological specialization dynamics. He.

  16. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Evolutionary systems biology of amino acid biosynthetic cost in yeast.

    Directory of Open Access Journals (Sweden)

    Michael D Barton

    2010-08-01

    Full Text Available Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental

  18. Teaching evolutionary biology

    Directory of Open Access Journals (Sweden)

    Rosana Tidon

    2004-01-01

    Full Text Available Evolutionary Biology integrates several disciplines of Biology in a complex and interactive manner, where a deep understanding of the subject demands knowledge in diverse areas. Since this knowledge is often inaccessible to the majority of specialized professionals, including the teachers, we present some reflections in order to stimulate discussions aimed at the improvement of the conditions of education in this area. We examine the profile of evolutionary teaching in Brazil, based on questionnaires distributed to teachers in Secondary Education in the Federal District, on data provided by the "National Institute for Educational Studies and Research", and on information collected from teachers working in various regions of this country. Issues related to biological misconceptions, curriculum and didactic material are discussed, and some proposals are presented with the objective of aiding discussions aimed at the improvement of the teaching of evolutionary biology.

  19. Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

    Science.gov (United States)

    O'Malley, Maureen A

    2012-01-01

    Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

  20. Evolutionary synthetic biology.

    Science.gov (United States)

    Peisajovich, Sergio G

    2012-06-15

    Signaling networks process vast amounts of environmental information to generate specific cellular responses. As cellular environments change, signaling networks adapt accordingly. Here, I will discuss how the integration of synthetic biology and directed evolution approaches is shedding light on the molecular mechanisms that guide the evolution of signaling networks. In particular, I will review studies that demonstrate how different types of mutations, from the replacement of individual amino acids to the shuffling of modular domains, lead to markedly different evolutionary trajectories and consequently to diverse network rewiring. Moreover, I will argue that intrinsic evolutionary properties of signaling proteins, such as the robustness of wild type functions, the promiscuous nature of evolutionary intermediates, and the modular decoupling between binding and catalysis, play important roles in the evolution of signaling networks. Finally, I will argue that rapid advances in our ability to synthesize DNA will radically alter how we study signaling network evolution at the genome-wide level.

  1. The cell biology of the endocytic system from an evolutionary perspective.

    Science.gov (United States)

    Wideman, Jeremy G; Leung, Ka Fai; Field, Mark C; Dacks, Joel B

    2014-04-01

    Evolutionary cell biology can afford an interdisciplinary comparative view that gives insights into both the functioning of modern cells and the origins of cellular systems, including the endocytic organelles. Here, we explore several recent evolutionary cell biology studies, highlighting investigations into the origin and diversity of endocytic systems in eukaryotes. Beginning with a brief overview of the eukaryote tree of life, we show how understanding the endocytic machinery in a select, but diverse, array of organisms provides insights into endocytic system origins and predicts the likely configuration in the last eukaryotic common ancestor (LECA). Next, we consider three examples in which a comparative approach yielded insight into the function of modern cellular systems. First, using ESCRT-0 as an example, we show how comparative cell biology can discover both lineage-specific novelties (ESCRT-0) as well as previously ignored ancient proteins (Tom1), likely of both evolutionary and functional importance. Second, we highlight the power of comparative cell biology for discovery of previously ignored but potentially ancient complexes (AP5). Finally, using examples from ciliates and trypanosomes, we show that not all organisms possess canonical endocytic pathways, but instead likely evolved lineage-specific mechanisms. Drawing from these case studies, we conclude that a comparative approach is a powerful strategy for advancing knowledge about the general mechanisms and functions of endocytic systems.

  2. Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems

    Science.gov (United States)

    Carroll, Scott P

    2011-01-01

    Biotic invaders and similar anthropogenic novelties such as domesticates, transgenics, and cancers can alter ecology and evolution in environmental, agricultural, natural resource, public health, and medical systems. The resulting biological changes may either hinder or serve management objectives. For example, biological control and eradication programs are often defeated by unanticipated resistance evolution and by irreversibility of invader impacts. Moreover, eradication may be ill-advised when nonnatives introduce beneficial functions. Thus, contexts that appear to call for eradication may instead demand managed coexistence of natives with nonnatives, and yet applied biologists have not generally considered the need to manage the eco-evolutionary dynamics that commonly result from interactions of natives with nonnatives. Here, I advocate a conciliatory approach to managing systems where novel organisms cannot or should not be eradicated. Conciliatory strategies incorporate benefits of nonnatives to address many practical needs including slowing rates of resistance evolution, promoting evolution of indigenous biological control, cultivating replacement services and novel functions, and managing native–nonnative coevolution. Evolutionary links across disciplines foster cohesion essential for managing the broad impacts of novel biotic systems. Rather than signaling defeat, conciliation biology thus utilizes the predictive power of evolutionary theory to offer diverse and flexible pathways to more sustainable outcomes. PMID:25567967

  3. Outline of a unified Darwinian evolutionary theory for physical and biological systems.

    Science.gov (United States)

    Baladrón, Carlos; Khrennikov, Andrei

    2017-11-01

    The scheme of a unified Darwinian evolutionary theory for physical and biological systems is described. Every physical system is methodologically endowed with a classical information processor, which turns every system into an agent being also susceptible to evolution. Biological systems retain this structure as natural extensions of physical systems from which they are built up. Optimization of information flows turns out to be the key element to study the possible emergence of quantum behavior and the unified Darwinian description of physical and biological systems. The Darwinian natural selection scheme is completed by the Lamarckian component in the form of the anticipation of states of surrounding bio-physical systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Can systems biology help to separate evolutionary analogies (convergent homoplasies) from homologies?

    Science.gov (United States)

    Gordon, Malcolm S; Notar, Julia C

    2015-01-01

    Convergent evolutionary analogies (homoplasies) of many kinds occur in diverse phylogenetic clades/lineages on both the animal and plant branches of the Tree of Life. Living organisms whose last common ancestors lived millions to hundreds of millions of years ago have later converged morphologically, behaviorally or at other levels of functionality (from molecular genetics through biochemistry, physiology and other organismic processes) as a result of long term strong natural selection that has constrained and channeled evolutionary processes. This happens most often when organisms belonging to different clades occupy ecological niches, habitats or environments sharing major characteristics that select for a relatively narrow range of organismic properties. Systems biology, broadly defined, provides theoretical and methodological approaches that are beginning to make it possible to answer a perennial evolutionary biological question relating to convergent homoplasies: Are at least some of the apparent analogies actually unrecognized homologies? This review provides an overview of the current state of knowledge of important aspects of this topic area. It also provides a resource describing many homoplasies that may be fruitful subjects for systems biological research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Evolutionary biology redux.

    Science.gov (United States)

    Torday, John S

    2013-01-01

    This article offers a novel, enlightened concept for determining the mechanism of evolution. It is based on homeostasis, which distinguishes life from non-life and as such is the universal mechanism for the evolution of all living organisms. This view of evolution is logical, mechanistic, non-scalar, predictive, testable, and falsifiable, and it illuminates the epistemological relationships between physics and biology, ontogeny and phylogeny, development and aging, ultimate and proximate causation, health and disease. In addition to validating Haeckel's biogenetic law and Lamarckian epigenetics, reflecting the enabling value of the cellular approach, this perspective also expresses the evolutionary process at the cell-molecular level, since the mechanism of cell communication itself is universal in biology, in keeping with a Kuhnian paradigm shift. This approach may even elucidate the nature and evolution of consciousness as a manifestation of the cellular continuum from unicellular to multicellular life. We need such a functional genomic mechanism for the process of evolution if we are to make progress in biology and medicine. Like Copernican heliocentrism, a cellular approach to evolution may fundamentally change humankind's perceptions about our place in the universe.

  6. Comparative genomics and evolutionary biology.

    Science.gov (United States)

    Kondrashov, A S

    1999-12-01

    Data of large-scale DNA sequencing are relevant to some of the most fundamental issues in evolutionary biology: suboptimality, homology, hierarchy, ancestry, novelties, the role of natural selection, and the relative importance of directional versus stabilizing selection. Already, these data provided the best available evidence for some evolutionary phenomena, and in several cases led to refinement of old concepts. Still, the Darwinian evolutionary paradigm will successfully accommodate comparative genomics.

  7. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  8. Evolutionary transition from biological to social systems via generation of reflexive models of externality.

    Science.gov (United States)

    Igamberdiev, Abir U

    2017-12-01

    Evolutionary transition from biological to social systems corresponds to the emergence of the structure of subject that incorporates the internal image of the external world. This structure, established on the basis of referral of the subject (self) to its symbolic image, acquires a potential to rationally describe the external world through the semiotic structure of human language. It has been modelled in reflexive psychology using the algebra of simple relations (Lefebvre, V.A., J. Soc. Biol. Struct. 10, 129-175, 1987). The model introduces a substantial opposition of the two basic complementary types of reflexion defined as Western (W) and Eastern (E). These types generate opposite models of behavior and opposite organizations of societies. Development of human societies involves the interactions of W and E types not only between the societies but also within one society underlying its homeostasis and dynamics. Invention of new ideas and implementation of new technologies shift the probability pattern of reflexive choices, appearing as internal assessments of the individual agents within a society, and direct changes in the preference of reflexive types. The dynamics of societies and of interactions between societies is based on the interference of opposite reflexive structures and on the establishment of different patterns during such interference. At different times in the history of human civilization these changing patterns resulted in the formation and splitting of large empires, the development and spreading of new technologies, the consecutive periods of wellness and decline. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Never in neutral: a systems biology and evolutionary perspective on how aneuploidy contributes to human diseases.

    Science.gov (United States)

    Pavelka, N; Rancati, G

    2013-01-01

    Whereas germline-inherited whole-chromosome aneuploidy has long been known to cause miscarriages and developmental abnormalities, somatically acquired aneuploidies have been observed in cancer cells and more recently also in cells of the normal liver and brain. Furthermore, aneuploidy is being increasingly reported in clinical isolates of pathogenic microbes such as fungi and parasites. Whereas many efforts have been devoted to the dissection of the molecular mechanisms that lead to aneuploidy, we have only recently started to investigate how aneuploidy alters the phenotypic makeup of a cell. Here we review recent evidence supporting the idea that aneuploidy is a large-effect mutation that introduces large changes in the cellular phenome. From a systems biology perspective, this can be explained by the extensive changes that aneuploidy brings about in both the transcriptome and the proteome of a cell. We further provide an evolutionary perspective on how aneuploidy-induced phenotypic variation may contribute to the exacerbation of human pathologies such as cancer and infectious diseases, by conferring selectable traits such as increased virulence and drug resistance. Copyright © 2013 S. Karger AG, Basel.

  10. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  11. Is evolutionary biology strategic science?

    Science.gov (United States)

    Meagher, Thomas R

    2007-01-01

    There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field.

  12. Quantum Mechanics predicts evolutionary biology.

    Science.gov (United States)

    Torday, J S

    2018-01-11

    Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018. Published by Elsevier Ltd.

  13. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  14. What's wrong with evolutionary biology?

    Science.gov (United States)

    Welch, John J

    2017-01-01

    There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.

  15. Artificial Neural Networks, and Evolutionary Algorithms as a systems biology approach to a data-base on fetal growth restriction.

    Science.gov (United States)

    Street, Maria E; Buscema, Massimo; Smerieri, Arianna; Montanini, Luisa; Grossi, Enzo

    2013-12-01

    One of the specific aims of systems biology is to model and discover properties of cells, tissues and organisms functioning. A systems biology approach was undertaken to investigate possibly the entire system of intra-uterine growth we had available, to assess the variables of interest, discriminate those which were effectively related with appropriate or restricted intrauterine growth, and achieve an understanding of the systems in these two conditions. The Artificial Adaptive Systems, which include Artificial Neural Networks and Evolutionary Algorithms lead us to the first analyses. These analyses identified the importance of the biochemical variables IL-6, IGF-II and IGFBP-2 protein concentrations in placental lysates, and offered a new insight into placental markers of fetal growth within the IGF and cytokine systems, confirmed they had relationships and offered a critical assessment of studies previously performed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Making evolutionary biology a basic science for medicine

    Science.gov (United States)

    Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

    2010-01-01

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

  17. Evolutionary Biology Needs Wild Microbiomes.

    Science.gov (United States)

    Hird, Sarah M

    2017-01-01

    The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.

  18. Comparative systems biology across an evolutionary gradient within the Shewanella genus

    Energy Technology Data Exchange (ETDEWEB)

    Konstantinidis, Kostas; Serres, Margrethe H.; Romine, Margaret F.; Rodrigues, Jorge L.M.; Auchutung, Jennifer M.; McCue, Lee Ann; Lipton, Mary S.; Obraztsova, Anna; Giometti, Carol S.; Nealson, Kenneth H.; Fredrickson, Jim K.; Tiedje, James M.

    2009-09-15

    To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology such as the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of ten closely related Shewanella organisms to provide quantitative insights into this issue. Our analyses revealed that, despite the extensive horizontal gene transfer characterizing these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended, however, on the degree of ecological specialization of the organisms evaluated. Using the unprecedented genetic gradient formed by these genomes, we were able to isolate the effect of ecology from the effect of evolutionary divergence and rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms when grown under identical conditions were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information towards beginning a system level understanding of bacterial species and genera.

  19. Evolutionary problems in centrosome and centriole biology.

    Science.gov (United States)

    Ross, L; Normark, B B

    2015-05-01

    Centrosomes have been an enigma to evolutionary biologists. Either they have been the subject of ill-founded speculation or they have been ignored. Here, we highlight evolutionary paradoxes and problems of centrosome and centriole evolution and seek to understand them in the light of recent advances in centrosome biology. Most evolutionary accounts of centrosome evolution have been based on the hypothesis that centrosomes are replicators, independent of the nucleus and cytoplasm. It is now clear, however, that this hypothesis is not tenable. Instead, centrosomes are formed de novo each cell division, with the presence of an old centrosome regulating, but not essential for, the assembly of a new one. Centrosomes are the microtubule-organizing centres of cells. They can potentially affect sensory and motor characters (as the basal body of cilia), as well as the movements of chromosomes during cell division. This latter role does not seem essential, however, except in male meiosis, and the reasons for this remain unclear. Although the centrosome is absent in some taxa, when it is present, its structure is extraordinarily conserved: in most taxa across eukaryotes, it does not appear to evolve at all. And yet a few insect groups display spectacular hypertrophy of the centrioles. We discuss how this might relate to the unusual reproductive system found in these insects. Finally, we discuss why the fate of centrosomes in sperm and early embryos might differ between different groups of animals. © 2015 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

  20. Evolutionary developmental biology its roots and characteristics.

    Science.gov (United States)

    Morange, Michel

    2011-09-01

    The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Evolutionary Biology in the Medical School Curriculum.

    Science.gov (United States)

    Neese, Randolph M.; Schiffman, Joshua D.

    2003-01-01

    Presents a study in which a questionnaire was given to deans at North American medical schools to determine which aspects of evolutionary biology are included in the curricula and the factors that influence this. Suggests that most future physicians should learn evolutionary biology as undergraduates if they are to learn it at all. (Author/NB)

  2. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  3. Evolutionary cell biology: two origins, one objective.

    Science.gov (United States)

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-02

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  4. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  5. Introducing Flexibility to Complex, Resilient Socio-Ecological Systems: A Comparative Analysis of Economics, Flexible Manufacturing Systems, Evolutionary Biology, and Supply Chain Management

    Directory of Open Access Journals (Sweden)

    Vivek Anand Asokan

    2017-06-01

    Full Text Available In this paper, a framework incorporating flexibility as a characteristic is proposed for designing complex, resilient socio-ecological systems. In an interconnected complex system, flexibility allows prompt deployment of resources where they are needed and is crucial for both innovation and robustness. A comparative analysis of flexible manufacturing systems, economics, evolutionary biology, and supply chain management is conducted to identify the most important characteristics of flexibility. Evolutionary biology emphasises overlapping functions and multi-functionality, which allow a system with structurally different elements to perform the same function, enhancing resilience. In economics, marginal cost and marginal expected profit are factors that are considered to be important in incorporating flexibility while making changes to the system. In flexible manufacturing systems, the size of choice sets is important in creating flexibility, as initial actions preserve more options for future actions that will enhance resilience. Given the dynamic nature of flexibility, identifying the characteristics that can lead to flexibility will introduce a crucial dimension to designing resilient and sustainable socio-ecological systems with a long-term perspective in mind.

  6. the evolutionary biology and biotechnology applications of ...

    Indian Academy of Sciences (India)

    play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These ... [Bonchev G. N. 2016 Useful parasites: the evolutionary biology and biotechnology applications of transposable elements. J. Genet. ... update of the plant genome size database containing data for.

  7. Evolutionary Biology Instruction: What Students Gain from Learning through Inquiry.

    Science.gov (United States)

    Dremock, Fae, Ed.

    2002-01-01

    This bulletin features articles on real world evolutionary biology, revolutionary classroom science, a review of new curricula in evolutionary biology, and the use of case studies to illustrate points in evolutionary biology. The articles are: (1) "'Real World' Evolutionary Biology: A Pragmatic Quest. Interview with BioQUEST's John Jungck" (Harvey…

  8. Evolutionary biology of centipedes (Myriapoda: Chilopoda).

    Science.gov (United States)

    Edgecombe, Gregory D; Giribet, Gonzalo

    2007-01-01

    New insights into the anatomy, systematics, and biogeography of centipedes have put these predatory terrestrial arthropods at the forefront of evolutionary studies. Centipedes have also played a pivotal role in understanding high-level arthropod relationships. Their deep evolutionary history, with a fossil record spanning 420 million years, explains their current worldwide distribution. Recent analyses of combined morphological and molecular data provide a stable phylogeny that underpins evolutionary interpretations of their biology. The centipede trunk, with its first pair of legs modified into a venom-delivering organ followed by 15 to 191 leg pairs, is a focus of arthropod segmentation studies. Gene expression studies and phylogenetics shed light on key questions in evolutionary developmental biology concerning the often group-specific fixed number of trunk segments, how some centipedes add segments after hatching whereas others hatch with the complete segment count, the addition of segments through evolution, and the invariably odd number of leg-bearing trunk segments.

  9. Evolutionary biology of harvestmen (Arachnida, Opiliones).

    Science.gov (United States)

    Giribet, Gonzalo; Sharma, Prashant P

    2015-01-07

    Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.

  10. Evolutionary Biology: Its Value to Society

    Science.gov (United States)

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  11. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology.

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties observed in biological systems at different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be enough to confer intrinsic robustness in order to tolerate intrinsic parameter fluctuations, genetic robustness for buffering genetic variations, and environmental robustness for resisting environmental disturbances. With this, the phenotypic stability of biological network can be maintained, thus guaranteeing phenotype robustness. This paper presents a survey on biological systems and then develops a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation in systems and evolutionary biology. Further, from the unifying mathematical framework, it was discovered that the phenotype robustness criterion for biological networks at different levels relies upon intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness. When this is true, the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in systems and evolutionary biology can also be investigated through their corresponding phenotype robustness criterion from the systematic point of view.

  12. Evolutionary perspectives into placental biology and disease.

    Science.gov (United States)

    Chuong, Edward B; Hannibal, Roberta L; Green, Sherril L; Baker, Julie C

    2013-12-01

    In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.

  13. Evolutionary perspectives into placental biology and disease

    Directory of Open Access Journals (Sweden)

    Edward B. Chuong

    2013-12-01

    Full Text Available In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal–fetal conflict shapes both basic placental and reproductive biology – in all species – will provide key insights into diseases of pregnancy.

  14. The future of evolutionary developmental biology.

    Science.gov (United States)

    Holland, P W

    1999-12-02

    Combining fields as diverse as comparative embryology, palaeontology, molecular phylogenetics and genome analysis, the new discipline of evolutionary developmental biology aims at explaining how developmental processes and mechanisms become modified during evolution, and how these modifications produce changes in animal morphology and body plans. In the next century this should give us far greater mechanistic insight into how evolution has produced the vast diversity of living organisms, past and present.

  15. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  16. Language as an evolutionary system

    Science.gov (United States)

    Brighton, Henry; Smith, Kenny; Kirby, Simon

    2005-09-01

    John Maynard Smith and Eörs Szathmáry argued that human language signified the eighth major transition in evolution: human language marked a new form of information transmission from one generation to another [Maynard Smith J, Szathmáry E. The major transitions in evolution. Oxford: Oxford Univ. Press; 1995]. According to this view language codes cultural information and as such forms the basis for the evolution of complexity in human culture. In this article we develop the theory that language also codes information in another sense: languages code information on their own structure. As a result, languages themselves provide information that influences their own survival. To understand the consequences of this theory we discuss recent computational models of linguistic evolution. Linguistic evolution is the process by which languages themselves evolve. This article draws together this recent work on linguistic evolution and highlights the significance of this process in understanding the evolution of linguistic complexity. Our conclusions are that: (1) the process of linguistic transmission constitutes the basis for an evolutionary system, and (2), that this evolutionary system is only superficially comparable to the process of biological evolution.

  17. Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

    Science.gov (United States)

    Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

    2010-01-26

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

  18. An extended synthesis for evolutionary biology.

    Science.gov (United States)

    Pigliucci, Massimo

    2009-06-01

    Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo-devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that--like its predecessor--will probably take decades to complete.

  19. Colour spaces in ecology and evolutionary biology.

    Science.gov (United States)

    Renoult, Julien P; Kelber, Almut; Schaefer, H Martin

    2017-02-01

    The recognition that animals sense the world in a different way than we do has unlocked important lines of research in ecology and evolutionary biology. In practice, the subjective study of natural stimuli has been permitted by perceptual spaces, which are graphical models of how stimuli are perceived by a given animal. Because colour vision is arguably the best-known sensory modality in most animals, a diversity of colour spaces are now available to visual ecologists, ranging from generalist and basic models allowing rough but robust predictions on colour perception, to species-specific, more complex models giving accurate but context-dependent predictions. Selecting among these models is most often influenced by historical contingencies that have associated models to specific questions and organisms; however, these associations are not always optimal. The aim of this review is to provide visual ecologists with a critical perspective on how models of colour space are built, how well they perform and where their main limitations are with regard to their most frequent uses in ecology and evolutionary biology. We propose a classification of models based on their complexity, defined as whether and how they model the mechanisms of chromatic adaptation and receptor opponency, the nonlinear association between the stimulus and its perception, and whether or not models have been fitted to experimental data. Then, we review the effect of modelling these mechanisms on predictions of colour detection and discrimination, colour conspicuousness, colour diversity and diversification, and for comparing the perception of colour traits between distinct perceivers. While a few rules emerge (e.g. opponent log-linear models should be preferred when analysing very distinct colours), in general model parameters still have poorly known effects. Colour spaces have nonetheless permitted significant advances in ecology and evolutionary biology, and more progress is expected if ecologists

  20. Evolutionary explanations for natural language: criteria from evolutionary biology

    NARCIS (Netherlands)

    Zuidema, W.; de Boer, B.

    2008-01-01

    Theories of the evolutionary origins of language must be informed by empirical and theoretical results from a variety of different fields. Complementing recent surveys of relevant work from linguistics, animal behaviour and genetics, this paper surveys the requirements on evolutionary scenarios that

  1. The state of software for evolutionary biology.

    Science.gov (United States)

    Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

    2018-01-29

    With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C ++ (e.g., MrBayes, MAFFT, SweepFinder etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Since, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Evolutionary biology through the lens of budding yeast comparative genomics.

    Science.gov (United States)

    Marsit, Souhir; Leducq, Jean-Baptiste; Durand, Éléonore; Marchant, Axelle; Filteau, Marie; Landry, Christian R

    2017-10-01

    The budding yeast Saccharomyces cerevisiae is a highly advanced model system for studying genetics, cell biology and systems biology. Over the past decade, the application of high-throughput sequencing technologies to this species has contributed to this yeast also becoming an important model for evolutionary genomics. Indeed, comparative genomic analyses of laboratory, wild and domesticated yeast populations are providing unprecedented detail about many of the processes that govern evolution, including long-term processes, such as reproductive isolation and speciation, and short-term processes, such as adaptation to natural and domestication-related environments.

  3. Toward an integration of evolutionary biology and ecosystem science.

    Science.gov (United States)

    Matthews, Blake; Narwani, Anita; Hausch, Stephen; Nonaka, Etsuko; Peter, Hannes; Yamamichi, Masato; Sullam, Karen E; Bird, Kali C; Thomas, Mridul K; Hanley, Torrance C; Turner, Caroline B

    2011-07-01

    At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes. © 2011 Blackwell Publishing Ltd/CNRS.

  4. The tragedy of the commons in evolutionary biology.

    OpenAIRE

    Rankin DJ; Bargum K; Kokko H.

    2007-01-01

    Garrett Hardin's tragedy of the commons is an analogy that shows how individuals driven by self-interest can end up destroying the resource upon which they all depend. The proposed solutions for humans rely on highly advanced skills such as negotiation, which raises the question of how non-human organisms manage to resolve similar tragedies. In recent years, this question has promoted evolutionary biologists to apply the tragedy of the commons to a wide range of biological systems. Here, we p...

  5. The Best and the Worst of Times for Evolutionary Biology.

    Science.gov (United States)

    Avise, John C.

    2003-01-01

    Discusses opportunities and challenges for the field of evolutionary biology, particularly in areas related to molecular genetic technologies, the environment, biodiversity, and public education. (Author/KHR)

  6. Engineering reduced evolutionary potential for synthetic biology.

    Science.gov (United States)

    Renda, Brian A; Hammerling, Michael J; Barrick, Jeffrey E

    2014-07-01

    The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales.

  7. Evolutionary biology of bacterial and fungal pathogens

    National Research Council Canada - National Science Library

    Baquero, F

    2008-01-01

    ... and Evolutionary Dynamics of Pathogens * 21 Keith A. Crandall and Marcos Pérez-Losada II. Evolutionary Genetics of Microbial Pathogens 4. Environmental and Social Influences on Infectious Disea...

  8. A Modeling Approach to Teaching Evolutionary Biology in High Schools.

    Science.gov (United States)

    Passmore, Cynthia; Stewart, Jim

    2002-01-01

    Describes the commitments and research that went into the design of a 9-week high school course in evolutionary biology designed to bring students to an understanding of the practice of evolutionary biology by engaging them in developing, elaborating, and using one of the discipline's most important explanatory models. (Contains 39 references.)…

  9. Evolutionary Ideas Held by Experienced South African Biology Teachers

    Science.gov (United States)

    Kyriacou, Xenia; de Beer, Josef; Ramnarain, Umesh

    2015-01-01

    With evolutionary biology relatively recently introduced into the South African school curriculum, the need arose to explore practising teachers' knowledge of the subject. A number of anticipated as well as unanticipated cognitive and affective barriers to the understanding of evolutionary biology were identified from a questionnaire with…

  10. What have humans done for evolutionary biology? Contributions from genes to populations.

    Science.gov (United States)

    Briga, Michael; Griffin, Robert M; Berger, Vérane; Pettay, Jenni E; Lummaa, Virpi

    2017-11-15

    Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. © 2017 The Author(s).

  11. Michael Akam and the rise of evolutionary developmental biology.

    Science.gov (United States)

    Stern, David L; Dawes-Hoang, Rachel E

    2010-01-01

    Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michaels contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologists.

  12. Democratizing evolutionary biology, lessons from insects

    DEFF Research Database (Denmark)

    Dunn, Robert Roberdeau; Beasley, DeAnna E.

    2016-01-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This ...

  13. Evolutionary Information System Development

    DEFF Research Database (Denmark)

    Kristensen, Jan

    This paper offers advice to companies and professionals that implement e-commerce systems in business organizations. Implementing e-commerce systems is different from traditional IT implementation and thus requires a new set of tools and skills. The need for a novel approach is illustrated...... of business priorities. On a more theoretical level this suggests that we must revise our current understanding of systems development to cope....

  14. Developmental dynamics: toward a biologically plausible evolutionary psychology.

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    There has been a conceptual revolution in the biological sciences over the past several decades. Evidence from genetics, embryology, and developmental biology has converged to offer a more epigenetic, contingent, and dynamic view of how organisms develop. Despite these advances, arguments for the heuristic value of a gene-centered, predeterministic approach to the study of human behavior and development have become increasingly evident in the psychological sciences during this time. In this article, the authors review recent advances in genetics, embryology, and developmental biology that have transformed contemporary developmental and evolutionary theory and explore how these advances challenge gene-centered explanations of human behavior that ignore the complex, highly coordinated system of regulatory dynamics involved in development and evolution.

  15. Regulatory Evolution and Theoretical Arguments in Evolutionary Biology

    Science.gov (United States)

    Ioannidis, Stavros

    2013-01-01

    The "cis"-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for "cis"-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current…

  16. Useful parasites: the evolutionary biology and biotechnology ...

    Indian Academy of Sciences (India)

    , transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we ... research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  17. Evolutionary biology as a link between religion and knowledge

    Directory of Open Access Journals (Sweden)

    C. W. du Toit

    2000-01-01

    Full Text Available It would appear that the epistemological tradition of the West is culminating in the present science-religion debate. The evolutionary model is being used increasingly in different disciplines as a guideline to understand humans and their action in the world. The struggle for explaining the action of God has shifted from the world of history and texts to the invisible level of quantum physics and molecular biology. It seems that levels of indeterminacy in quantum mechanics and autopoietic systems offer space to explain the action of God. On the human level integrity is sought by linking the highest level of consciousness and rationality to the very basic level of molecular and genetic structures. These issues are dealt with and specific attention is given to autopoietic systems and the biological roots of rationality.

  18. Zebrafish Xenograft: An Evolutionary Experiment in Tumour Biology.

    Science.gov (United States)

    Wyatt, Rachael A; Trieu, Nhu P V; Crawford, Bryan D

    2017-09-05

    Though the cancer research community has used mouse xenografts for decades more than zebrafish xenografts, zebrafish have much to offer: they are cheap, easy to work with, and the embryonic model is relatively easy to use in high-throughput assays. Zebrafish can be imaged live, allowing us to observe cellular and molecular processes in vivo in real time. Opponents dismiss the zebrafish model due to the evolutionary distance between zebrafish and humans, as compared to mice, but proponents argue for the zebrafish xenograft's superiority to cell culture systems and its advantages in imaging. This review places the zebrafish xenograft in the context of current views on cancer and gives an overview of how several aspects of this evolutionary disease can be addressed in the zebrafish model. Zebrafish are missing homologs of some human proteins and (of particular interest) several members of the matrix metalloproteinase (MMP) family of proteases, which are known for their importance in tumour biology. This review draws attention to the implicit evolutionary experiment taking place when the molecular ecology of the xenograft host is significantly different than that of the donor.

  19. Democratizing evolutionary biology, lessons from insects.

    Science.gov (United States)

    Dunn, Robert R; Beasley, DeAnna E

    2016-12-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This review highlights how insect-based citizen science has led to the expansion of specimen collections and reframed research questions in light of new observations and unexpected discoveries. Given the rapid expansion of human-modified (and inhabited) environments, the degree to which the public can participate in insect-based citizen science will allow us to track and monitor evolutionary trends at a global scale. Copyright © 2016. Published by Elsevier Inc.

  20. Indoor Thermal Comfort, an Evolutionary Biology Perspective

    Energy Technology Data Exchange (ETDEWEB)

    Stoops, John L.

    2006-04-15

    As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?

  1. the evolutionary biology and biotechnology applications of ...

    Indian Academy of Sciences (India)

    of many genetic disorders, such as haemophilia A, Apert syndrome .... Examples of adaptive mutations and exaptations provided by transposable elements. .... adaptive variation. However, such surveys should be under- taken in a wider range of species to reliably estimate the impact of TEs on their evolutionary ecology.

  2. Evolutionary convergence and biologically embodied cognition

    NARCIS (Netherlands)

    Keijzer, Franciscus

    2017-01-01

    The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in

  3. Evolutionary Autonomous Health Monitoring System (EAHMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — For supporting NASA's Robotics, Tele-Robotics and Autonomous Systems Roadmap, we are proposing the "Evolutionary Autonomous Health Monitoring System" (EAHMS) for...

  4. Bridging developmental systems theory and evolutionary psychology using dynamic optimization.

    Science.gov (United States)

    Frankenhuis, Willem E; Panchanathan, Karthik; Clark Barrett, H

    2013-07-01

    Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic optimization integrates developmental systems theorists' focus on dynamics and contingency with the 'design stance' of evolutionary psychology. It provides a theoretical framework as well as a set of tools for exploring the properties of developmental systems that natural selection might favor, given particular evolutionary ecologies. We also discuss limitations of the approach. © 2013 Blackwell Publishing Ltd.

  5. Women in evolution - highlighting the changing face of evolutionary biology.

    Science.gov (United States)

    Wellenreuther, Maren; Otto, Sarah

    2016-01-01

    The face of science has changed. Women now feature alongside men at the forefront of many fields, and this is particularly true in evolutionary biology. This special issue celebrates the outstanding achievements and contributions of women in evolutionary biology, by highlighting a sample of their research and accomplishments. In addition to original research contributions, this collection of articles contains personal reflections to provide perspective and advice on succeeding as a woman in science. By showcasing the diversity and research excellence of women and drawing on their experiences, we wish to enhance the visibility of female scientists and provide inspiration as well as role models. These are exciting times for evolutionary biology, and the field is richer and stronger for the diversity of voices contributing to the field.

  6. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Cognitive innovations and the evolutionary biology of expertise.

    Science.gov (United States)

    Dukas, Reuven

    2017-12-05

    Animal life can be perceived as the selective use of information for maximizing survival and reproduction. All organisms including bacteria and protists rely on genetic networks to build and modulate sophisticated structures and biochemical mechanisms for perceiving information and responding to environmental changes. Animals, however, have gone through a series of innovations that dramatically increased their capacity to acquire, retain and act upon information. Multicellularity was associated with the evolution of the nervous system, which took over many tasks of internal communication and coordination. This paved the way for the evolution of learning, initially based on individual experience and later also via social interactions. The increased importance of social learning also led to the evolution of language in a single lineage. Individuals' ability to dramatically increase performance via learning may have led to an evolutionary cycle of increased lifespan and greater investment in cognitive abilities, as well as in the time necessary for the development and refinement of expertise. We still know little, however, about the evolutionary biology, genetics and neurobiological mechanisms that underlie such expertise and its development.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

  8. Measuring the evolutionary rewiring of biological networks.

    Directory of Open Access Journals (Sweden)

    Chong Shou

    Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

  9. Evolutionary crossroads in developmental biology: annelids.

    Science.gov (United States)

    Ferrier, David E K

    2012-08-01

    Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology. With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen. As one of the major phyla within Lophotrochozoa, Annelida are playing an important role in deducing the developmental biology of the last common ancestor of the protostomes and deuterostomes, an animal from which >98% of all described animal species evolved.

  10. Evolutionary game theory as a framework for studying biological invasions.

    Science.gov (United States)

    Pintor, Lauren M; Brown, Joel S; Vincent, Thomas L

    2011-04-01

    Although biological invasions pose serious threats to biodiversity, they also provide the opportunity to better understand interactions between the ecological and evolutionary processes structuring populations and communities. However, ecoevolutionary frameworks for studying species invasions are lacking. We propose using game theory and the concept of an evolutionarily stable strategy (ESS) as a conceptual framework for integrating the ecological and evolutionary dynamics of invasions. We suggest that the pathways by which a recipient community may have no ESS provide mechanistic hypotheses for how such communities may be vulnerable to invasion and how invaders can exploit these vulnerabilities. We distinguish among these pathways by formalizing the evolutionary contexts of the invader relative to the recipient community. We model both the ecological and the adaptive dynamics of the interacting species. We show how the ESS concept provides new mechanistic hypotheses for when invasions result in long- or short-term increases in biodiversity, species replacement, and subsequent evolutionary changes.

  11. The evolutionary biology of dance without frills.

    Science.gov (United States)

    Ravignani, Andrea; Cook, Peter F

    2016-10-10

    Recently psychologists have taken up the question of whether dance is reliant on unique human adaptations, or whether it is rooted in neural and cognitive mechanisms shared with other species [1,2]. In its full cultural complexity, human dance clearly has no direct analog in animal behavior. Most definitions of dance include the consistent production of movement sequences timed to an external rhythm. While not sufficient for dance, modes of auditory-motor timing, such as synchronization and entrainment, are experimentally tractable constructs that may be analyzed and compared between species. In an effort to assess the evolutionary precursors to entrainment and social features of human dance, Laland and colleagues [2] have suggested that dance may be an incidental byproduct of adaptations supporting vocal or motor imitation - referred to here as the 'imitation and sequencing' hypothesis. In support of this hypothesis, Laland and colleagues rely on four convergent lines of evidence drawn from behavioral and neurobiological research on dance behavior in humans and rhythmic behavior in other animals. Here, we propose a less cognitive, more parsimonious account for the evolution of dance. Our 'timing and interaction' hypothesis suggests that dance is scaffolded off of broadly conserved timing mechanisms allowing both cooperative and antagonistic social coordination. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:

  13. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    during his life that spanned a century, Ernst Mayr (1904-2005) made outstanding contributions to our understanding of the pat- tern and process of evolution. An ornithologist and systematist by training, Mayr embraced Darwinism and championed the cause of evolutionary biology throughout his long and highly productive.

  14. Biochemistry and evolutionary biology: Two disciplines that need ...

    Indian Academy of Sciences (India)

    Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the ...

  15. Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws

    NARCIS (Netherlands)

    Van Hezewijk, René

    2008-01-01

    Published as a chapter in Van Hezewijk, R. (2003). Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws. In N. Stephenson, L. Radtke, R. Jorna & H. J. Stam (Eds.), Theoretical psychology; Critical contributions (pp. 405-415). Concord, Ontario: Captus Press.

  16. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  17. Teaching evolutionary biology: Pressures, stress, and coping

    Science.gov (United States)

    Griffith, Joyce A.; Brem, Sarah K.

    2004-10-01

    Understanding what teachers need to be more comfortable and confident in their profession is crucial to the future of effective teachers and scientific literacy in public schools. This study focuses on the experiences of Arizona biology teachers in teaching evolution, using a clinical model of stress to identify sources of pressure, the resulting stresses, and coping strategies they employ to alleviate these stresses. We conducted focus groups, one-on-one interviews, and written surveys with 15 biology teachers from the Phoenix area. On the basis of their responses, teachers were clustered into three categories: Conflicted, who struggle with their own beliefs and the possible impact of their teaching, Selective, who carefully avoid difficult topics and situations, and Scientists, who see no place for controversial social issues in their science classroom. Teachers from each group felt that they could be more effective in teaching evolution if they possessed the most up-to-date information about evolution and genomics, a safe space in which to reflect on the possible social and personal implications with their peers, and access to richer lesson plans for teaching evolution that include not only science but personal stories regarding how the lessons arose, and what problems and opportunities they created.

  18. [Evolutionary medicine: an introduction. Evolutionary biology, a missing element in medical teaching].

    Science.gov (United States)

    Swynghedauw, Bernard

    2009-05-01

    The aim of this brief review article is to help to reconcile medicine with evolutionary biology, a subject that should be taught in medical school. Evolutionary medicine takes the view that contemporary ills are related to an incompatibility between the environment in which humans currently live and their genomes, which have been shaped by diferent environmental conditions during biological evolution. Human activity has recently induced acute environmental modifications that have profoundly changed the medical landscape. Evolutionary biology is an irreversible, ongoing and discontinuous process characterized by periods of stasis followed by accelerations. Evolutionary biology is determined by genetic mutations, which are selected either by Darwinian selective pressure or randomly by genetic drift. Most medical events result from a genome/environment conflict. Some may be purely genetic, as in monogenic diseases, and others purely environmental, such as traffic accidents. Nevertheless, in most common diseases the clinical landscape is determined by the conflict between these two factors, the genetic elements of which are gradually being unraveled Three examples are examined in depth:--The medical consequences of the greenhouse effect. The absence of excess mortality during recent heat waves suggests that the main determinant of mortality in the 2003 heatwave was heatstroke and old age. The projected long-term effects of global warming call for research on thermolysis, a forgotten branch of physiology.--The hygiene hypothesis postulates that the exponential rise in autoimmune and allergic diseases is linked to lesser exposure to infectious agents, possibly involving counter-regulatory factors such as IL-10.--The recent rise in the incidence of obesity and type 2 diabetes in rich countries can be considered to result from a conflict between a calorie-rich environment and gene variants that control appetite. These variants are currently being identified by genome

  19. Evolution, Science and Society: Evolutionary Biology and the National Research Agenda.

    Science.gov (United States)

    Futuyma, Douglas J.; Meagher, Thomas R.

    2001-01-01

    Discusses ways of advancing understanding of evolutionary biology which seeks to explain all the characteristics of organisms. Describes the goals of evolutionary biology, why it is important, and how it contributes to society and basic science. (ASK)

  20. phyloXML: XML for evolutionary biology and comparative genomics.

    Science.gov (United States)

    Han, Mira V; Zmasek, Christian M

    2009-10-27

    Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

  1. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    consisting of differential equations describing the rate of change of concentration of each of the metabolites can be constructed. Such a system of equations can then be solved to obtain insights about the essentiality of each component. For example, a math- ematical model of glycolysis in T. brucei has been built, based on.

  2. Integrating Functional, Developmental and Evolutionary Biology into Biology Curricula

    Science.gov (United States)

    Haave, Neil

    2012-01-01

    A complete understanding of life involves how organisms are able to function in their environment and how they arise. Understanding how organisms arise involves both their evolution and development. Thus to completely comprehend living things, biology must study their function, development and evolution. Previous proposals for standardized…

  3. Fewer invited talks by women in evolutionary biology symposia.

    Science.gov (United States)

    Schroeder, J; Dugdale, H L; Radersma, R; Hinsch, M; Buehler, D M; Saul, J; Porter, L; Liker, A; De Cauwer, I; Johnson, P J; Santure, A W; Griffin, A S; Bolund, E; Ross, L; Webb, T J; Feulner, P G D; Winney, I; Szulkin, M; Komdeur, J; Versteegh, M A; Hemelrijk, C K; Svensson, E I; Edwards, H; Karlsson, M; West, S A; Barrett, E L B; Richardson, D S; van den Brink, V; Wimpenny, J H; Ellwood, S A; Rees, M; Matson, K D; Charmantier, A; Dos Remedios, N; Schneider, N A; Teplitsky, C; Laurance, W F; Butlin, R K; Horrocks, N P C

    2013-09-01

    Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001-2011, 9-23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  4. Anticipatory Mechanisms in Evolutionary Living Systems

    Science.gov (United States)

    Dubois, Daniel M.; Holmberg, Stig C.

    2010-11-01

    This paper deals firstly with a revisiting of Darwin's theory of Natural Selection. Darwin in his book never uses the word "evolution", but shows a clear position about mutability of species. Darwin's Natural Selection was mainly inspired by the anticipatory Artificial Selection by humans in domestication, and the Malthus struggle for existence. Darwin showed that the struggle for existence leads to the preservation of the most divergent offspring of any one species. He cited several times the canon of "Natura non facit saltum". He spoke about the origin of life from some one primordial form, into which life was first breathed. Finally, Darwin made anticipation about the future researches in psychology. This paper cites the work of Ernst Mayr who was the first, after 90 years of an intense scientific debate, to present a new and stable Darwinian paradigm as the "Evolutionary Synthesis" in 1942. To explain what is life, the Living Systems Theory (LST) by J. G. Miller is presented. It is showed that the Autopoietic Systems Theory of Varela et al is also a fundamental component of living systems. In agreement with Darwin, the natural selection is a necessary condition for transformation of biological systems, but is not a sufficient condition. Thus, in this paper we conjecture that an anticipatory evolutionary mechanism exists with the genetic code that is a self-replicating and self-modifying anticipatory program. As demonstrated by Nobel laureate McClintock, evolution in genomes is programmed. The word "program" comes from "pro-gram" meaning to write before, by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes of behavioural responses, that is part of an organism. For example, cell death may be programmed by what is called the apoptosis. This definitively is a great breakthrough in our understanding of biological evolution. Hence

  5. Bridging Developmental Systems Theory and Evolutionary Psychology Using Dynamic Optimization

    Science.gov (United States)

    Frankenhuis, Willem E.; Panchanathan, Karthik; Clark Barrett, H.

    2013-01-01

    Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic…

  6. Evolutionary biology today and the call for an extended synthesis.

    Science.gov (United States)

    Futuyma, Douglas J

    2017-10-06

    Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation

  7. Complex evolutionary systems in behavioral finance

    NARCIS (Netherlands)

    Hommes, C.; Wagener, F.

    2008-01-01

    Traditional finance is built on the rationality paradigm. This chapter discusses simple models from an alternative approach in which financial markets are viewed as complex evolutionary systems. Agents are boundedly rational and base their investment decisions upon market forecasting heuristics.

  8. Financial Markets as Nonlinear Adaptive Evolutionary Systems

    OpenAIRE

    Hommes, C.H.

    2001-01-01

    This paper gives an overview of joint work with Buz Brock, on evolutionary adaptive belief systems (ABS) for modelling financial markets. Recent work with Andrea Gaunersdorfer is also reviewed and some recent experimental work on expectation formation in financial markets is also discussed. Financial markets are viewed as evolutionary systems between different, competing trading strategies. Agents are boundedly rational in the sense that they tend to follow strategies that have performed well...

  9. The application of statistical physics to evolutionary biology.

    Science.gov (United States)

    Sella, Guy; Hirsh, Aaron E

    2005-07-05

    A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

  10. Gilbert Gottlieb: intermediator between psychology and evolutionary biology.

    Science.gov (United States)

    Rosenblatt, Jay S

    2007-12-01

    This article describes and evaluates Gilbert Gottlieb's role as an intermediator between psychology and evolutionary biology. He proposed that altered developmental conditions gave rise to new behavioral phenotypes (behavioral neophenotypes) that could provide the basis for initiating speciation. As an example, Gottlieb cited sympatric speciation of two species of fruit flies (Rhageletis pomella), which he believed was based on an ontogenetic shift in pupal feeding on apples or hawthorn fruit which determined their adult selection of apple or hawthorn trees for ovipositing. Recent evidence has provided additional links in the process of speciation of these fruit flies. Unlike other efforts to incorporate evolution in psychology, Gottlieb's theoretical contribution was based on actual evolutionary processes including recent developments in the field of evo-devo.

  11. Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

    Science.gov (United States)

    Koonin, Eugene V; Wolf, Yuri I

    2012-01-01

    When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain "ribosomal Tree of Life" that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability, i.e., dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary biology.

  12. Evolution of microbes and viruses: A paradigm shift in evolutionary biology?

    Directory of Open Access Journals (Sweden)

    Eugene V. Koonin

    2012-09-01

    Full Text Available When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain ‘ribosomal Tree of Life’ that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: i pervasive horizontal gene transfer (HGT, in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment of the Tree of Life concept, ii Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and iii evolution of evolvability, i.e. dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary

  13. Mating systems in caridean shrimp (Decapoda: Caridea and their evolutionary consequences for sexual dimorphism and reproductive biology Sistemas de apareamiento en camarones carideos (Decapoda: Caridea y sus consecuencias evolutivas en el dimorfismo sexual y biología reproductiva

    Directory of Open Access Journals (Sweden)

    CRISTIÁN CORREA

    2003-06-01

    Full Text Available In this paper we review functional and evolutionary relationships among mating systems of caridean shrimp and specific traits such as general biology/ecology, sexual systems, behavior and morphology. Four mating systems are described based on reports from available literature, and a fifth system is recognized but published information is insufficient to describe it in detail. `Monogamy' occurs in many species inhabiting monopolizable refuges or hosts, especially when environmental conditions restrict the probability of intraspecific interactions. In contrast, free-living species experience higher encounter rates and males can dominate or search. In `neighborhoods of dominance' mating systems, large males have higher reproductive success since they perform better in fights for receptive females. In `pure searching' mating systems, small and agile males do better because they search more efficiently for mates within the population. The fourth mating system is `search & attend' occurring in solitary symbionts, which experience variable ecological and demographic environments: depending on environmental conditions and ontogenetic stages it may either be profitable for males to search or to attend hosts with sexually attractive females. Sexual systems of caridean shrimp are characterized by their high diversity and intraspecific plasticity, including gonochorism and different forms of protandric or simultaneous hermaphroditism. The identified mating systems partially explained this diversity: In monogamous species, low encounter rates and lack of sexual dimorphism favors simultaneous hermaphroditism but gonochory usually occurs among these species probably because mates are not strictly faithful. Species with neighborhoods of dominance mating are gonochoristic because both sexes benefit from being large. Pure searching species have a wide opportunity for the evolution of protandry since small males benefit while the opposite is true for females. In

  14. [Theories of biological evolution from the viewpoint of the modern systemic biology].

    Science.gov (United States)

    Lashin, S A; Suslov, V V; Matushkin, Iu G

    2012-05-01

    Theories of biological evolution advanced in the last 200 years are reviewed from the viewpoint of advances of modern genetics. The theory of gene networks as a key direction of systemic biology is a link connecting different evolutionary theories.

  15. Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology

    Directory of Open Access Journals (Sweden)

    Minelli Alessandro

    2009-06-01

    Full Text Available Abstract As a result of the integration of molecular and morphological approaches for the reconstruction of phylogenies, and of the intertwining of developmental and evolutionary biology, further prospects are open for a fruitful interaction between these two fields in what we may call a phylo-evo-devo approach. Wiegmann et al.'s molecular phylogeny of the holometabolous insect orders, recently published in BMC Biology, offers a good opportunity to revisit the inverted positions of wings and halteres in the Diptera and the Strepsiptera in terms of a putative homeotic mutation in the Hox gene Ultrabithorax. The main finding of this paper is that Strepsiptera are closely related to the Coleoptera rather than Diptera, as recently claimed. Through this exemplary case, the paper demonstrates the value of the reciprocal illumination we can expect from the integration of a good phylogeny and a sound knowledge of the evolvability of developmental mechanisms.

  16. Biological causal links on physiological and evolutionary time scales.

    Science.gov (United States)

    Karmon, Amit; Pilpel, Yitzhak

    2016-04-26

    Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

  17. Evolutionary dynamics of language systems

    Science.gov (United States)

    Wu, Chieh-Hsi; Hua, Xia; Dunn, Michael; Levinson, Stephen C.; Gray, Russell D.

    2017-01-01

    Understanding how and why language subsystems differ in their evolutionary dynamics is a fundamental question for historical and comparative linguistics. One key dynamic is the rate of language change. While it is commonly thought that the rapid rate of change hampers the reconstruction of deep language relationships beyond 6,000–10,000 y, there are suggestions that grammatical structures might retain more signal over time than other subsystems, such as basic vocabulary. In this study, we use a Dirichlet process mixture model to infer the rates of change in lexical and grammatical data from 81 Austronesian languages. We show that, on average, most grammatical features actually change faster than items of basic vocabulary. The grammatical data show less schismogenesis, higher rates of homoplasy, and more bursts of contact-induced change than the basic vocabulary data. However, there is a core of grammatical and lexical features that are highly stable. These findings suggest that different subsystems of language have differing dynamics and that careful, nuanced models of language change will be needed to extract deeper signal from the noise of parallel evolution, areal readaptation, and contact. PMID:29073028

  18. The search for evolutionary developmental origins of aging in zebrafish: a novel intersection of developmental and senescence biology in the zebrafish model system.

    Science.gov (United States)

    Kishi, Shuji

    2011-09-01

    regulation. We wish to ascertain whether we can identify such genes promptly in a comprehensive manner. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes and small molecular compounds that can be linked to the senescence phenotype and thereby facilitates searching for the evolutionary and developmental origins of aging in vertebrates. Copyright © 2011 Wiley-Liss, Inc.

  19. Goldfish morphology as a model for evolutionary developmental biology.

    Science.gov (United States)

    Ota, Kinya G; Abe, Gembu

    2016-01-01

    Morphological variation of the goldfish is known to have been established by artificial selection for ornamental purposes during the domestication process. Chinese texts that date to the Song dynasty contain descriptions of goldfish breeding for ornamental purposes, indicating that the practice originated over one thousand years ago. Such a well-documented goldfish breeding process, combined with the phylogenetic and embryological proximities of this species with zebrafish, would appear to make the morphologically diverse goldfish strains suitable models for evolutionary developmental (evodevo) studies. However, few modern evodevo studies of goldfish have been conducted. In this review, we provide an overview of the historical background of goldfish breeding, and the differences between this teleost and zebrafish from an evolutionary perspective. We also summarize recent progress in the field of molecular developmental genetics, with a particular focus on the twin-tail goldfish morphology. Furthermore, we discuss unanswered questions relating to the evolution of the genome, developmental robustness, and morphologies in the goldfish lineage, with the goal of blazing a path toward an evodevo study paradigm using this teleost species as a new model species. For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs Developmental Biology published by Wiley Periodicals, Inc.

  20. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  1. Reconstructing nursing altruism using a biological evolutionary framework.

    Science.gov (United States)

    Haigh, Carol A

    2010-06-01

    This paper presents a discussion of the role of altruism in development of the discipline of nursing and an exploration of how nursing altruism compares with current thinking in biological evolutionary theory. There is an assumption that the role of the nurse has its foundations in altruistic behaviours; however, the source of this altruism is never analysed or debated. A search of the biological altruism, altruism and health-related literature encompassing the years 1975-2007 was performed using Google Scholar. The first element of the study is a brief overview of nursing altruism as a way of establishing the conceptual boundaries. Additionally, the major tenets of biological evolution are explored to clarify the theoretical underpinnings of the hypotheses presented. A key premise of this study is that nursing altruism is not solely a manifestation of disinterested sacrifice for the benefit of others, but is more concerned with ensuring the survival of a clearly defined social group. A re-evaluation of altruism as a motivating factor in nursing and as an element of the therapeutic relationship is long overdue. It is time that the nursing profession examined professional driving forces using more than traditional philosophical frameworks. Nursing altruism is programmed to ensure the survival of the meme rather than to act in the best interest of patients. Certainly patients reap the benefits of this selfish altruism, but that can be argued to be a side effect rather than a result.

  2. Natural Killer T Cells: An Ecological Evolutionary Developmental Biology Perspective

    Directory of Open Access Journals (Sweden)

    Amrendra Kumar

    2017-12-01

    Full Text Available Type I natural killer T (NKT cells are innate-like T lymphocytes that recognize glycolipid antigens presented by the MHC class I-like protein CD1d. Agonistic activation of NKT cells leads to rapid pro-inflammatory and immune modulatory cytokine and chemokine responses. This property of NKT cells, in conjunction with their interactions with antigen-presenting cells, controls downstream innate and adaptive immune responses against cancers and infectious diseases, as well as in several inflammatory disorders. NKT cell properties are acquired during development in the thymus and by interactions with the host microbial consortium in the gut, the nature of which can be influenced by NKT cells. This latter property, together with the role of the host microbiota in cancer therapy, necessitates a new perspective. Hence, this review provides an initial approach to understanding NKT cells from an ecological evolutionary developmental biology (eco-evo-devo perspective.

  3. Entrepreneurs and Evolutionary Biology: The Relationship between Testosterone and New Venture Creation

    Science.gov (United States)

    White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth

    2006-01-01

    Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…

  4. The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

    Science.gov (United States)

    O'Malley, Maureen A

    2017-10-04

    Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

  5. Computational systems chemical biology.

    Science.gov (United States)

    Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  6. Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology.

    Science.gov (United States)

    Skinner, Michael K; Savenkova, Marina I; Zhang, Bin; Gore, Andrea C; Crews, David

    2014-05-16

    Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female. The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant. Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.

  7. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America.

    Science.gov (United States)

    Marcellini, Sylvain; González, Favio; Sarrazin, Andres F; Pabón-Mora, Natalia; Benítez, Mariana; Piñeyro-Nelson, Alma; Rezende, Gustavo L; Maldonado, Ernesto; Schneider, Patricia Neiva; Grizante, Mariana B; Da Fonseca, Rodrigo Nunes; Vergara-Silva, Francisco; Suaza-Gaviria, Vanessa; Zumajo-Cardona, Cecilia; Zattara, Eduardo E; Casasa, Sofia; Suárez-Baron, Harold; Brown, Federico D

    2017-01-01

    Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community. © 2016 Wiley Periodicals, Inc.

  8. Evolutionary and Political Economic Influences on Biological Diversity in African Americans.

    Science.gov (United States)

    Jackson, Fatimah Linda Collier

    1993-01-01

    Examines existing data on biological diversity among Americans of African descent within the contexts of their evolutionary backgrounds and political and economic realities. Explores the origins of the diversity, and provides an evolutionary and political economy synthesis for evaluating the biological distinctions apparent among African…

  9. Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence.

    Science.gov (United States)

    Slijepcevic, Predrag

    2018-01-01

    Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research. The revamped programme may be tentatively called Research Programme for Distributed Biological Intelligence. Intelligence I define as the capacity of organisms to gain information about their environment, process that information internally, and translate it into phenotypic forms. This multistage progression may be expressed through the acronym IGPT (information-gain-process-translate). The key principles of the programme may be summarized as follows. (i) Intelligence, a universal biological phenomenon promoting individual fitness, is required for effective organism-environment interactions. Given that animals represent less than 0.01% of the planetary biomass, neural intelligence is not the evolutionary norm. (ii) The basic unit of intelligence is a single cell prokaryote. All other forms of intelligence are derived. (iii) Intelligence is hierarchical. It ranges from bacteria to the biosphere or Gaia. (iv) The concept of "information" acquires a new meaning because information processing is at the heart of biological intelligence. All biological systems, from bacteria to Gaia, are intelligent, open thermodynamic systems that exchange information, matter and energy with the environment. (v) The organism-environment interaction is cybernetic. As much as the organism changes due to the influence of the environment, the organism's responses to induced changes affect the environment and

  10. Evolutionary biology in biodiversity science, conservation, and policy: a call to action.

    Science.gov (United States)

    Hendry, Andrew P; Lohmann, Lúcia G; Conti, Elena; Cracraft, Joel; Crandall, Keith A; Faith, Daniel P; Häuser, Christoph; Joly, Carlos A; Kogure, Kazuhiro; Larigauderie, Anne; Magallón, Susana; Moritz, Craig; Tillier, Simon; Zardoya, Rafael; Prieur-Richard, Anne-Hélène; Walther, Bruno A; Yahara, Tetsukazu; Donoghue, Michael J

    2010-05-01

    Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant. We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans. We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology. In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

  11. A soul of truth in things erroneous: Popper's "amateurish" evolutionary philosophy in light of contemporary biology.

    Science.gov (United States)

    Vecchi, Davide; Baravalle, Lorenzo

    2015-01-01

    This paper will critically assess Popper's evolutionary philosophy. There exists a rich literature on the topic with which we have many reservations. We believe that Popper's evolutionary philosophy should be assessed in light of the intriguing theoretical insights offered, during the last 10 years or so, by the philosophy of biology, evolutionary biology and molecular biology. We will argue that, when analysed in this manner, Popper's ideas concerning the nature of selection, Lamarckism and the theoretical limits of neo-Darwinism can be appreciated in their full biological and philosophical value.

  12. Systems Biology of Metabolism.

    Science.gov (United States)

    Nielsen, Jens

    2017-06-20

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.

  13. Investigating Climate Change and Reproduction: Experimental Tools from Evolutionary Biology

    Directory of Open Access Journals (Sweden)

    Oliver Y. Martin

    2012-09-01

    Full Text Available It is now generally acknowledged that climate change has wide-ranging biological consequences, potentially leading to impacts on biodiversity. Environmental factors can have diverse and often strong effects on reproduction, with obvious ramifications for population fitness. Nevertheless, reproductive traits are often neglected in conservation considerations. Focusing on animals, recent progress in sexual selection and sexual conflict research suggests that reproductive costs may pose an underestimated hurdle during rapid climate change, potentially lowering adaptive potential and increasing extinction risk of certain populations. Nevertheless, regime shifts may have both negative and positive effects on reproduction, so it is important to acquire detailed experimental data. We hence present an overview of the literature reporting short-term reproductive consequences of exposure to different environmental factors. From the enormous diversity of findings, we conclude that climate change research could benefit greatly from more coordinated efforts incorporating evolutionary approaches in order to obtain cross-comparable data on how individual and population reproductive fitness respond in the long term. Therefore, we propose ideas and methods concerning future efforts dealing with reproductive consequences of climate change, in particular by highlighting the advantages of multi-generational experimental evolution experiments.

  14. Improving the reviewing process in Ecology and Evolutionary Biology

    Directory of Open Access Journals (Sweden)

    Grossman, G. D.

    2014-06-01

    Full Text Available I discuss current issues in reviewing and editorial practices in ecology and evolutionary biology and suggest possible solutions for current problems. The reviewing crisis is unlikely to change unless steps are taken by journals to provide greater inclusiveness and incentives to reviewers. In addition, both journals and institutions should reduce their emphasis on publication numbers (least publishable units and impact factors and focus instead on article synthesis and quality which will require longer publications. Academic and research institutions should consider reviewing manuscripts and editorial positions an important part of a researcher’s professional activities and reward them accordingly. Rewarding reviewers either monetarily or via other incentives such as free journal subscriptions may encourage participation in the reviewing process for both profit and non–profit journals. Reviewer performance will likely be improved by measures that increase inclusiveness, such as sending reviews and decision letters to reviewers. Journals may be able to evaluate the efficacy of their reviewing process by comparing citations of rejected but subsequently published papers with those published within the journal at similar times. Finally, constructive reviews: 1 identify important shortcomings and suggest solutions when possible, 2 distinguish trivial from non–trivial problems, and 3 include editor’s evaluations of the reviews including identification of trivial versus substantive comments (i.e., those that must be addressed.

  15. Adaptation and novelty: teleological explanations in evolutionary biology.

    Science.gov (United States)

    Ayala, F J

    1999-01-01

    Knives, birds' wings, and mountain slopes are used for certain purposes: cutting, flying, and climbing. A bird's wings have in common with knives that they have been 'designed' for the purpose they serve, which purpose accounts for their existence, whereas mountain slopes have come about by geological processes independently of their uses for climbing. A bird's wings differ from a knife in that they have not been designed or produced by any conscious agent; rather, the wings, like the slopes, are outcomes of natural processes without any intentional causation. Evolutionary biologists use teleological language and teleological explanations. I propose that this use is appropriate, because teleological explanations are hypotheses that can be subject to empirical testing. The distinctiveness of teleological hypotheses is that they account for the existence of a feature in terms of the function it serves; for example, wings have evolved and persist because flying is beneficial to birds by increasing their chances of surviving and reproducing. Features of organisms that are explained with teleological hypotheses include structures, such as wings; processes, such as development from egg to adult; and behaviours, such as nest building. A proximate explanation of these features is the function they serve; an ultimate explanation that they all share is their contribution to the reproductive fitness of the organisms. I distinguish several kinds of teleological explanations, such as natural and artificial, as well as bounded and unbounded, some of which but not others apply to biological explanations.

  16. New insights into the evolutionary history of biological nitrogen fixation

    Directory of Open Access Journals (Sweden)

    Eric eBoyd

    2013-08-01

    Full Text Available Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2 to ammonia (NH3, accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of this fundamental biological process. One key question is whether the limited availability of fixed nitrogen was a factor in life’s origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth’s biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained by deep phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex and life sustaining process.

  17. Bridging Evolutionary Biology and Developmental Psychology: Toward An Enduring Theoretical Infrastructure.

    Science.gov (United States)

    Frankenhuis, Willem E; Tiokhin, Leonid

    2018-01-16

    Bjorklund synthesizes promising research directions in developmental psychology using an evolutionary framework. In general terms, we agree with Bjorklund: Evolutionary theory has the potential to serve as a metatheory for developmental psychology. However, as currently used in psychology, evolutionary theory is far from reaching this potential. In evolutionary biology, formal mathematical models are the norm. In developmental psychology, verbal models are the norm. In order to reach its potential, evolutionary developmental psychology needs to embrace formal modeling. © 2018 The Authors. Child Development © 2018 Society for Research in Child Development, Inc.

  18. How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology.

    Science.gov (United States)

    Bonier, Frances; Martin, Paul R

    2016-11-30

    An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution. © 2016 The Author(s).

  19. Complex systems biology

    OpenAIRE

    Ma'ayan, Avi

    2017-01-01

    Complex systems theory is concerned with identifying and characterizing common design elements that are observed across diverse natural, technological and social complex systems. Systems biology, a more holistic approach to study molecules and cells in biology, has advanced rapidly in the past two decades. However, not much appreciation has been granted to the realization that the human cell is an exemplary complex system. Here, I outline general design principles identified in many complex s...

  20. The Design and Transformation of Biofundamentals: A Nonsurvey Introductory Evolutionary and Molecular Biology Course

    Science.gov (United States)

    Klymkowsky, Michael W.; Rentsch, Jeremy D.; Begovic, Emina; Cooper, Melanie M.

    2016-01-01

    Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students’ ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master. The original Web-based course’s design presaged many of the recommendations of the Vision and Change report; in particular, a focus on social evolutionary mechanisms, stochastic (evolutionary and molecular) processes, and core ideas (cellular continuity, evolutionary homology, molecular interactions, coupled chemical reactions, and molecular machines). Inspired by insights from the Chemistry, Life, the Universe & Everything general chemistry project, we transformed the original Web version into a (freely available) book with a more unified narrative flow and a set of formative assessments delivered through the beSocratic system. We outline how student responses to course materials are guiding future course modifications, in particular a more concerted effort at helping students to construct logical, empirically based arguments, explanations, and models. PMID:27909020

  1. The Design and Transformation of Biofundamentals: A Nonsurvey Introductory Evolutionary and Molecular Biology Course.

    Science.gov (United States)

    Klymkowsky, Michael W; Rentsch, Jeremy D; Begovic, Emina; Cooper, Melanie M

    2016-01-01

    Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master. The original Web-based course's design presaged many of the recommendations of the Vision and Change report; in particular, a focus on social evolutionary mechanisms, stochastic (evolutionary and molecular) processes, and core ideas (cellular continuity, evolutionary homology, molecular interactions, coupled chemical reactions, and molecular machines). Inspired by insights from the Chemistry, Life, the Universe & Everything general chemistry project, we transformed the original Web version into a (freely available) book with a more unified narrative flow and a set of formative assessments delivered through the beSocratic system. We outline how student responses to course materials are guiding future course modifications, in particular a more concerted effort at helping students to construct logical, empirically based arguments, explanations, and models. © 2016 M. W. Klymkowsky 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).

  2. Evolutionary Computing for Intelligent Power System Optimization and Control

    DEFF Research Database (Denmark)

    This new book focuses on how evolutionary computing techniques benefit engineering research and development tasks by converting practical problems of growing complexities into simple formulations, thus largely reducing development efforts. This book begins with an overview of the optimization the...... theory and modern evolutionary computing techniques, and goes on to cover specific applications of evolutionary computing to power system optimization and control problems....

  3. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  4. Controversies in modern evolutionary biology: the imperative for error detection and quality control.

    Science.gov (United States)

    Prosdocimi, Francisco; Linard, Benjamin; Pontarotti, Pierre; Poch, Olivier; Thompson, Julie D

    2012-01-04

    The data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biology, for example, has led to many interesting, but often controversial studies. It has been suggested that part of the conflict may be due to errors in the initial sequences. Most gene sequences are predicted by bioinformatics programs and a number of quality issues have been raised, concerning DNA sequencing errors or badly predicted coding regions, particularly in eukaryotes. We investigated the impact of these errors on evolutionary studies and specifically on the identification of important genetic events. We focused on the detection of asymmetric evolution after duplication, which has been the subject of controversy recently. Using the human genome as a reference, we established a reliable set of 688 duplicated genes in 13 complete vertebrate genomes, where significantly different evolutionary rates are observed. We estimated the rates at which protein sequence errors occur and are accumulated in the higher-level analyses. We showed that the majority of the detected events (57%) are in fact artifacts due to the putative erroneous sequences and that these artifacts are sufficient to mask the true functional significance of the events. Initial errors are accumulated throughout the evolutionary analysis, generating artificially high rates of event predictions and leading to substantial uncertainty in the conclusions. This study emphasizes the urgent need for error detection and quality control strategies in order to efficiently extract knowledge from the new genome data. © 2012 Prosdocimi et al; licensee BioMed Central Ltd.

  5. Proposal for Teaching Evolutionary Biology: A Bridge between Research and Educational Practice

    Science.gov (United States)

    Alvarez Pérez, Eréndira; Ruiz Gutiérrez, Rosaura

    2016-01-01

    We present quantitative results for the doctoral thesis of the first-named author of this article. The objective was to recommend and test a teaching proposal for core knowledge of evolutionary biology in secondary education. The focus of the study is "Problem cores in teaching". The "Weaving evolutionary thinking" teaching…

  6. Expansion of biological pathways based on evolutionary inference.

    Science.gov (United States)

    Li, Yang; Calvo, Sarah E; Gutman, Roee; Liu, Jun S; Mootha, Vamsi K

    2014-07-03

    The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Epigenetic Regulation of Biological Rhythms: An Evolutionary Ancient Molecular Timer.

    Science.gov (United States)

    Stevenson, Tyler J

    2017-12-05

    Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms. The model also provides a novel framework for the timing of epigenetic modifications during the lifespan and transgenerational inheritance of an organism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Systems biology and medicine

    Indian Academy of Sciences (India)

    Immunology Group, International Centre for Genetic Engineering and Biotechnology,. Aruna Asaf ... simple laws. As a result, the most obvious strat- egy for understanding complex natural systems in general was to reduce the system into smaller, sim- pler, and .... networked organization of biological system would emerge ...

  9. An overview of ecological and evolutionary research on disease in natural systems: an annotated reference list

    Science.gov (United States)

    Helen M. Alexander

    2012-01-01

    The Fourth International Workshop on the Genetics of Host-Parasite Interactions in Forestry (July 31-August 5, 2011) included a session on “Ecology and Evolutionary Biology of Resistance and Tolerance, Natural Systems.” Within this session, I gave a talk entitled “An overview of ecological and evolutionary research on disease in ‘natural’ systems” that reviewed...

  10. Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

    Directory of Open Access Journals (Sweden)

    Julie D. Thompson

    2008-01-01

    Full Text Available The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting, interactomes (based on the presence and degree of conservation of interacting proteins, and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression. Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.

  11. The Comparative Organismal Approach in Evolutionary Developmental Biology: Insights from Ascidians and Cavefish.

    Science.gov (United States)

    Jeffery, William R

    2016-01-01

    Important contributions to evolutionary developmental biology have been made using the comparative organismal approach. As examples, I describe insights obtained from studies of Molgula ascidians and Astyanax cavefish. © 2016 Elsevier Inc. All rights reserved.

  12. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  13. Systems biology in animal sciences

    OpenAIRE

    Woelders, H.; Pas, te, M.F.W.; Bannink, A.; Veerkamp, R. F.; Smits, M A

    2011-01-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aim...

  14. Latitudinal clines: an evolutionary view on biological rhythms†,‡

    Science.gov (United States)

    Hut, Roelof A.; Paolucci, Silvia; Dor, Roi; Kyriacou, Charalambos P.; Daan, Serge

    2013-01-01

    Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian phenotypes as well as in polymorphisms of circadian clock genes and their possible association with annual timing. The use of latitudinal (and altitudinal) clines in identifying selective forces acting on biological rhythms is discussed, and we evaluate how these studies can reveal novel molecular and physiological components of these rhythms. PMID:23825204

  15. Latitudinal clines: an evolutionary view on biological rhythms.

    Science.gov (United States)

    Hut, Roelof A; Paolucci, Silvia; Dor, Roi; Kyriacou, Charalambos P; Daan, Serge

    2013-08-22

    Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian phenotypes as well as in polymorphisms of circadian clock genes and their possible association with annual timing. The use of latitudinal (and altitudinal) clines in identifying selective forces acting on biological rhythms is discussed, and we evaluate how these studies can reveal novel molecular and physiological components of these rhythms.

  16. Selective evolutionary generation systems: Theory and applications

    Science.gov (United States)

    Menezes, Amor A.

    This dissertation is devoted to the problem of behavior design, which is a generalization of the standard global optimization problem: instead of generating the optimizer, the generalization produces, on the space of candidate optimizers, a probability density function referred to as the behavior. The generalization depends on a parameter, the level of selectivity, such that as this parameter tends to infinity, the behavior becomes a delta function at the location of the global optimizer. The motivation for this generalization is that traditional off-line global optimization is non-resilient and non-opportunistic. That is, traditional global optimization is unresponsive to perturbations of the objective function. On-line optimization methods that are more resilient and opportunistic than their off-line counterparts typically consist of the computationally expensive sequential repetition of off-line techniques. A novel approach to inexpensive resilience and opportunism is to utilize the theory of Selective Evolutionary Generation Systems (SECS), which sequentially and probabilistically selects a candidate optimizer based on the ratio of the fitness values of two candidates and the level of selectivity. Using time-homogeneous, irreducible, ergodic Markov chains to model a sequence of local, and hence inexpensive, dynamic transitions, this dissertation proves that such transitions result in behavior that is called rational; such behavior is desirable because it can lead to both efficient search for an optimizer as well as resilient and opportunistic behavior. The dissertation also identifies system-theoretic properties of the proposed scheme, including equilibria, their stability and their optimality. Moreover, this dissertation demonstrates that the canonical genetic algorithm with fitness proportional selection and the (1+1) evolutionary strategy are particular cases of the scheme. Applications in three areas illustrate the versatility of the SECS theory: flight

  17. Evolutionary biology: a basic science for medicine in the 21st century.

    Science.gov (United States)

    Perlman, Robert L

    2011-01-01

    Evolutionary biology was a poorly developed discipline at the time of the Flexner Report and was not included in Flexner's recommendations for premedical or medical education. Since that time, however, the value of an evolutionary approach to medicine has become increasingly recognized. There are several ways in which an evolutionary perspective can enrich medical education and improve medical practice. Evolutionary considerations rationalize our continued susceptibility or vulnerability to disease; they call attention to the idea that the signs and symptoms of disease may be adaptations that prevent or limit the severity of disease; they help us understand the ways in which our interventions may affect the evolution of microbial pathogens and of cancer cells; and they provide a framework for thinking about population variation and risk factors for disease. Evolutionary biology should become a foundational science for the medical education of the future.

  18. [The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

    Science.gov (United States)

    Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

    2010-01-01

    The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

  19. Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

    Science.gov (United States)

    Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

    2016-01-01

    In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

  20. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  1. The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

    Science.gov (United States)

    Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

    2016-09-01

    Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A backtracking evolutionary algorithm for power systems

    Directory of Open Access Journals (Sweden)

    Chiou Ji-Pyng

    2017-01-01

    Full Text Available This paper presents a backtracking variable scaling hybrid differential evolution, called backtracking VSHDE, for solving the optimal network reconfiguration problems for power loss reduction in distribution systems. The concepts of the backtracking, variable scaling factor, migrating, accelerated, and boundary control mechanism are embedded in the original differential evolution (DE to form the backtracking VSHDE. The concepts of the backtracking and boundary control mechanism can increase the population diversity. And, according to the convergence property of the population, the scaling factor is adjusted based on the 1/5 success rule of the evolution strategies (ESs. A larger population size must be used in the evolutionary algorithms (EAs to maintain the population diversity. To overcome this drawback, two operations, acceleration operation and migrating operation, are embedded into the proposed method. The feeder reconfiguration of distribution systems is modelled as an optimization problem which aims at achieving the minimum loss subject to voltage and current constraints. So, the proper system topology that reduces the power loss according to a load pattern is an important issue. Mathematically, the network reconfiguration system is a nonlinear programming problem with integer variables. One three-feeder network reconfiguration system from the literature is researched by the proposed backtracking VSHDE method and simulated annealing (SA. Numerical results show that the perfrmance of the proposed method outperformed the SA method.

  3. EVOLUTIONARY ASPECTS OF THE GEORGIAN BANKING SYSTEM

    Directory of Open Access Journals (Sweden)

    Tamar ATANELISHVILI

    2016-08-01

    Full Text Available Georgian monetary relations have a centuries-old history. Credit associations were first founded in 11-13th centuries. Network of credit institutions became larger in the 19th century – independent commercial banks were established in the second half of the 19th century. Central State Bank of Georgia was established in the Democratic Republic of Georgia in the beginning of the 20th century. At the same time, there were efforts to create independent two-level banking system, although those efforts failed due to forceful sovietization of Georgia. But still, independent banking system was founded in Georgia after the collapse of the former Soviet Union. This work examines afore-mentioned evolutionary processes and some of peculiarities of modern banking system. The research shows that modern Georgian banking system is growing fast but it contains signs of oligopoly which contradicts the interests of vast masses of population and entrepreneurial development, while stimulating retaining of high interest rates and devaluation of national currency.

  4. Evolutionary biology and the determinants of morality 2 | Odozor ...

    African Journals Online (AJOL)

    biological factors, such as education, family integration and upbringing, religion, socialisation and culture, which even go beyond biology to determine the very contents of human morality. This second essay continues the reflection on this ...

  5. Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

    Science.gov (United States)

    Zhang, Shi-Jian; Liu, Chu-Jun; Yu, Peng; Zhong, Xiaoming; Chen, Jia-Yu; Yang, Xinzhuang; Peng, Jiguang; Yan, Shouyu; Wang, Chenqu; Zhu, Xiaotong; Xiong, Jingwei; Zhang, Yong E; Tan, Bertrand Chin-Ming; Li, Chuan-Yun

    2014-05-01

    With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, RhesusBase2 refined the fine-scale structures in 30% of the macaque Ensembl transcripts, reporting an accurate, up-to-date set of macaque gene models. On the basis of these annotations and accurate macaque gene models, we further developed an NGS-oriented Molecular Evolution Gateway to access and visualize macaque annotations in reference to human orthologous genes and associated regulations (www.rhesusbase.org/molEvo). We highlighted the application of this well-annotated genomic framework in generating hypothetical link of human-biased regulations to human-specific traits, by using mechanistic characterization of the DIEXF gene as an example that provides novel clues to the understanding of digestive system reduction in human evolution. On a global scale, we also identified a catalog of 9,295 human-biased regulatory events, which may represent novel elements that have a substantial impact on shaping human transcriptome and possibly underpin recent human phenotypic evolution. Taken together, we provide an NGS data-driven, information-rich framework that will broadly benefit genomics research in general and serves as an important resource for in-depth evolutionary studies of human biology.

  6. Pancreatic cancer biology and genetics from an evolutionary perspective.

    Science.gov (United States)

    Makohon-Moore, Alvin; Iacobuzio-Donahue, Christine A

    2016-09-01

    Cancer is an evolutionary disease, containing the hallmarks of an asexually reproducing unicellular organism subject to evolutionary paradigms. Pancreatic ductal adenocarcinoma (hereafter referred to as pancreatic cancer) is a particularly robust example of this phenomenon. Genomic features indicate that pancreatic cancer cells are selected for fitness advantages when encountering the geographic and resource-depleted constraints of the microenvironment. Phenotypic adaptations to these pressures help disseminated cells to survive in secondary sites, a major clinical problem for patients with this disease. In this Review we gather the wide-ranging aspects of pancreatic cancer research into a single concept rooted in Darwinian evolution, with the goal of identifying novel insights and opportunities for study.

  7. Pancreatic cancer biology and genetics from an evolutionary perspective

    Science.gov (United States)

    Makohon-Moore, Alvin; Iacobuzio-Donahue, Christine A.

    2017-01-01

    Cancer is an evolutionary disease, containing the hallmarks of an asexually reproducing unicellular organism subject to evolutionary paradigms. Pancreatic ductal adenocarcinoma (hereafter referred to as pancreatic cancer) is a particularly robust example of this phenomenon. Genomic features indicate that pancreatic cancer cells are selected for fitness advantages when encountering the geographic and resource-depleted constraints of the microenvironment. Phenotypic adaptations to these pressures help disseminated cells to survive in secondary sites, a major clinical problem for patients with this disease. In this Review we gather the wide-ranging aspects of pancreatic cancer research into a single concept rooted in Darwinian evolution, with the goal of identifying novel insights and opportunities for study. PMID:27444064

  8. Biological system interactions.

    Science.gov (United States)

    Adomian, G; Adomian, G E; Bellman, R E

    1984-05-01

    Mathematical modeling of cellular population growth, interconnected subsystems of the body, blood flow, and numerous other complex biological systems problems involves nonlinearities and generally randomness as well. Such problems have been dealt with by mathematical methods often changing the actual model to make it tractable. The method presented in this paper (and referenced works) allows much more physically realistic solutions.

  9. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  10. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  11. Charles Darwin and the Origins of Plant Evolutionary Developmental Biology

    Science.gov (United States)

    Friedman, William E.; Diggle, Pamela K.

    2011-01-01

    Much has been written of the early history of comparative embryology and its influence on the emergence of an evolutionary developmental perspective. However, this literature, which dates back nearly a century, has been focused on metazoans, without acknowledgment of the contributions of comparative plant morphologists to the creation of a developmental view of biodiversity. We trace the origin of comparative plant developmental morphology from its inception in the eighteenth century works of Wolff and Goethe, through the mid nineteenth century discoveries of the general principles of leaf and floral organ morphogenesis. Much like the stimulus that von Baer provided as a nonevolutionary comparative embryologist to the creation of an evolutionary developmental view of animals, the comparative developmental studies of plant morphologists were the basis for the first articulation of the concept that plant (namely floral) evolution results from successive modifications of ontogeny. Perhaps most surprisingly, we show that the first person to carefully read and internalize the remarkable advances in the understanding of plant morphogenesis in the 1840s and 1850s is none other than Charles Darwin, whose notebooks, correspondence, and (then) unpublished manuscripts clearly demonstrate that he had discovered the developmental basis for the evolutionary transformation of plant form. PMID:21515816

  12. Charles Darwin and the origins of plant evolutionary developmental biology.

    Science.gov (United States)

    Friedman, William E; Diggle, Pamela K

    2011-04-01

    Much has been written of the early history of comparative embryology and its influence on the emergence of an evolutionary developmental perspective. However, this literature, which dates back nearly a century, has been focused on metazoans, without acknowledgment of the contributions of comparative plant morphologists to the creation of a developmental view of biodiversity. We trace the origin of comparative plant developmental morphology from its inception in the eighteenth century works of Wolff and Goethe, through the mid nineteenth century discoveries of the general principles of leaf and floral organ morphogenesis. Much like the stimulus that von Baer provided as a nonevolutionary comparative embryologist to the creation of an evolutionary developmental view of animals, the comparative developmental studies of plant morphologists were the basis for the first articulation of the concept that plant (namely floral) evolution results from successive modifications of ontogeny. Perhaps most surprisingly, we show that the first person to carefully read and internalize the remarkable advances in the understanding of plant morphogenesis in the 1840s and 1850s is none other than Charles Darwin, whose notebooks, correspondence, and (then) unpublished manuscripts clearly demonstrate that he had discovered the developmental basis for the evolutionary transformation of plant form.

  13. Not just a theory--the utility of mathematical models in evolutionary biology.

    Directory of Open Access Journals (Sweden)

    Maria R Servedio

    2014-12-01

    Full Text Available Progress in science often begins with verbal hypotheses meant to explain why certain biological phenomena exist. An important purpose of mathematical models in evolutionary research, as in many other fields, is to act as “proof-of-concept” tests of the logic in verbal explanations, paralleling the way in which empirical data are used to test hypotheses. Because not all subfields of biology use mathematics for this purpose, misunderstandings of the function of proof-of-concept modeling are common. In the hope of facilitating communication, we discuss the role of proof-of-concept modeling in evolutionary biology.

  14. Not just a theory--the utility of mathematical models in evolutionary biology.

    Science.gov (United States)

    Servedio, Maria R; Brandvain, Yaniv; Dhole, Sumit; Fitzpatrick, Courtney L; Goldberg, Emma E; Stern, Caitlin A; Van Cleve, Jeremy; Yeh, D Justin

    2014-12-01

    Progress in science often begins with verbal hypotheses meant to explain why certain biological phenomena exist. An important purpose of mathematical models in evolutionary research, as in many other fields, is to act as “proof-of-concept” tests of the logic in verbal explanations, paralleling the way in which empirical data are used to test hypotheses. Because not all subfields of biology use mathematics for this purpose, misunderstandings of the function of proof-of-concept modeling are common. In the hope of facilitating communication, we discuss the role of proof-of-concept modeling in evolutionary biology.

  15. Biology Teachers' Conceptions of the Diversity of Life and the Historical Development of Evolutionary Concepts

    Science.gov (United States)

    da Silva, Paloma Rodrigues; de Andrade, Mariana A. Bologna Soares; de Andrade Caldeira, Ana Maria

    2015-01-01

    Biology is a science that involves study of the diversity of living organisms. This diversity has always generated questions and has motivated cultures to seek plausible explanations for the differences and similarities between types of organisms. In biology teaching, these issues are addressed by adopting an evolutionary approach. The aim of this…

  16. Stability properties of nonlinear dynamical systems and evolutionary stable states

    Science.gov (United States)

    Gleria, Iram; Brenig, Leon; Rocha Filho, Tarcísio M.; Figueiredo, Annibal

    2017-03-01

    In this paper we address the problem of stability in a general class of non-linear systems. We establish a link between the concepts of asymptotic stable interior fixed points of square Quasi-Polynomial systems and evolutionary stable states, a property of some payoff matrices arising from evolutionary games.

  17. Evolutionary Computation and Its Applications in Neural and Fuzzy Systems

    Directory of Open Access Journals (Sweden)

    Biaobiao Zhang

    2011-01-01

    Full Text Available Neural networks and fuzzy systems are two soft-computing paradigms for system modelling. Adapting a neural or fuzzy system requires to solve two optimization problems: structural optimization and parametric optimization. Structural optimization is a discrete optimization problem which is very hard to solve using conventional optimization techniques. Parametric optimization can be solved using conventional optimization techniques, but the solution may be easily trapped at a bad local optimum. Evolutionary computation is a general-purpose stochastic global optimization approach under the universally accepted neo-Darwinian paradigm, which is a combination of the classical Darwinian evolutionary theory, the selectionism of Weismann, and the genetics of Mendel. Evolutionary algorithms are a major approach to adaptation and optimization. In this paper, we first introduce evolutionary algorithms with emphasis on genetic algorithms and evolutionary strategies. Other evolutionary algorithms such as genetic programming, evolutionary programming, particle swarm optimization, immune algorithm, and ant colony optimization are also described. Some topics pertaining to evolutionary algorithms are also discussed, and a comparison between evolutionary algorithms and simulated annealing is made. Finally, the application of EAs to the learning of neural networks as well as to the structural and parametric adaptations of fuzzy systems is also detailed.

  18. Optimal immunity meets natural variation: the evolutionary biology of host defence.

    Science.gov (United States)

    Graham, A L

    2013-11-01

    This editorial introduces the seven articles that comprise the Parasite Immunology special issue on the Evolutionary Biology of Host Defence. The rationale for an evolutionary approach to immunoparasitology is briefly outlined, and then the articles are placed in that broader context. A central aim of each article is to explain the generation and maintenance of immunological heterogeneity among hosts in nature. The authors describe new tools and approaches that enable unprecedented insight into evolutionary and immunological processes in both the laboratory and the wild. The examples discussed include insects, birds and mammals (as hosts) and trypanosomes, apicomplexans and nematodes (as parasites). © 2013 John Wiley & Sons Ltd.

  19. Coevolution takes the sting out of it: Evolutionary biology and mechanisms of toxin resistance in animals.

    Science.gov (United States)

    Arbuckle, Kevin; Rodríguez de la Vega, Ricardo C; Casewell, Nicholas R

    2017-10-27

    Understanding how biotic interactions shape the genomes of the interacting species is a long-sought goal of evolutionary biology that has been hampered by the scarcity of tractable systems in which specific genomic features can be linked to complex phenotypes involved in interspecific interactions. In this review we present the compelling case of evolved resistance to the toxic challenge of venomous or poisonous animals as one such system. Animal venoms and poisons can be comprised of few or of many individual toxins. Here we show that resistance to animal toxins has evolved multiple times across metazoans, although it has been documented more often in phyla that feed on chemically-armed animals than in prey of venomous predators. We review three types of gene-product based resistance: 1) toxin scavenging, where molecules produced by the envenomed organism bind and inactivate the toxins; 2) target-site insensitivity, including landmark cases of convergent changes that make the molecules normally targeted by animal toxins refractory, and; 3) off-target repurposing, where envenomed organisms overcome toxicity by exploiting the function of toxins to alter their physiological effect. We finish by discussing the evolutionary processes that likely played a role in the origin and maintenance of toxin resistance. We conclude that antagonistic interactions involving poisonous or venomous animals are unparalleled models for investigating microevolutionary processes involved in coevolution and linking them to macroevolutionary patterns. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  1. Stability properties of nonlinear dynamical systems and evolutionary stable states

    Energy Technology Data Exchange (ETDEWEB)

    Gleria, Iram, E-mail: iram@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL (Brazil); Brenig, Leon [Faculté des Sciences, Université Libre de Bruxelles, 1050 Brussels (Belgium); Rocha Filho, Tarcísio M.; Figueiredo, Annibal [Instituto de Física and International Center for Condensed Matter Physics, Universidade de Brasília, 70919-970 Brasília-DF (Brazil)

    2017-03-18

    Highlights: • We address the problem of equilibrium stability in a general class of non-linear systems. • We link Evolutionary Stable States (ESS) to stable fixed points of square quasi-polynomial (QP) systems. • We show that an interior ES point may be related to stable interior fixed points of QP systems. - Abstract: In this paper we address the problem of stability in a general class of non-linear systems. We establish a link between the concepts of asymptotic stable interior fixed points of square Quasi-Polynomial systems and evolutionary stable states, a property of some payoff matrices arising from evolutionary games.

  2. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  3. Public health evolutionary biology of antimicrobial resistance: priorities for intervention.

    Science.gov (United States)

    Baquero, Fernando; Lanza, Val F; Cantón, Rafael; Coque, Teresa M

    2015-03-01

    The three main processes shaping the evolutionary ecology of antibiotic resistance (AbR) involve the emergence, invasion and occupation by antibiotic-resistant genes of significant environments for human health. The process of emergence in complex bacterial populations is a high-frequency, continuous swarming of ephemeral combinatory genetic and epigenetic explorations inside cells and among cells, populations and communities, expanding in different environments (migration), creating the stochastic variation required for evolutionary progress. Invasion refers to the process by which AbR significantly increases in frequency in a given (invaded) environment, led by external invaders local multiplication and spread, or by endogenous conversion. Conversion occurs because of the spread of AbR genes from an exogenous resistant clone into an established (endogenous) bacterial clone(s) colonizing the environment; and/or because of dissemination of particular resistant genetic variants that emerged within an endogenous clonal population. Occupation of a given environment by a resistant variant means a permanent establishment of this organism in this environment, even in the absence of antibiotic selection. Specific interventions on emergence influence invasion, those acting on invasion also influence occupation and interventions on occupation determine emergence. Such interventions should be simultaneously applied, as they are not simple solutions to the complex problem of AbR.

  4. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  5. Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

    Science.gov (United States)

    Liao, David; Tlsty, Thea D

    2014-08-06

    Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

  6. Are humans prone to autoimmunity? Implications from evolutionary changes in hominin sialic acid biology.

    Science.gov (United States)

    Varki, Ajit

    2017-09-01

    Given varied intrinsic and extrinsic challenges to the immune system, it is unsurprising that each evolutionary lineage evolves distinctive features of immunoreactivity, and that tolerance mechanisms fail, allowing autoimmunity. Humans appear prone to many autoimmune diseases, with mechanisms both genetic and environmental. Another rapidly evolving biological system involves sialic acids, a family of monosaccharides that are terminal caps on cell surface and secreted molecules of vertebrates, and play multifarious roles in immunity. We have explored multiple genomic changes in sialic acid biology that occurred in human ancestors (hominins), some with implications for enhanced immunoreactivity, and hence for autoimmunity. Human ancestors lost the enzyme synthesizing the common mammalian sialic acid Neu5Gc, with an accumulation of the precursor sialic acid Neu5Ac. Resulting changes include an enhanced reactivity by some immune cells and increased ability of macrophages to kill bacteria, at the cost of increased endotoxin sensitivity. There are also multiple human-specific evolutionary changes in inhibitory and activating Siglecs, immune cell receptors that recognize sialic acids as "self-associated molecular patterns" (SAMPs) to modulate immunity, but can also be hijacked by pathogen molecular mimicry of SAMPs. Altered expression patterns and fixed or polymorphic SIGLEC pseudogenization in humans has modulated both innate and adaptive immunity, sometimes favoring over-reactivity. Meanwhile, dietary intake of Neu5Gc (derived primarily from red meats) allows metabolic incorporation of this non-human molecule into human cells--apparently the first example of "xeno-autoimmunity" involving "xeno-autoantigen" interactions with circulating "xeno-autoantibodies". Taken together, some of these factors may contribute to the apparent human propensity for autoimmunity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Physical methods for investigating structural colours in biological systems

    NARCIS (Netherlands)

    Vukusic, P.; Stavenga, D. G.

    2009-01-01

    Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in

  8. Evolutionary cell biology: functional insight from "endless forms most beautiful".

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication 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).

  9. Infrastructure system restoration planning using evolutionary algorithms

    Science.gov (United States)

    Corns, Steven; Long, Suzanna K.; Shoberg, Thomas G.

    2016-01-01

    This paper presents an evolutionary algorithm to address restoration issues for supply chain interdependent critical infrastructure. Rapid restoration of infrastructure after a large-scale disaster is necessary to sustaining a nation's economy and security, but such long-term restoration has not been investigated as thoroughly as initial rescue and recovery efforts. A model of the Greater Saint Louis Missouri area was created and a disaster scenario simulated. An evolutionary algorithm is used to determine the order in which the bridges should be repaired based on indirect costs. Solutions were evaluated based on the reduction of indirect costs and the restoration of transportation capacity. When compared to a greedy algorithm, the evolutionary algorithm solution reduced indirect costs by approximately 12.4% by restoring automotive travel routes for workers and re-establishing the flow of commodities across the three rivers in the Saint Louis area.

  10. Systems biology in animal sciences.

    Science.gov (United States)

    Woelders, H; Te Pas, M F W; Bannink, A; Veerkamp, R F; Smits, M A

    2011-05-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed 'omics' technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A 'system' approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with 'system approaches' in animal sciences, providing exciting opportunities to predict and modulate animal traits.

  11. Systems biology in animal sciences

    NARCIS (Netherlands)

    Woelders, H.; Pas, te M.F.W.; Bannink, A.; Veerkamp, R.F.; Smits, M.A.

    2011-01-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes

  12. NEW SYMMETRIC ENCRYPTION SYSTEM BASED ON EVOLUTIONARY ALGORITHM

    OpenAIRE

    A. Mouloudi

    2015-01-01

    In this article, we present a new symmetric encryption system which is a combination of our ciphering evolutionary system SEC [1] and a new ciphering method called “fragmentation”. This latter allows the alteration of the appearance frequencies of characters from a given text. Our system has at its disposed two keys, the first one is generated by the evolutionary algorithm, the second one is generated after “fragmentation” part. Both of them are symmetric, session keys and strengt...

  13. Children's Ability to Learn Evolutionary Explanations for Biological Adaptation

    Science.gov (United States)

    Shtulman, Andrew; Neal, Cara; Lindquist, Gabrielle

    2016-01-01

    Research Findings: Evolution by natural selection is often relegated to the high school curriculum on the assumption that younger students cannot grasp its complexity. We sought to test that assumption by teaching children ages 4-12 (n = 96) a selection-based explanation for biological adaptation and comparing their success to that of adults…

  14. Evolutionary Biology and the Determinants of Morality | Odozor ...

    African Journals Online (AJOL)

    Against the background of traditional ethics, this paper examined morality as a product of human effort and training, in contrast to its view as an outcome of mere human biological constitution. Conscientious training of the moral faculties, together with the requisite socialization process, enables the human moral nature to be ...

  15. Improving the reviewing process in Ecology and Evolutionary Biology

    OpenAIRE

    Grossman, G. D.

    2014-01-01

    Mejora del proceso de revisión de artículos en ecología y biología evolutiva Se debaten los problemas actuales de la revisión y las prácticas editoriales en los campos de la ecología y la biología evolutiva, y se sugieren posibles soluciones para los mismos. La crisis por la que está pasando la revisión no cambiará a menos que las revistas tomen medidas para aumentar la inclusividad de los revisores y los incentivos a los mismos. Asimismo, tanto las revistas como las instituciones debería...

  16. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  17. Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights.

    Science.gov (United States)

    Jiang, Chao; Caccamo, Paul D; Brun, Yves V

    2015-04-01

    How Darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating "evolutionary thinking" into bacterial cell biology in the genomic era. © 2015 WILEY Periodicals, Inc.

  18. Remembering the Forest While Viewing the Trees: Evolutionary Thinking in the Teaching of Molecular Biology

    Science.gov (United States)

    Saraswati, Sitaraman; Sitaraman, Ramakrishnan

    2014-01-01

    Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of…

  19. A Course in Evolutionary Biology: Engaging Students in the "Practice" of Evolution. Research Report.

    Science.gov (United States)

    Passmore, Cynthia; Stewart, James

    Recent education reform documents emphasize the need for students to develop a rich understanding of evolution's power to integrate knowledge of the natural world. This paper describes a nine-week high school course designed to help students understand evolutionary biology by engaging them in developing, elaborating, and using Charles Darwin's…

  20. Inherit the Policy: A Sociocultural Approach to Understanding Evolutionary Biology Policy in South Carolina

    Science.gov (United States)

    Moore, Gregory D.

    2012-01-01

    South Carolina biology Indicator 5.6 calls for students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory" (South Carolina Department of Education, 2006). Levinson and Sutton (2001) offered a sociocultural approach to policy that considers cultural…

  1. Remembering the forest while viewing the trees: evolutionary thinking in the teaching of molecular biology.

    Science.gov (United States)

    Saraswati, Sitaraman; Sitaraman, Ramakrishnan

    2014-01-01

    Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of evolution in diverse contexts, including those where it is not explicitly mentioned. © 2013 by The International Union of Biochemistry and Molecular Biology.

  2. The significance and scope of evolutionary developmental biology: a vision for the 21st century.

    Science.gov (United States)

    Moczek, Armin P; Sears, Karen E; Stollewerk, Angelika; Wittkopp, Patricia J; Diggle, Pamela; Dworkin, Ian; Ledon-Rettig, Cristina; Matus, David Q; Roth, Siegfried; Abouheif, Ehab; Brown, Federico D; Chiu, Chi-Hua; Cohen, C Sarah; Tomaso, Anthony W De; Gilbert, Scott F; Hall, Brian; Love, Alan C; Lyons, Deirdre C; Sanger, Thomas J; Smith, Joel; Specht, Chelsea; Vallejo-Marin, Mario; Extavour, Cassandra G

    2015-01-01

    Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century. © 2015 Wiley Periodicals, Inc.

  3. Culture extends the scope of evolutionary biology in the great apes.

    Science.gov (United States)

    Whiten, Andrew

    2017-07-24

    Discoveries about the cultures and cultural capacities of the great apes have played a leading role in the recognition emerging in recent decades that cultural inheritance can be a significant factor in the lives not only of humans but also of nonhuman animals. This prominence derives in part from these primates being those with whom we share the most recent common ancestry, thus offering clues to the origins of our own thoroughgoing reliance on cumulative cultural achievements. In addition, the intense research focus on these species has spawned an unprecedented diversity of complementary methodological approaches, the results of which suggest that cultural phenomena pervade the lives of these apes, with potentially major implications for their broader evolutionary biology. Here I review what this extremely broad array of observational and experimental methodologies has taught us about the cultural lives of chimpanzees, gorillas, and orangutans and consider the ways in which this knowledge extends our wider understanding of primate biology and the processes of adaptation and evolution that shape it. I address these issues first by evaluating the extent to which the results of cultural inheritance echo a suite of core principles that underlie organic Darwinian evolution but also extend them in new ways and then by assessing the principal causal interactions between the primary, genetically based organic processes of evolution and the secondary system of cultural inheritance that is based on social learning from others.

  4. Incorporating tree-thinking and evolutionary time scale into developmental biology.

    Science.gov (United States)

    Kuraku, Shigehiro; Feiner, Nathalie; Keeley, Sean D; Hara, Yuichiro

    2016-01-01

    Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples. © 2016 Japanese Society of Developmental Biologists.

  5. Structural Equation Modeling: Applications in ecological and evolutionary biology research

    Science.gov (United States)

    Pugesek, Bruce H.; von Eye, Alexander; Tomer, Adrian

    2003-01-01

    This book presents an introduction to the methodology of structural equation modeling, illustrates its use, and goes on to argue that it has revolutionary implications for the study of natural systems. A major theme of this book is that we have, up to this point, attempted to study systems primarily using methods (such as the univariate model) that were designed only for considering individual processes. Understanding systems requires the capacity to examine simultaneous influences and responses. Structural equation modeling (SEM) has such capabilities. It also possesses many other traits that add strength to its utility as a means of making scientific progress. In light of the capabilities of SEM, it can be argued that much of ecological theory is currently locked in an immature state that impairs its relevance. It is further argued that the principles of SEM are capable of leading to the development and evaluation of multivariate theories of the sort vitally needed for the conservation of natural systems. Supplementary information can be found at the authors website, http://www.jamesbgrace.com/. • Details why multivariate analyses should be used to study ecological systems • Exposes unappreciated weakness in many current popular analyses • Emphasizes the future methodological developments needed to advance our understanding of ecological systems.

  6. Latitudinal clines : An evolutionary view on biological rhythms

    NARCIS (Netherlands)

    Hut, Roelof A.; Paolucci, Silvia; Dor, Roi; Kyriacou, Charalambos P.; Daan, Serge

    2013-01-01

    Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian

  7. Genotype- or Phenotype-Targeting Anticancer Therapies? Lessons from Tumor Evolutionary Biology.

    Science.gov (United States)

    Escargueil, Alexandre E; Prado, Soizic; Dezaire, Ambre; Clairambault, Jean; Larsen, Annette K; Soares, Daniele G

    2016-01-01

    Despite the efficacy of most cancer therapies, drug resistance remains a major problem in the clinic. The eradication of the entire tumor and the cure of the patient by chemotherapy alone are rare, in particular for advanced disease. From an evolutionary perspective, the selective pressure exerted by chemotherapy leads to the emergence of resistant clones where resistance can be associated with many different functional mechanisms at the single cell level or can involve changes in the tumor micro-environment. In the last decade, tumor genomics has contributed to the improvement of our understanding of tumorigenesis and has led to the identification of numerous cellular targets for the development of novel therapies. However, since tumors are by nature extremely heterogeneous, the drug efficacy and economical sustainability of this approach is now debatable. Importantly, tumor cell heterogeneity depends not only on genetic modifications but also on non-genetic processes involving either stochastic events or epigenetic modifications making genetic biomarkers of uncertain utility. In this review, we wish to highlight how evolutionary biology can impact our understanding of carcinogenesis and resistance to therapies. We will discuss new approaches based on applied ecology and evolution dynamics that can be used to convert the cancer into a chronic disease where the drugs would control tumor growth. Finally, we will discuss the way metabolic dysfunction or phenotypic changes can help developing new delivery systems or phenotypetargeted drugs and how exploring new sources of active compounds can conduct to the development of drugs with original mechanisms of action. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. The Physics behind Systems Biology

    Directory of Open Access Journals (Sweden)

    Radde Nicole E.

    2016-12-01

    Full Text Available Systems Biology is a young and rapidly evolving research field, which combines experimental techniques and mathematical modeling in order to achieve a mechanistic understanding of processes underlying the regulation and evolution of living systems. Systems Biology is often associated with an Engineering approach: The purpose is to formulate a data-rich, detailed simulation model that allows to perform numerical (‘in silico’ experiments and then draw conclusions about the biological system. While methods from Engineering may be an appropriate approach to extending the scope of biological investigations to experimentally inaccessible realms and to supporting data-rich experimental work, it may not be the best strategy in a search for design principles of biological systems and the fundamental laws underlying Biology. Physics has a long tradition of characterizing and understanding emergent collective behaviors in systems of interacting units and searching for universal laws. Therefore, it is natural that many concepts used in Systems Biology have their roots in Physics. With an emphasis on Theoretical Physics, we will here review the ‘Physics core’ of Systems Biology, show how some success stories in Systems Biology can be traced back to concepts developed in Physics, and discuss how Systems Biology can further benefit from its Theoretical Physics foundation.

  9. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants.

    Science.gov (United States)

    Plattner, Helmut

    2017-07-18

    During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in

  10. Puzzles in modern biology. II. Language, cancer and the recursive processes of evolutionary innovation.

    Science.gov (United States)

    Frank, Steven A

    2016-01-01

    Human language emerged abruptly. Diverse body forms evolved suddenly. Seed-bearing plants spread rapidly. How do complex evolutionary innovations arise so quickly? Resolving alternative claims remains difficult. The great events of the past happened a long time ago. Cancer provides a model to study evolutionary innovation. A tumor must evolve many novel traits to become an aggressive cancer. I use what we know or could study about cancer to describe the key processes of innovation. In general, evolutionary systems form a hierarchy of recursive processes. Those recursive processes determine the rates at which innovations are generated, spread and transmitted. I relate the recursive processes to abrupt evolutionary innovation.

  11. The Depressed Brain: An Evolutionary Systems Theory.

    Science.gov (United States)

    Badcock, Paul B; Davey, Christopher G; Whittle, Sarah; Allen, Nicholas B; Friston, Karl J

    2017-03-01

    Major depression is a debilitating condition characterised by diverse neurocognitive and behavioural deficits. Nevertheless, our species-typical capacity for depressed mood implies that it serves an adaptive function. Here we apply an interdisciplinary theory of brain function to explain depressed mood and its clinical manifestations. Combining insights from the free-energy principle (FEP) with evolutionary theorising in psychology, we argue that depression reflects an adaptive response to perceived threats of aversive social outcomes (e.g., exclusion) that minimises the likelihood of surprising interpersonal exchanges (i.e., those with unpredictable outcomes). We suggest that psychopathology typically arises from ineffectual attempts to alleviate interpersonal difficulties and/or hyper-reactive neurobiological responses to social stress (i.e., uncertainty), which often stems from early experience that social uncertainty is difficult to resolve. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Annelids in evolutionary developmental biology and comparative genomics.

    Science.gov (United States)

    McDougall, C; Hui, J H L; Monteiro, A; Takahashi, T; Ferrier, D E K

    2008-09-01

    Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.

  13. Annelids in evolutionary developmental biology and comparative genomics

    Directory of Open Access Journals (Sweden)

    Mcdougall C.

    2008-09-01

    Full Text Available Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.

  14. Evolutionary design of discrete controllers for hybrid mechatronic systems

    DEFF Research Database (Denmark)

    Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

    2015-01-01

    This paper investigates the issue of evolutionary design of controllers for hybrid mechatronic systems. Finite State Automaton (FSA) is selected as the representation for a discrete controller due to its interpretability, fast execution speed and natural extension to a statechart, which is very...... popular in industrial applications. A case study of a two-tank system is used to demonstrate that the proposed evolutionary approach can lead to a successful design of an FSA controller for the hybrid mechatronic system, represented by a hybrid bond graph. Generalisation of the evolved FSA controller...... of the evolutionary design of controllers for hybrid mechatronic systems. Finally, some important future research directions are pointed out, leading to the major work of the succeeding part of the research....

  15. Evolutionary steps in the reproductive biology of Annonaceae

    Directory of Open Access Journals (Sweden)

    Gerhard Gottsberger

    2014-01-01

    Full Text Available Flowers of Annonaceae are characterized by fleshy petals, many stamens with hard connective shields and numerous carpels with sessile stigmas often covered by sticky secretions. The petals of many representatives during anthesis form a closed pollination chamber. Protogynous dichogamy with strong scent emissions especially during the pistillate stage is a character of nearly all species. Scent emissions can be enhanced by thermogenesis. The prevailing reproductive system in the family seems to be self-compatibility. The basal genus Anaxagorea besides exhibiting several ancestral morphological characters has also many characters which reappear in other genera. Strong fruit-like scents consisting of fruit-esters and alcohols mainly attract small fruit-beetles (genus Colopterus, Nitidulidae as pollinators, as well as several other beetles (Curculionidae, Chrysomelidae and fruit-flies (Drosophilidae, which themselves gnaw on the thick petals or their larvae are petal or ovule predators. The flowers and the thick petals are thus a floral brood substrate for the visitors and the thick petals of Anaxagorea have to be interpreted as an antipredator structure. Another function of the closed thick petals is the production of heat by accumulated starch, which enhances scent emission and provides a warm shelter for the attracted beetles. Insight into floral characters and floral ecology of Anaxagorea, the sister group of the rest of the Annonaceae, is particularly important for understanding functional evolution and diversification of the family as a whole. As beetle pollination (cantharophily is plesiomorphic in Anaxagorea and in Annonaceae, characters associated with beetle pollination appear imprinted in members of the whole family. Pollination by beetles (cantharophily is the predominant mode of the majority of species worldwide. Examples are given of diurnal representatives (e.g., Guatteria, Duguetia, Annona which function on the basis of fruit

  16. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  17. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  18. Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions.

    Science.gov (United States)

    Olsson, Lennart; Levit, Georgy S; Hossfeld, Uwe

    2010-11-01

    Evolutionary theory has been likened to a "universal acid" (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research--evolutionary developmental biology--has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin's Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the "Jena school" of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about "biometabolic modi" are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research--heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of

  19. Ancestor of the new archetypal biology: Goethe's dynamic typology as a model for contemporary evolutionary developmental biology.

    Science.gov (United States)

    Riegner, Mark F

    2013-12-01

    As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo). Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Thermodynamics, ecology and evolutionary biology: A bridge over troubled water or common ground?

    Science.gov (United States)

    Skene, Keith R.

    2017-11-01

    This paper addresses a key issue confronting ecological and evolutionary biology, namely the challenge of a cohesive approach to these fields given significant differences in the concepts and foundations of their study. Yet these two areas of scientific research are paramount in terms addressing the spatial and temporal dynamics and distribution of diversity, an understanding of which is needed if we are to resolve the current crisis facing the biosphere. The importance of understanding how nature responds to change is now of essential rather than of metaphysical interest as our planet struggles with increasing anthropogenic damage. Ecology and evolutionary biology can no longer remain disjointed. While some progress has been made in terms of synthetic thinking across these areas, this has often been in terms of bridge building, where thinking in one aspect is extended over to the other side. We review these bridges and the success or otherwise of such efforts. This paper then suggests that in order to move from a descriptive to a mechanistic understanding of the biosphere, we may need to re-evaluate our approach to the studies of ecology and evolutionary biology, finding a common denominator that will enable us to address the critical issues facing us, particularly in terms of understanding what drives change, what determines tempo and how communities function. Common ground, we argue, is essential if we are to comprehend how resilience operates in the natural world and how diversification can counter increasing extinction rates. This paper suggests that thermodynamics may provide a bridge between ecology and evolutionary biology, and that this will enable us to move forward with otherwise intractable problems.

  1. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  2. 18th Asia Pacific Symposium on Intelligent and Evolutionary Systems

    CERN Document Server

    Ishibuchi, Hisao; Ong, Yew-Soon; Tan, Kay-Chen

    2015-01-01

    This book contains a collection of the papers accepted in the 18th Asia Pacific Symposium on Intelligent and Evolutionary Systems (IES 2014), which was held in Singapore from 10-12th November 2014. The papers contained in this book demonstrate notable intelligent systems with good analytical and/or empirical results.

  3. Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions

    Science.gov (United States)

    Olsson, Lennart; Levit, Georgy S.; Hoßfeld, Uwe

    2010-11-01

    Evolutionary theory has been likened to a “universal acid” (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research—evolutionary developmental biology—has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin’s Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the “Jena school” of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about “biometabolic modi” are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research—heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the

  4. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  5. Plant systems biology: network matters.

    Science.gov (United States)

    Lucas, Mikaël; Laplaze, Laurent; Bennett, Malcolm J

    2011-04-01

    Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology. © 2011 Blackwell Publishing Ltd.

  6. The Neural Systems of Forgiveness: An Evolutionary Psychological Perspective

    Directory of Open Access Journals (Sweden)

    Joseph Billingsley

    2017-05-01

    Full Text Available Evolution-minded researchers posit that the suite of human cognitive adaptations may include forgiveness systems. According to these researchers, forgiveness systems regulate interpersonal motivation toward a transgressor in the wake of harm by weighing multiple factors that influence both the potential gains of future interaction with the transgressor and the likelihood of future harm. Although behavioral research generally supports this evolutionary model of forgiveness, the model’s claims have not been examined with available neuroscience specifically in mind, nor has recent neuroscientific research on forgiveness generally considered the evolutionary literature. The current review aims to help bridge this gap by using evolutionary psychology and cognitive neuroscience to mutually inform and interrogate one another. We briefly summarize the evolutionary research on forgiveness, then review recent neuroscientific findings on forgiveness in light of the evolutionary model. We emphasize neuroscientific research that links desire for vengeance to reward-based areas of the brain, that singles out prefrontal areas likely associated with inhibition of vengeful feelings, and that correlates the activity of a theory-of-mind network with assessments of the intentions and blameworthiness of those who commit harm. In addition, we identify gaps in the existing neuroscientific literature, and propose future research directions that might address them, at least in part.

  7. The Neural Systems of Forgiveness: An Evolutionary Psychological Perspective.

    Science.gov (United States)

    Billingsley, Joseph; Losin, Elizabeth A R

    2017-01-01

    Evolution-minded researchers posit that the suite of human cognitive adaptations may include forgiveness systems. According to these researchers, forgiveness systems regulate interpersonal motivation toward a transgressor in the wake of harm by weighing multiple factors that influence both the potential gains of future interaction with the transgressor and the likelihood of future harm. Although behavioral research generally supports this evolutionary model of forgiveness, the model's claims have not been examined with available neuroscience specifically in mind, nor has recent neuroscientific research on forgiveness generally considered the evolutionary literature. The current review aims to help bridge this gap by using evolutionary psychology and cognitive neuroscience to mutually inform and interrogate one another. We briefly summarize the evolutionary research on forgiveness, then review recent neuroscientific findings on forgiveness in light of the evolutionary model. We emphasize neuroscientific research that links desire for vengeance to reward-based areas of the brain, that singles out prefrontal areas likely associated with inhibition of vengeful feelings, and that correlates the activity of a theory-of-mind network with assessments of the intentions and blameworthiness of those who commit harm. In addition, we identify gaps in the existing neuroscientific literature, and propose future research directions that might address them, at least in part.

  8. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  9. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  10. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  11. Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

    Science.gov (United States)

    Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

    2017-02-01

    Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. What will result from the interaction between functional and evolutionary biology?

    Science.gov (United States)

    Morange, Michel

    2011-03-01

    The modern synthesis has been considered to be wrongly called a "synthesis", since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a "new synthesis". My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

    Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology.

    Science.gov (United States)

    Vianello, Angelo; Passamonti, Sabina

    2016-02-09

    Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote causes). Are these divergent views on what is life? The epistemological role of functional biology (molecular biology, but also biochemistry, physiology, cell biology and so forth) appears essential, for its capacity to identify several mechanisms of natural selection of new characters, individuals and populations. Nevertheless, several issues remain unsolved, such as orphan metabolic activities, i.e., adaptive functions still missing the identification of the underlying genes and proteins, and orphan genes, i.e., genes that bear no signature of evolutionary history, yet provide an organism with improved adaptation to environmental changes. In the framework of the Extended Synthesis, we suggest that the adaptive roles of any known function/structure are reappraised in terms of their capacity to warrant constancy of the internal environment (homeostasis), a concept that encompasses both proximal and remote causes.

  15. Investigation on Evolutionary Computation Techniques of a Nonlinear System

    Directory of Open Access Journals (Sweden)

    Tran Trong Dao

    2011-01-01

    Full Text Available The main aim of this work is to show that such a powerful optimizing tool like evolutionary algorithms (EAs can be in reality used for the simulation and optimization of a nonlinear system. A nonlinear mathematical model is required to describe the dynamic behaviour of batch process; this justifies the use of evolutionary method of the EAs to deal with this process. Four algorithms from the field of artificial intelligent—differential evolution (DE, self-organizing migrating algorithm (SOMA, genetic algorithm (GA, and simulated annealing (SA—are used in this investigation. The results show that EAs are used successfully in the process optimization.

  16. NASA's Evolutionary Xenon Thruster (NEXT) Ion Propulsion System Information Summary

    Science.gov (United States)

    Pencil, Eirc S.; Benson, Scott W.

    2008-01-01

    This document is a guide to New Frontiers mission proposal teams. The document describes the development and status of the NASA's Evolutionary Xenon Thruster (NEXT) ion propulsion system (IPS) technology, its application to planetary missions, and the process anticipated to transition NEXT to the first flight mission.

  17. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  18. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  19. Electromagnetic fields in biological systems

    CERN Document Server

    Lin, James C

    2016-01-01

    As wireless technology becomes more sophisticated and accessible to more users, the interactions of electromagnetic fields with biological systems have captured the interest not only of the scientific community but also the general public. Unintended or deleterious biological effects of electromagnetic fields and radiation may indicate grounds for health and safety precautions in their use. Spanning static fields to terahertz waves, Electromagnetic Fields in Biological Systems explores the range of consequences these fields have on the human body. With contributions by an array of experts, topics discussed include: Essential interactions and field coupling phenomena, highlighting their importance in research on biological effects and in scientific, industrial, and medical applications Electric field interactions in cells, focusing on ultrashort, pulsed high-intensity fields The effect of exposure to naturally occurring and human-made static, low-frequency, and pulsed magnetic fields in biological systems Dosi...

  20. Decentralized control of ecological and biological networks through Evolutionary Network Control

    Directory of Open Access Journals (Sweden)

    Alessandro Ferrarini

    2016-09-01

    Full Text Available Evolutionary Network Control (ENC has been recently introduced to allow the control of any kind of ecological and biological networks, with an arbitrary number of nodes and links, acting from inside and/or outside. To date, ENC has been applied using a centralized approach where an arbitrary number of network nodes and links could be tamed. This approach has shown to be effective in the control of ecological and biological networks. However a decentralized control, where only one node and the correspondent input/output links are controlled, could be more economic from a computational viewpoint, in particular when the network is very large (i.e. big data. In this view, ENC is upgraded here to realize the decentralized control of ecological and biological nets.

  1. The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology

    Directory of Open Access Journals (Sweden)

    Silva Larissa

    2012-11-01

    Full Text Available Abstract Background Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding of the relevant host-parasite interactions, and the possible treatments are limited by the emergence of resistant strains and the absence of a vaccine. The S. mansoni genome was completely sequenced and still under continuous annotation. Nevertheless, more than 45% of the encoded proteins remain without experimental characterization or even functional prediction. To improve our knowledge regarding the biology of this parasite, we conducted a proteome-wide evolutionary analysis to provide a broad view of the S. mansoni’s proteome evolution and to improve its functional annotation. Results Using a phylogenomic approach, we reconstructed the S. mansoni phylome, which comprises the evolutionary histories of all parasite proteins and their homologs across 12 other organisms. The analysis of a total of 7,964 phylogenies allowed a deeper understanding of genomic complexity and evolutionary adaptations to a parasitic lifestyle. In particular, the identification of lineage-specific gene duplications pointed to the diversification of several protein families that are relevant for host-parasite interaction, including proteases, tetraspanins, fucosyltransferases, venom allergen-like proteins, and tegumental-allergen-like proteins. In addition to the evolutionary knowledge, the phylome data enabled us to automatically re-annotate 3,451 proteins through a phylogenetic-based approach rather than solely sequence similarity searches. To allow further exploitation of this valuable data, all information has been made available at PhylomeDB (http://www.phylomedb.org. Conclusions In this study, we used an evolutionary approach to assess S. mansoni parasite biology, improve genome/proteome functional annotation, and provide insights into

  2. The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology.

    Science.gov (United States)

    Silva, Larissa Lopes; Marcet-Houben, Marina; Nahum, Laila Alves; Zerlotini, Adhemar; Gabaldón, Toni; Oliveira, Guilherme

    2012-11-13

    Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding of the relevant host-parasite interactions, and the possible treatments are limited by the emergence of resistant strains and the absence of a vaccine. The S. mansoni genome was completely sequenced and still under continuous annotation. Nevertheless, more than 45% of the encoded proteins remain without experimental characterization or even functional prediction. To improve our knowledge regarding the biology of this parasite, we conducted a proteome-wide evolutionary analysis to provide a broad view of the S. mansoni's proteome evolution and to improve its functional annotation. Using a phylogenomic approach, we reconstructed the S. mansoni phylome, which comprises the evolutionary histories of all parasite proteins and their homologs across 12 other organisms. The analysis of a total of 7,964 phylogenies allowed a deeper understanding of genomic complexity and evolutionary adaptations to a parasitic lifestyle. In particular, the identification of lineage-specific gene duplications pointed to the diversification of several protein families that are relevant for host-parasite interaction, including proteases, tetraspanins, fucosyltransferases, venom allergen-like proteins, and tegumental-allergen-like proteins. In addition to the evolutionary knowledge, the phylome data enabled us to automatically re-annotate 3,451 proteins through a phylogenetic-based approach rather than solely sequence similarity searches. To allow further exploitation of this valuable data, all information has been made available at PhylomeDB (http://www.phylomedb.org). In this study, we used an evolutionary approach to assess S. mansoni parasite biology, improve genome/proteome functional annotation, and provide insights into host-parasite interactions. Taking advantage of a proteome

  3. Efficient design of hybrid renewable energy systems using evolutionary algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Bernal-Agustin, Jose L.; Dufo-Lopez, Rodolfo [Department of Electrical Engineering, University of Zaragoza, Calle Maria de Luna, 3. 50018 Zaragoza (Spain)

    2009-03-15

    This paper shows an exhaustive study that has obtained the best values for the control parameters of an evolutionary algorithm developed by the authors, which permits the efficient design and control of hybrid systems of electrical energy generation, obtaining good solutions but needing low computational effort. In particular, for this study, a complex photovoltaic (PV)-wind-diesel-batteries-hydrogen system has been considered. In order to appropriately evaluate the behaviour of the evolutionary algorithm, the global optimal solution has been obtained (the one in which total net present cost presents a minor value) by an enumerative method. Next, a large number of designs were created using the evolutionary algorithm and modifying the values of the parameters that control its functioning. Finally, from the obtained results, it has been possible to determine the size of the population, the number of generations, the ratios of crossing and mutation, as well as the type of mutation most suitable to assure a probability near 100% of obtaining the global optimal design using the evolutionary algorithm. (author)

  4. Systems biology of human atherosclerosis.

    Science.gov (United States)

    Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H

    2014-01-01

    Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

  5. Text mining for systems biology.

    Science.gov (United States)

    Fluck, Juliane; Hofmann-Apitius, Martin

    2014-02-01

    Scientific communication in biomedicine is, by and large, still text based. Text mining technologies for the automated extraction of useful biomedical information from unstructured text that can be directly used for systems biology modelling have been substantially improved over the past few years. In this review, we underline the importance of named entity recognition and relationship extraction as fundamental approaches that are relevant to systems biology. Furthermore, we emphasize the role of publicly organized scientific benchmarking challenges that reflect the current status of text-mining technology and are important in moving the entire field forward. Given further interdisciplinary development of systems biology-orientated ontologies and training corpora, we expect a steadily increasing impact of text-mining technology on systems biology in the future. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  7. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  8. On the origins of anticipation as an evolutionary framework: functional systems perspective

    Science.gov (United States)

    Kurismaa, Andres

    2015-08-01

    This paper discusses the problem of anticipation from an evolutionary and systems-theoretical perspective, developed in the context of Russian/Soviet evolutionary biological and neurophysiological schools in the early and mid-twentieth century. On this background, an outline is given of the epigenetic interpretation of anticipatory capacities formulated and substantiated by the eminent Russian neurophysiologist academician Peter K. Anokhin in the framework of functional systems theory. It is considered that several key positions of this theory are well confirmed by recent evidence on anticipation as an evolutionarily basic adaptive capacity, possibly inherent to the organization of life. In the field of neuroscience, the theory of functional systems may potentially facilitate future studies at the intersection of learning, development and evolution by representing an integrative approach to the problem of anticipation.

  9. The future of Evo-Devo: the inaugural meeting of the Pan American Society for evolutionary developmental biology.

    Science.gov (United States)

    Lesoway, Maryna P

    2016-01-01

    What is the future of evolutionary developmental biology? This question and more were discussed at the inaugural meeting for the Pan American Society for Evolutionary Developmental Biology, held August 5-9, 2015, in Berkeley, California, USA. More than 300 participants attended the first meeting of the new society, representing the current diversity of Evo-Devo. Speakers came from throughout the Americas, presenting work using an impressive range of study systems, techniques, and approaches. Current research draws from themes including the role of gene regulatory networks, plasticity and the role of the environment, novelty, population genetics, and regeneration, using new and emerging techniques as well as traditional tools. Multiple workshops and a discussion session covered subjects both practical and theoretical, providing an opportunity for members to discuss the current challenges and future directions for Evo-Devo. The excitement and discussion generated over the course of the meeting demonstrates the current dynamism of the field, suggesting that the future of Evo-Devo is bright indeed. © 2016 Wiley Periodicals, Inc.

  10. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Biological invasions in agricultural settings: insights from evolutionary biology and population genetics.

    Science.gov (United States)

    Guillemaud, Thomas; Ciosi, Marc; Lombaert, Eric; Estoup, Arnaud

    2011-03-01

    Invasion biology and agriculture are intimately related for several reasons and in particular because many agricultural pest species are recent invaders. In this article we suggest that the reconstruction of invasion routes with population genetics-based methods can address fundamental questions in ecology and practical aspects of the management of biological invasions in agricultural settings. We provide a brief description of the methods used to reconstruct invasion routes and describe their main characteristics. In particular, we focus on a scenario--the bridgehead invasion scenario --which had been overlooked until recently. We show that this scenario, in which an invasive population is the source of other invasive populations, is evolutionarily parsimonious and may have played a crucial role in shaping the distribution of many recent agricultural pests. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  12. Evolutionary design of discrete controllers for hybrid mechatronic systems

    Science.gov (United States)

    Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

    2015-01-01

    This paper investigates the issue of evolutionary design of controllers for hybrid mechatronic systems. Finite State Automaton (FSA) is selected as the representation for a discrete controller due to its interpretability, fast execution speed and natural extension to a statechart, which is very popular in industrial applications. A case study of a two-tank system is used to demonstrate that the proposed evolutionary approach can lead to a successful design of an FSA controller for the hybrid mechatronic system, represented by a hybrid bond graph. Generalisation of the evolved FSA controller to unknown control targets is also tested. Further, a comparison with another type of controller, a lookahead controller, is conducted, with advantages and disadvantages of each discussed. The comparison sheds light on which type of controller representation is a better choice to use in various stages of the evolutionary design of controllers for hybrid mechatronic systems. Finally, some important future research directions are pointed out, leading to the major work of the succeeding part of the research.

  13. Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology

    Science.gov (United States)

    Hiatt, Anna; Davis, Gregory K.; Trujillo, Caleb; Terry, Mark; French, Donald P.; Price, Rebecca M.; Perez, Kathryn E.

    2013-01-01

    To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution. Based on results of surveys and interviews with students, we suggest that teaching core concepts (CCs) within a framework that integrates supporting concepts (SCs) from both evolutionary and developmental biology can improve evo-devo instruction. We articulate CCs, SCs, and foundational concepts (FCs) that provide an integrative framework to help students master evo-devo concepts and to help educators address specific conceptual difficulties their students have with evo-devo. We then identify the difficulties that undergraduates have with these concepts. Most of these difficulties are of two types: those that are ubiquitous among students in all areas of biology and those that stem from an inadequate understanding of FCs from developmental, cell, and molecular biology. PMID:24006397

  14. Circadian systems biology in Metazoa.

    Science.gov (United States)

    Lin, Li-Ling; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-11-01

    Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  15. A Free Energy Principle for Biological Systems.

    Science.gov (United States)

    Karl, Friston

    2012-11-01

    This paper describes a free energy principle that tries to explain the ability of biological systems to resist a natural tendency to disorder. It appeals to circular causality of the sort found in synergetic formulations of self-organization (e.g., the slaving principle) and models of coupled dynamical systems, using nonlinear Fokker Planck equations. Here, circular causality is induced by separating the states of a random dynamical system into external and internal states, where external states are subject to random fluctuations and internal states are not. This reduces the problem to finding some (deterministic) dynamics of the internal states that ensure the system visits a limited number of external states; in other words, the measure of its (random) attracting set, or the Shannon entropy of the external states is small. We motivate a solution using a principle of least action based on variational free energy (from statistical physics) and establish the conditions under which it is formally equivalent to the information bottleneck method. This approach has proved useful in understanding the functional architecture of the brain. The generality of variational free energy minimisation and corresponding information theoretic formulations may speak to interesting applications beyond the neurosciences; e.g., in molecular or evolutionary biology.

  16. Exploring the Factors Related to Acceptance of Evolutionary Theory among Turkish Preservice Biology Teachers: Toward a More Informative Conceptual Ecology for Biological Evolution

    Science.gov (United States)

    Deniz, Hasan; Donnelly, Lisa A.; Yilmaz, Irfan

    2008-01-01

    In this study, using multiple regression analysis, we aimed to explore the factors related to acceptance of evolutionary theory among preservice Turkish biology teachers using conceptual ecology for biological evolution as a theoretical lens. We aimed to determine the extent to which we can account for the variance in acceptance of evolutionary…

  17. Internationality of Publications, Co-Authorship, References and Citations in Brazilian Evolutionary Biology

    Directory of Open Access Journals (Sweden)

    Dirce Maria Santin

    2016-02-01

    Full Text Available The international dimensions of contemporary science have significantly impacted production and use patterns of scientific knowledge, which, in turn, requires new insights of librarians, publishers and academic institutions. Despite the recognized importance of internationality in science, studies on the internationalization of scientific output are still limited and dedicated exclusively to analyzing of its diffusion and international collaboration. This study analyzes the national/international character of articles, international collaboration, references and citations of Brazilian scientific output in Evolutionary Biology in order to understand the contribution to the internationalization of science in Brazil. Analyses are based on data from the Science Citation Index of Web of Science and include 1450 articles, 60,454 references and 18,059 citing documents. Results reveal similar internationality patterns, with 99.6% of articles published in foreign journals, 90.5% international references, and 88.5% international citations. Despite recording the lowest value among the indicators (51.9%, international collaboration surpasses the national and international average and is an important characteristic in the field in Brazil, contributing to increasing the number of references and the impact of articles. Evolutionary Biology is considered a predominantly international field, whose internationality patterns increase the audience for the studies and provide greater visibility for Brazilian science.

  18. [Medical applications of systems biology].

    Science.gov (United States)

    Demongeot, Jacques

    2009-01-01

    We illustrate in this review some applications of systems biology in the medical and biological areas. After a brief summary of time scales experienced by medical -observations and of the general scheme of dynamic systems, we describe how some techniques underlying the complex systems theory can be applied to model medical issues in immunology, medical genetics, developmental morphogenesis, biochemistry, epidemiology, telemedecine and multiple platforms of expertise. In concluding, we will discuss the issue of "clinomics" coupling clinical and -omics data in a unique patient-specific file.

  19. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  20. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  1. Diversity matters: the importance of comparative studies and the potential for synergy between neuroscience and evolutionary biology.

    Science.gov (United States)

    Carlson, Bruce A

    2012-08-01

    Basic research in neuroscience and clinical research on neurological disorders synergistically increase our understanding of the human brain. Traditionally, functional and clinical studies of the human brain were limited to postmortem histology, "natural experiments" (eg, lesions to brain areas caused by trauma or disease), and crude measures of electrical activity such as electroencephalography. More recently, the development of transcranial magnetic stimulation and rapid advances in imaging technology have greatly facilitated human brain research. In rare cases in which treating a neurological disorder involves implanting electrodes, researchers can even record the electrical activity of individual neurons. Although these approaches have led to important insights, they do not allow for a precise dissection of the underlying mechanisms by which the brain mediates perception, cognition, and behavior. Thus, neuroscientists and neurologists remain severely limited in the types of experiments they can perform on human subjects and much of our understanding of brain structure and function is based on research in animal models. In this article, I highlight the enormous potential for synergy between neuroscience and evolutionary biology. Nervous systems have been shaped by evolution, and comparative approaches take advantage of the resulting diversity to gain insight into the neural mechanisms of behavior. On the other hand, nervous systems and the behaviors and perceptions they mediate can play a fundamental role in the evolutionary processes that generate this diversity. To emphasize these points, I describe recent findings from research on African fishes that use electricity to communicate and navigate in their dark underwater world.

  2. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  3. Insights from Systems Biology in Physiological Studies: Learning from Context

    Directory of Open Access Journals (Sweden)

    Pedro Henrique Imenez Silva

    2017-06-01

    Full Text Available Systems biology presents an integrated view of biological systems, focusing on the relations between elements, whether functional or evolutionary, and providing a rich framework for the comprehension of life. At the same time, many low-throughput experimental studies are performed without influence from this integrated view, whilst high-throughput experiments use low-throughput results in their validation and interpretation. We propose an inversion in this logic, and ask which benefits could be obtained from a holistic view coming from high-throughput studies―and systems biology in particular―in interpreting and designing low-throughput experiments. By exploring some key examples from the renal and adrenal physiology, we try to show that network and modularity theory, along with observed patterns of association between elements in a biological system, can have profound effects on our ability to draw meaningful conclusions from experiments.

  4. Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

    Directory of Open Access Journals (Sweden)

    Saito Shigeru

    2010-05-01

    Full Text Available Abstract Background Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages. Results In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events. Conclusions Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

  5. Evolutionary multi-agent systems from inspirations to applications

    CERN Document Server

    Byrski, Aleksander

    2017-01-01

    This book addresses agent-based computing, concentrating in particular on evolutionary multi-agent systems (EMAS), which have been developed since 1996 at the AGH University of Science and Technology in Cracow, Poland. It provides the relevant background information on and a detailed description of this computing paradigm, along with key experimental results. Readers will benefit from the insightful discussion, which primarily concerns the efficient implementation of computing frameworks for developing EMAS and similar computing systems, as well as a detailed formal model. Theoretical deliberations demonstrating that computing with EMAS always helps to find the optimal solution are also included, rounding out the coverage.

  6. Systems biology of cellular rhythms.

    Science.gov (United States)

    Goldbeter, A; Gérard, C; Gonze, D; Leloup, J-C; Dupont, G

    2012-08-31

    Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise.

  7. Toward a synthesis of developmental biology with evolutionary theory and ecology.

    Science.gov (United States)

    Sommer, Ralf J; Mayer, Melanie G

    2015-01-01

    The evolutionary conservation of developmental mechanisms is a truism in biology, but few attempts have been made to integrate development with evolutionary theory and ecology. To work toward such a synthesis, we summarize studies in the nematode model Pristionchus pacificus, focusing on the development of the dauer, a stress-resistant, alternative larval stage. Integrative approaches combining molecular and genetic principles of development with natural variation and ecological studies in wild populations have identified a key role for a developmental switch mechanism in dauer development and evolution, one that involves the nuclear hormone receptor DAF-12. DAF-12 is a crucial regulator and convergence point for different signaling inputs, and its function is conserved among free-living and parasitic nematodes. Furthermore, DAF-12 is the target of regulatory loops that rely on novel or fast-evolving components to control the intraspecific competition of dauer larvae. We propose developmental switches as paradigms for understanding the integration of development, evolution, and ecology at the molecular level.

  8. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  9. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  10. Why Control Activity? Evolutionary Selection Pressures Affecting the Development of Physical Activity Genetic and Biological Regulation

    Directory of Open Access Journals (Sweden)

    J. Timothy Lightfoot

    2013-01-01

    Full Text Available The literature strongly suggests that daily physical activity is genetically and biologically regulated. Potential identities of the responsible mechanisms are unclear, but little has been written concerning the possible evolutionary selection pressures leading to the development of genetic/biological controls of physical activity. Given the weak relationship between exercise endurance and activity levels and the differential genomic locations associated with the regulation of endurance and activity, it is probable that regulation of endurance and activity evolved separately. This hypothesis paper considers energy expenditures and duration of activity in hunter/gatherers, pretechnology farmers, and modern Western societies and considers the potential of each to selectively influence the development of activity regulation. Food availability is also considered given the known linkage of caloric restriction on physical activity as well as early data relating food oversupply to physical inactivity. Elucidating the selection pressures responsible for the genetic/biological control of activity will allow further consideration of these pressures on activity in today’s society, especially the linkages between food and activity. Further, current food abundance is removing the cues for activity that were present for the first 40,000 years of human evolution, and thus future research should investigate the effects of this abundance upon the mechanisms regulating activity.

  11. Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

    Science.gov (United States)

    Morris, Dylan H; Gostic, Katelyn M; Pompei, Simone; Bedford, Trevor; Łuksza, Marta; Neher, Richard A; Grenfell, Bryan T; Lässig, Michael; McCauley, John W

    2017-10-30

    Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Developed through data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Collaboration Networks in the Brazilian Scientific Output in Evolutionary Biology: 2000-2012.

    Science.gov (United States)

    Santin, Dirce M; Vanz, Samile A S; Stumpf, Ida R C

    2016-03-01

    This article analyzes the existing collaboration networks in the Brazilian scientific output in Evolutionary Biology, considering articles published during the period from 2000 to 2012 in journals indexed by Web of Science. The methodology integrates bibliometric techniques and Social Network Analysis resources to describe the growth of Brazilian scientific output and understand the levels, dynamics and structure of collaboration between authors, institutions and countries. The results unveil an enhancement and consolidation of collaborative relationships over time and suggest the existence of key institutions and authors, whose influence on research is expressed by the variety and intensity of the relationships established in the co-authorship of articles. International collaboration, present in more than half of the publications, is highly significant and unusual in Brazilian science. The situation indicates the internationalization of scientific output and the ability of the field to take part in the science produced by the international scientific community.

  13. Effects of demographic stochasticity on biological community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke

    2010-04-13

    We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.

  14. The expiry date of man: a synthesis of evolutionary biology and public health.

    Science.gov (United States)

    Bonneux, L; Barendregt, J J; Van der Maas, P J

    1998-10-01

    In industrialised countries, mortality and morbidity are dominated by age related chronic degenerative diseases. The health and health care needs of future populations will be heavily determined by these conditions of old age. Two opposite scenarios of future morbidity exist: morbidity might decrease ("compress"), because life span is limited, and the incidence of disease is postponed. Or morbidity might increase ("expand"), because death is delayed more than disease incidence. Optimality theory in evolutionary biology explains senescence as a by product of an optimised life history. The theory clarifies how senescence is timed by the competing needs for reproduction and survival, and why this leads to a generalised deterioration of many functions at many levels. As death and disease are not independent, future morbidity will depend on duration and severity of the process of senescence, partly determined by health care, palliating the disease severity but increasing the disease duration by postponing death. Even if morbidity might be compressed, health care needs will surely expand.

  15. Collaboration Networks in the Brazilian Scientific Output in Evolutionary Biology: 2000-2012

    Directory of Open Access Journals (Sweden)

    Dirce M. Santin

    2016-03-01

    Full Text Available This article analyzes the existing collaboration networks in the Brazilian scientific output in Evolutionary Biology, considering articles published during the period from 2000 to 2012 in journals indexed by Web of Science. The methodology integrates bibliometric techniques and Social Network Analysis resources to describe the growth of Brazilian scientific output and understand the levels, dynamics and structure of collaboration between authors, institutions and countries. The results unveil an enhancement and consolidation of collaborative relationships over time and suggest the existence of key institutions and authors, whose influence on research is expressed by the variety and intensity of the relationships established in the co-authorship of articles. International collaboration, present in more than half of the publications, is highly significant and unusual in Brazilian science. The situation indicates the internationalization of scientific output and the ability of the field to take part in the science produced by the international scientific community.

  16. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  17. The causal pie model: an epidemiological method applied to evolutionary biology and ecology.

    Science.gov (United States)

    Wensink, Maarten; Westendorp, Rudi G J; Baudisch, Annette

    2014-05-01

    A general concept for thinking about causality facilitates swift comprehension of results, and the vocabulary that belongs to the concept is instrumental in cross-disciplinary communication. The causal pie model has fulfilled this role in epidemiology and could be of similar value in evolutionary biology and ecology. In the causal pie model, outcomes result from sufficient causes. Each sufficient cause is made up of a "causal pie" of "component causes". Several different causal pies may exist for the same outcome. If and only if all component causes of a sufficient cause are present, that is, a causal pie is complete, does the outcome occur. The effect of a component cause hence depends on the presence of the other component causes that constitute some causal pie. Because all component causes are equally and fully causative for the outcome, the sum of causes for some outcome exceeds 100%. The causal pie model provides a way of thinking that maps into a number of recurrent themes in evolutionary biology and ecology: It charts when component causes have an effect and are subject to natural selection, and how component causes affect selection on other component causes; which partitions of outcomes with respect to causes are feasible and useful; and how to view the composition of a(n apparently homogeneous) population. The diversity of specific results that is directly understood from the causal pie model is a test for both the validity and the applicability of the model. The causal pie model provides a common language in which results across disciplines can be communicated and serves as a template along which future causal analyses can be made.

  18. The system-biological GLOBE 3D Genome Platform. : A new holistic genome viewer for molecular genetics

    NARCIS (Netherlands)

    M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); T.A. Knoch (Tobias)

    2009-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the

  19. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  20. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  1. Evolutionary Development of the Simulation by Logical Modeling System (SIBYL)

    Science.gov (United States)

    Wu, Helen

    1995-01-01

    Through the evolutionary development of the Simulation by Logical Modeling System (SIBYL) we have re-engineered the expensive and complex IBM mainframe based Long-term Hardware Projection Model (LHPM) to a robust cost-effective computer based mode that is easy to use. We achieved significant cost reductions and improved productivity in preparing long-term forecasts of Space Shuttle Main Engine (SSME) hardware. The LHPM for the SSME is a stochastic simulation model that projects the hardware requirements over 10 years. SIBYL is now the primary modeling tool for developing SSME logistics proposals and Program Operating Plan (POP) for NASA and divisional marketing studies.

  2. An Evolutionary Approach to Regional Systems of Innovation

    DEFF Research Database (Denmark)

    Gunnarsson, Jan Sture Gunnar; Wallin, Torsten

    This article examines how the birth and the development of regional systems of innovation are connected with economic selection and points to implications for regional-level policies. The research questions are explored using an evolutionary model, which emphasises geographical spaces...... using computer simulations. The primary findings are, firstly, that the model generates predictions suited for empirical research on how economic selection influences cooperative behaviour of innovative factors. Secondly, we demonstrate how a region's entrepreneurial activity and growth can...... be controlled in a decentralised way by regions....

  3. System biology of gene regulation.

    Science.gov (United States)

    Baitaluk, Michael

    2009-01-01

    ) questions of biological relevance. Thus systems biology could be treated as such a socioscientific phenomenon and a new approach to both experiments and theory that is defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel.

  4. Electron Transfer in Biological Systems

    Science.gov (United States)

    Evenson, Jeffrey Wayne

    1993-01-01

    A review of electron transfer in biology is provided. Chemiosmotic theory, a phenomenological discussion of electron transfer in the bacterial reaction center, and a general formalism for treating electron transfer in condensed systems (including biological systems) are presented. The effective electronic donor/acceptor coupling (H_{DA}) for a bridged electron transfer system is defined. An expression for H_{DA} in terms of the bridge Green's function is developed for systems represented by a tight-binding Hamiltonian. H_{DA } is computed exactly for two systems, and the existence of a dimensionless parameter which determines whether the effective coupling oscillates or decays with increasing donor/acceptor distance is shown. A numerical technique for computing H_{DA} is developed and shown to be significantly more powerful than the conventional Larsson technique. The inverse matrix technique and pathway methods for computing the effective coupling in bridged electron transfer systems are defined and compared. The inverse matrix technique is found to be more powerful on general theoretical grounds and more accurate for numerical calculations of the effective coupling for the butane-1-4-diyl diradical and dimethylene cyclohexane. Parameters for electron transfer Hamiltonians and multi-pathway effects are discussed. Calculations for a simple model electron transfer system and tuna cytochrome c demonstrate a dichotomy in the behavior of the effective coupling distance dependence. In one regime the effective coupling varies exponentially with distance and depends only on the average properties of the bridging material; in the other regime the effective coupling has a complex distance dependence and is sensitive to the details of the bridging material. Experiments and theory indicate that both regimes occur in biological systems, providing a new perspective on a recent controversy over the nature of the distance dependence. We review the status of effective coupling

  5. [Circadian rhythms and systems biology].

    Science.gov (United States)

    Goldbeter, Albert; Gérard, Claude; Leloup, Jean-Christophe

    2010-01-01

    Cellular rhythms represent a field of choice for studies in system biology. The examples of circadian rhythms and of the cell cycle show how the experimental and modeling approaches contribute to clarify the conditions in which periodic behavior spontaneously arises in regulatory networks at the cellular level. Circadian rhythms originate from intertwined positive and negative feedback loops controlling the expression of several clock genes. Models can be used to address the dynamical bases of physiological disorders related to dysfunctions of the mammalian circadian clock. The cell cycle is driven by a network of cyclin-dependent kinases (Cdks). Modeled in the form of four modules coupled through multiple regulatory interactions, the Cdk network operates in an oscillatory manner in the presence of sufficient amounts of growth factor. For circadian rhythms and the cell cycle, as for other recently observed cellular rhythms, periodic behavior represents an emergent property of biological systems related to their regulatory structure.

  6. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  7. HVAC system optimization for energy management by evolutionary programming

    Energy Technology Data Exchange (ETDEWEB)

    Fong, K.F.; Chow, T.T. [City University of Hong Kong, Kowloon (China). Division of Building Science and Technology; Hanby, V.I. [De Montfort Univ., Leicester (United Kingdom). Inst. of Energy and Sustainable Development

    2006-03-15

    Energy management of heating, ventilating and air-conditioning (HVAC) systems is a primary concern in building projects, since the energy consumption in electricity has the highest percentage in HVAC among all building services installations and electric appliances. Without sacrifice of thermal comfort, to reset the suitable operating parameters, such as the chilled water temperature and supply air temperature, would have energy saving with immediate effect. For the typical commercial building projects, it is not difficult to acquire the reference settings for efficient operation. However, for some special projects, due to the specific design and control of the HVAC system, conventional settings may not be necessarily energy-efficient in daily operation. In this paper, the simulation-optimization approach was proposed for the effective energy management of HVAC system. Due to the complicated interrelationship of the entire HVAC system, which commonly includes the water side and air side systems, it is necessary to suggest optimum settings for different operations in response to the dynamic cooling loads and changing weather conditions throughout a year. A metaheuristic simulation-EP (evolutionary programming) coupling approach was developed using evolutionary programming, which can effectively handle the discrete, non-linear and highly constrained optimization problems, such as those related to HVAC systems. The effectiveness of this simulation-EP coupling suite was demonstrated through the establishment of a monthly optimum reset scheme for both the chilled water and supply air temperatures of the HVAC installations of a local project. This reset scheme would have a saving potential of about 7% as compared to the existing operational settings, without any extra cost. (author)

  8. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  9. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  10. Wiener-Hammerstein system identification - an evolutionary approach

    Science.gov (United States)

    Naitali, Abdessamad; Giri, Fouad

    2016-01-01

    The problem of identifying parametric Wiener-Hammerstein (WH) systems is addressed within the evolutionary optimisation context. Specifically, a hybrid culture identification method is developed that involves model structure adaptation using genetic recombination and model parameter learning using particle swarm optimisation. The method enjoys three interesting features: (1) the risk of premature convergence of model parameter estimates to local optima is significantly reduced, due to the constantly maintained diversity of model candidates; (2) no prior knowledge is needed except for upper bounds on the system structure indices; (3) the method is fully autonomous as no interaction is needed with the user during the optimum search process. The performances of the proposed method will be illustrated and compared to alternative methods using a well-established WH benchmark.

  11. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  12. Identifying the evolutionary building blocks of the cardiac conduction system.

    Directory of Open Access Journals (Sweden)

    Bjarke Jensen

    Full Text Available The endothermic state of mammals and birds requires high heart rates to accommodate the high rates of oxygen consumption. These high heart rates are driven by very similar conduction systems consisting of an atrioventricular node that slows the electrical impulse and a His-Purkinje system that efficiently activates the ventricular chambers. While ectothermic vertebrates have similar contraction patterns, they do not possess anatomical evidence for a conduction system. This lack amongst extant ectotherms is surprising because mammals and birds evolved independently from reptile-like ancestors. Using conserved genetic markers, we found that the conduction system design of lizard (Anolis carolinensis and A. sagrei, frog (Xenopus laevis and zebrafish (Danio rerio adults is strikingly similar to that of embryos of mammals (mouse Mus musculus, and man and chicken (Gallus gallus. Thus, in ectothermic adults, the slow conducting atrioventricular canal muscle is present, no fibrous insulating plane is formed, and the spongy ventricle serves the dual purpose of conduction and contraction. Optical mapping showed base-to-apex activation of the ventricles of the ectothermic animals, similar to the activation pattern of mammalian and avian embryonic ventricles and to the His-Purkinje systems of the formed hearts. Mammalian and avian ventricles uniquely develop thick compact walls and septum and, hence, form a discrete ventricular conduction system from the embryonic spongy ventricle. Our study uncovers the evolutionary building plan of heart and indicates that the building blocks of the conduction system of adult ectothermic vertebrates and embryos of endotherms are similar.

  13. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  14. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  15. An evolutionary approach to regional systems of innovation

    DEFF Research Database (Denmark)

    Gunnarsson, Jan Sture Gunnar; Wallin, Torsten

    2011-01-01

    and production of intermediate goods. In particular we are concerned with how cooperative behaviour of technology producers is affected by the need to protect technological secrecies and of being financially constrained by firms demanding innovative input. Based on the theoretical model, we provide an analysis...... using computer simulations. The primary findings are, firstly, that the model generates predictions suited for empirical research on how economic selection influences cooperative behaviour of innovative actors. Secondly, we demonstrate how a region's entrepreneurial activity and growth can be controlled......This article examines how the birth and the development of regional systems of innovation are connected with economic selection and points to implications for regional-level policies. The research questions are explored using an evolutionary model, which emphasises geographical spaces...

  16. Altruism, egoism, or neither: A cognitive-efficiency-based evolutionary biological perspective on helping behavior.

    Science.gov (United States)

    Schulz, Armin W

    2016-04-01

    I argue for differences in the cognitive efficiency of different psychologies underlying helping behavior, and present an account of the adaptive pressures that result from these differences. Specifically, I argue that organisms often face pressure to move away from only being egoistically motivated to help: non-egoistic organisms are often able to determine how to help other organisms more quickly and with less recourse to costly cognitive resources like concentration and attention. Furthermore, I also argue that, while these pressures away from pure egoism can lead to the evolution of altruists, they can also lead to the evolution of reciprocation-focused behaviorist helpers or even of reflex-driven helpers (who are neither altruists nor egoists). In this way, I seek to broaden the set of considerations typically taken into account when assessing the evolution of the psychology of helping behavior-which tend to be restricted to matters of reliability-and also try to make clearer the role of evolutionary biological considerations in the discussion of this apparently straightforwardly psychological phenomenon. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Useful parasites: the evolutionary biology and biotechnology applications of transposable elements.

    Science.gov (United States)

    Bonchev, Georgi N

    2016-12-01

    Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  18. Evolutionary Cell Biology of Division Mode in the Bacterial Planctomycetes-Verrucomicrobia- Chlamydiae Superphylum.

    Science.gov (United States)

    Rivas-Marín, Elena; Canosa, Inés; Devos, Damien P

    2016-01-01

    Bacteria from the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum are exceptions to the otherwise dominant mode of division by binary fission, which is based on the interaction between the FtsZ protein and the peptidoglycan (PG) biosynthesis machinery. Some PVC bacteria are deprived of the FtsZ protein and were also thought to lack PG. How these bacteria divide is still one of the major mysteries of microbiology. The presence of PG has recently been revealed in Planctomycetes and Chlamydiae, and proteins related to PG synthesis have been shown to be implicated in the division process in Chlamydiae, providing important insights into PVC mechanisms of division. Here, we review the historical lack of observation of PG in PVC bacteria, its recent detection in two phyla and its involvement in chlamydial cell division. Based on the detection of PG-related proteins in PVC proteomes, we consider the possible evolution of the diverse division mechanisms in these bacteria. We conclude by summarizing what is known and what remains to be understood about the evolutionary cell biology of PVC division modes.

  19. The social production of health: critical contributions from evolutionary, biological, and cultural anthropology.

    Science.gov (United States)

    Levin, Betty Wolder; Browner, C H

    2005-08-01

    In 1946, the newly formed World Health Organization boldly sought to conceptualize "health" as wellbeing in the positive sense, "not merely the absence of disease or infirmity." Yet nearly six decades later, researchers are still principally concerned with pathology and its characteristics and consequences. This special issue is the result of an effort to broaden the focus. Anthropologists working from evolutionary, biological and sociocultural perspectives and in diverse geographic regions were asked to examine meanings associated with health and/or to identify social conditions and practices that have contributed to positive physiological and psychological states in particular cultures, times, or across time. Most notable, perhaps, was discovering how difficult it is for Western social scientists to move beyond pathology-based thinking; most authors represented here regard health primarily as the absence of disease. Still, these papers articulate and address questions key to understanding health in and of itself, including: How is health conceptualized? What kinds of social conditions lead to health? And, how do social inequalities affect health? This introduction critically discusses previous work on the subject to contextualize the original research papers offered here.

  20. Explanations for adaptations, just-so stories, and limitations on evidence in evolutionary biology.

    Science.gov (United States)

    Smith, Richard J

    2016-11-01

    Explanations of the historical origin of specific individual traits are a key part of the research program in paleontology and evolutionary biology. Why did bipedalism evolve in the human lineage? Why did some dinosaurs and related species have head crests? Why did viviparity evolve in some reptiles? Why did the common ancestor of primates evolve stereoscopic vision, grasping hands and feet, nails instead of claws, and large brains? These are difficult questions. To varying degrees, an explanation must grapple with (1) judgments about changes in fitness that might follow from a change in morphology - without actually observing behavior or measuring reproductive success, (2) the relationship between genes and traits, (3) limitations on doing relevant experiments, (4) the interpretation of causes that are almost certainly contingent, multifactorial, interactive, hierarchical, nonlinear, emergent, and probabilistic rather than deterministic, (5) limited information about variation and ontogeny, (6) a dataset based on the random fortunes of the historical record, including only partial hard-tissue morphology and no soft-tissue morphology, (7) an equally partial and problematic (for example, time-averaged) record of the environment, (8) the compression of all data into a geological time scale that is likely to miss biologically important events or fluctuations, (9) dependence on a process that can only be inferred ("form and even behavior may leave fossil traces, but forces like natural selection do not", 1:130 ) and finally, (10) the assumption of the "adaptationist programme"2 that the trait in question is in fact an adaptation rather than a consequence of genetic drift, correlated evolution, pleiotropy, exaptation, or other mechanisms. © 2016 Wiley Periodicals, Inc.

  1. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  2. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  3. Towards Engineering Biological Systems in a Broader Context.

    Science.gov (United States)

    Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

    2016-02-27

    Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Species diversity vs. morphological disparity in the light of evolutionary developmental biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-04-01

    Two indicators of a clade's success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs). Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review. From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and the extent and the possible

  5. Transforming Biology Assessment with Machine Learning: Automated Scoring of Written Evolutionary Explanations

    Science.gov (United States)

    Nehm, Ross H.; Ha, Minsu; Mayfield, Elijah

    2012-01-01

    This study explored the use of machine learning to automatically evaluate the accuracy of students' written explanations of evolutionary change. Performance of the Summarization Integrated Development Environment (SIDE) program was compared to human expert scoring using a corpus of 2,260 evolutionary explanations written by 565 undergraduate…

  6. Evolutionary Explanations for Antibiotic Resistance in Daily Press, Online Websites and Biology Textbooks in Sweden

    Science.gov (United States)

    Bohlin, Gustav; Höst, Gunnar E.

    2015-01-01

    The present study explores the extent and precision of evolutionary explanations for antibiotic resistance in communication directed toward the Swedish public. Bacterial resistance develops through evolutionary mechanisms and knowledge of these helps to explain causes underlying the growing prevalence of resistant strains, as well as important…

  7. Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology.

    Science.gov (United States)

    Clutton-Brock, Tim; Sheldon, Ben C

    2010-10-01

    Many important questions in ecology and evolutionary biology can only be answered with data that extend over several decades and answering a substantial proportion of questions requires records of the life histories of recognisable individuals. We identify six advantages that long-term, individual based studies afford in ecology and evolution: (i) analysis of age structure; (ii) linkage between life history stages; (iii) quantification of social structure; (iv) derivation of lifetime fitness measures; (v) replication of estimates of selection; (vi) linkage between generations, and we review their impact on studies in six key areas of evolution and ecology. Our review emphasises the unusual opportunities and productivity of long-term, individual-based studies and documents the important role that they play in research on ecology and evolutionary biology as well as the difficulties they face. Copyright © 2010 Elsevier Ltd. All rights reserved.

  8. Biological species is the only possible form of existence for higher organisms: the evolutionary meaning of sexual reproduction

    Directory of Open Access Journals (Sweden)

    Shcherbakov Victor P

    2010-03-01

    Full Text Available Abstract Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is substantiated that the main advantage of sex is the opposite: the ability to counteract not only extinction but further evolution as well. Living systems live long owing to their ability to reproduce themselves with a high fidelity. Simple organisms (like bacteria reach the continued existence due to the high fidelity of individual genome replication. In organisms with a large genome and complex development, the achievable fidelity of DNA replication is not enough for the precise reproduction of the genome. Such species must be capable of surviving and must remain unchanged in spite of the continuous changes of their genes. This problem has no solution in the frame of asexual ("homeogenomic" lineages. They would rapidly degrade and become extinct or blurred out in the course of the reckless evolution. The core outcome of the transition to sexual reproduction was the creation of multiorganismic entity - biological species. Individual organisms forfeited their ability to reproduce autonomously. It implies that individual organisms forfeited their ability to substantive evolution. They evolve as a part of the biological species. In case of obligatory sexuality, there is no such a thing as synchronic multi-level selection. Natural selection cannot select anything that is not a unit of reproduction. Hierarchy in biology implies the functional predestination of the parts for the sake of the whole. A crucial feature of the sexual reproduction is the formation of genomes of individual organisms by random picking them over from the continuously shuffled gene pool instead of the direct replication of the ancestor's genome. A clear anti-evolutionary

  9. Biological species is the only possible form of existence for higher organisms: the evolutionary meaning of sexual reproduction.

    Science.gov (United States)

    Shcherbakov, Victor P

    2010-03-22

    Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is substantiated that the main advantage of sex is the opposite: the ability to counteract not only extinction but further evolution as well. Living systems live long owing to their ability to reproduce themselves with a high fidelity. Simple organisms (like bacteria) reach the continued existence due to the high fidelity of individual genome replication. In organisms with a large genome and complex development, the achievable fidelity of DNA replication is not enough for the precise reproduction of the genome. Such species must be capable of surviving and must remain unchanged in spite of the continuous changes of their genes. This problem has no solution in the frame of asexual ("homeogenomic") lineages. They would rapidly degrade and become extinct or blurred out in the course of the reckless evolution. The core outcome of the transition to sexual reproduction was the creation of multiorganismic entity - biological species. Individual organisms forfeited their ability to reproduce autonomously. It implies that individual organisms forfeited their ability to substantive evolution. They evolve as a part of the biological species. In case of obligatory sexuality, there is no such a thing as synchronic multi-level selection. Natural selection cannot select anything that is not a unit of reproduction. Hierarchy in biology implies the functional predestination of the parts for the sake of the whole. A crucial feature of the sexual reproduction is the formation of genomes of individual organisms by random picking them over from the continuously shuffled gene pool instead of the direct replication of the ancestor's genome. A clear anti-evolutionary consequence of

  10. Biological species is the only possible form of existence for higher organisms: the evolutionary meaning of sexual reproduction

    Science.gov (United States)

    2010-01-01

    Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is substantiated that the main advantage of sex is the opposite: the ability to counteract not only extinction but further evolution as well. Living systems live long owing to their ability to reproduce themselves with a high fidelity. Simple organisms (like bacteria) reach the continued existence due to the high fidelity of individual genome replication. In organisms with a large genome and complex development, the achievable fidelity of DNA replication is not enough for the precise reproduction of the genome. Such species must be capable of surviving and must remain unchanged in spite of the continuous changes of their genes. This problem has no solution in the frame of asexual ("homeogenomic") lineages. They would rapidly degrade and become extinct or blurred out in the course of the reckless evolution. The core outcome of the transition to sexual reproduction was the creation of multiorganismic entity - biological species. Individual organisms forfeited their ability to reproduce autonomously. It implies that individual organisms forfeited their ability to substantive evolution. They evolve as a part of the biological species. In case of obligatory sexuality, there is no such a thing as synchronic multi-level selection. Natural selection cannot select anything that is not a unit of reproduction. Hierarchy in biology implies the functional predestination of the parts for the sake of the whole. A crucial feature of the sexual reproduction is the formation of genomes of individual organisms by random picking them over from the continuously shuffled gene pool instead of the direct replication of the ancestor's genome. A clear anti-evolutionary consequence of

  11. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  12. Genes are information, so information theory is coming to the aid of evolutionary biology.

    Science.gov (United States)

    Sherwin, William B

    2015-11-01

    Speciation is central to evolutionary biology, and to elucidate it, we need to catch the early genetic changes that set nascent taxa on their path to species status (Via 2009). That challenge is difficult, of course, for two chief reasons: (i) serendipity is required to catch speciation in the act; and (ii) after a short time span with lingering gene flow, differentiation may be low and/or embodied only in rare alleles that are difficult to sample. In this issue of Molecular Ecology Resources, Smouse et al. (2015) have noted that optimal assessment of differentiation within and between nascent species should be robust to these challenges, and they identified a measure based on Shannon's information theory that has many advantages for this and numerous other tasks. The Shannon measure exhibits complete additivity of information at different levels of subdivision. Of all the family of diversity measures ('0' or allele counts, '1' or Shannon, '2' or heterozygosity, F(ST) and related metrics) Shannon's measure comes closest to weighting alleles by their frequencies. For the Shannon measure, rare alleles that represent early signals of nascent speciation are neither down-weighted to the point of irrelevance, as for level 2 measures, nor up-weighted to overpowering importance, as for level 0 measures (Chao et al. 2010, )2015. Shannon measures have a long history in population genetics, dating back to Shannon's PhD thesis in 1940 (Crow 2001), but have received only sporadic attention, until a resurgence of interest in the last ten years, as reviewed briefly by Smouse et al. (2015). © 2015 John Wiley & Sons Ltd.

  13. LA CONSERVACIÓN BIOLÓGICA Y SU PERSPECTIVA EVOLUTIVA Biological Conservation and its Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    OLGA L MONTENEGRO

    Full Text Available Este artículo revisa tres de las principales causas de amenaza a la diversidad biológica, como son la fragmentación y pérdida del hábitat, así como la invasión de especies exóticas, principalmente en lo que compete a sus implicaciones evolutivas. Los efectos de la fragmentación y/o pérdida del hábitat pueden revisarse a la luz de la sinergia entre factores demográficos y genéticos que moldean cambios evolutivos o que llevan a las poblaciones al vórtice de la extinción. Las invasiones biológicas, aunque han generado pérdidas considerables en la diversidad biológica, ofrecen un escenario interesante para estudiar procesos evolutivos contemporáneos.This paper reviews three of the main threats to biological diversity, such as habitat fragmentation /habitat loss, and invasion of exotic species, mainly from their evolutionary implications. Effects of habitat fragmentation/habitat loss could be addressed by looking at the synergy between demographic and genetic factors that together shape evolutionary changes or otherwise bring populations to extinction vortex. Biological invasions, in spite of their strong negative effects on biological diversity, offer an interesting scenario to study contemporary evolutionary processes.

  14. Integrating systems biology models and biomedical ontologies

    Science.gov (United States)

    2011-01-01

    Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms. PMID:21835028

  15. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  16. Primary Emotional Systems and Personality: An Evolutionary Perspective

    Science.gov (United States)

    Montag, Christian; Panksepp, Jaak

    2017-01-01

    The present article highlights important concepts of personality including stability issues from the perspective of situational demands and stability over the life-course. Following this more introductory section, we argue why individual differences in primary emotional systems may represent the phylogenetically oldest parts of human personality. Our argumentation leads to the need to increasingly consider individual differences in the raw affects/emotions of people to understand human personality in a bottom–up fashion, which can be coordinated with top–down perspectives. In support of this idea, we also review existing evidence linking individual differences in primal emotions as assessed with the Affective Neuroscience Personality Scales and the widely accepted Big Five Model of Personality. In this context, we provide additional evidence on the link between primal emotions and personality in German and Chinese sample populations. In short, this article addresses evolutionary perspectives in the evaluation of human personality, highlighting some of the ancestral emotional urges that probably still control variations in the construction of human personality structures. Moreover, we address how individual differences in primary emotional systems can illuminate linkages to major human psychopathologies and the potential advantages and disadvantages of carrying a certain personality trait within certain cultural/environmental niches. PMID:28443039

  17. Ludwig von Bertalanffy Forerunner of Evolutionary Systems Theory

    OpenAIRE

    Wolfgang, Hofkirchner

    2005-01-01

    Ludwig von Bertalanffy is known as founding father of the General System Theory (GST). When Ludwig von Bertalanffy created his GST amidst the last century, he was able to overcome the deep cleft between the controversial theoretical approaches to biology - mechanicism and vitalism. He did so by formulating laws of organisation ruling biota and after generalising them he successfully applied them to different domains such as medicine, psychology, psychotherapy. Methodologically, Bertalanffy re...

  18. A novel classification system for evolutionary aging theories.

    Science.gov (United States)

    Trindade, Lucas S; Aigaki, Toshiro; Peixoto, Alexandre A; Balduino, Alex; Mânica da Cruz, Ivana B; Heddle, Jonathan G

    2013-01-01

    Theories of lifespan evolution are a source of confusion amongst aging researchers. After a century of aging research the dispute over whether the aging process is active or passive persists and a comprehensive and universally accepted theoretical model remains elusive. Evolutionary aging theories primarily dispute whether the aging process is exclusively adapted to favor the kin or exclusively non-adapted to favor the individual. Interestingly, contradictory data and theories supporting both exclusively programmed and exclusively non-programmed theories continue to grow. However, this is a false dichotomy; natural selection favors traits resulting in efficient reproduction whether they benefit the individual or the kin. Thus, to understand the evolution of aging, first we must understand the environment-dependent balance between the advantages and disadvantages of extended lifespan in the process of spreading genes. As described by distinct theories, different niches and environmental conditions confer on extended lifespan a range of fitness values varying from highly beneficial to highly detrimental. Here, we considered the range of fitness values for extended lifespan and develop a fitness-based framework for categorizing existing theories. We show that all theories can be classified into four basic types: secondary (beneficial), maladaptive (neutral), assisted death (detrimental), and senemorphic aging (varying between beneficial to detrimental). We anticipate that this classification system will assist with understanding and interpreting aging/death by providing a way of considering theories as members of one of these classes rather than consideration of their individual details.

  19. Introducing systems biology for nursing science.

    Science.gov (United States)

    Founds, Sandra A

    2009-07-01

    Systems biology expands on general systems theory as the "omics'' era rapidly progresses. Although systems biology has been institutionalized as an interdisciplinary framework in the biosciences, it is not yet apparent in nursing. This article introduces systems biology for nursing science by presenting an overview of the theory. This framework for the study of organisms from molecular to environmental levels includes iterations of computational modeling, experimentation, and theory building. Synthesis of complex biological processes as whole systems rather than isolated parts is emphasized. Pros and cons of systems biology are discussed, and relevance of systems biology to nursing is described. Nursing research involving molecular, physiological, or biobehavioral questions may be guided by and contribute to the developing science of systems biology. Nurse scientists can proactively incorporate systems biology into their investigations as a framework for advancing the interdisciplinary science of human health care. Systems biology has the potential to advance the research and practice goals of the National Institute for Nursing Research in the National Institutes of Health Roadmap initiative.

  20. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  1. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

    Science.gov (United States)

    List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

    2016-08-20

    For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to

  2. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains......There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...

  3. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  4. Systems biology approaches in aging research.

    Science.gov (United States)

    Chauhan, Anuradha; Liebal, Ulf W; Vera, Julio; Baltrusch, Simone; Junghanß, Christian; Tiedge, Markus; Fuellen, Georg; Wolkenhauer, Olaf; Köhling, Rüdiger

    2015-01-01

    Aging is a systemic process which progressively manifests itself at multiple levels of structural and functional organization from molecular reactions and cell-cell interactions in tissues to the physiology of an entire organ. There is ever increasing data on biomedical relevant network interactions for the aging process at different scales of time and space. To connect the aging process at different structural, temporal and spatial scales, extensive systems biological approaches need to be deployed. Systems biological approaches can not only systematically handle the large-scale datasets (like high-throughput data) and the complexity of interactions (feedback loops, cross talk), but also can delve into nonlinear behaviors exhibited by several biological processes which are beyond intuitive reasoning. Several public-funded agencies have identified the synergistic role of systems biology in aging research. Using one of the notable public-funded programs (GERONTOSYS), we discuss how systems biological approaches are helping the scientists to find new frontiers in aging research. We elaborate on some systems biological approaches deployed in one of the projects of the consortium (ROSage). The systems biology field in aging research is at its infancy. It is open to adapt existing systems biological methodologies from other research fields and devise new aging-specific systems biological methodologies. 2015 S. Karger AG, Basel.

  5. The current status of REH theory. [Random Evolutionary Hits in biological molecular evolution

    Science.gov (United States)

    Holmquist, R.; Jukes, T. H.

    1981-01-01

    A response is made to the evaluation of Fitch (1980) of REH (random evolutionary hits) theory for the evolutionary divergence of proteins and nucleic acids. Correct calculations for the beta hemoglobin mRNAs of the human, mouse and rabbit in the absence and presence of selective constraints are summarized, and it is shown that the alternative evolutionary analysis of Fitch underestimates the total fixed mutations. It is further shown that the model used by Fitch to test for the completeness of the count of total base substitutions is in fact a variant of REH theory. Considerations of the variance inherent in evolutionary estimations are also presented which show the REH model to produce no more variance than other evolutionary models. In the reply, it is argued that, despite the objections raised, REH theory applied to proteins gives inaccurate estimates of total gene substitutions. It is further contended that REH theory developed for nucleic sequences suffers from problems relating to the frequency of nucleotide substitutions, the identity of the codons accepting silent and amino acid-changing substitutions, and estimate uncertainties.

  6. Systems biology and cardiac arrhythmias.

    Science.gov (United States)

    Grace, Andrew A; Roden, Dan M

    2012-10-27

    During the past few years, the development of effective, empirical technologies for treatment of cardiac arrhythmias has exceeded the pace at which detailed knowledge of the underlying biology has accumulated. As a result, although some clinical arrhythmias can be cured with techniques such as catheter ablation, drug treatment and prediction of the risk of sudden death remain fairly primitive. The identification of key candidate genes for monogenic arrhythmia syndromes shows that to bring basic biology to the clinic is a powerful approach. Increasingly sophisticated experimental models and methods of measurement, including stem cell-based models of human cardiac arrhythmias, are being deployed to study how perturbations in several biologic pathways can result in an arrhythmia-prone heart. The biology of arrhythmia is largely quantifiable, which allows for systematic analysis that could transform treatment strategies that are often still empirical into management based on molecular evidence. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Systems biology of personalized nutrition

    NARCIS (Netherlands)

    Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

    2017-01-01

    Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

  8. Generating minimal living systems from non-living materials and increasing their evolutionary abilities

    DEFF Research Database (Denmark)

    Rasmussen, Steen; Constantinescu, Adi; Svaneborg, Carsten

    2016-01-01

    We review lessons learned about evolutionary transitions from a bottom up construction of minimal life. We use a particular systemic protocell design process as a starting point for exploring two fundamental questions: (1) how may minimal living systems emerge from nonliving materials? - and (2) ...... computational and experimental protocellular investigations, and we conjecture how this design principle can be extended for enhancing the evolutionary potential for a wide range of given system.......We review lessons learned about evolutionary transitions from a bottom up construction of minimal life. We use a particular systemic protocell design process as a starting point for exploring two fundamental questions: (1) how may minimal living systems emerge from nonliving materials? - and (2......) how may minimal living systems support increasingly more evolutionary richness? Under (1) we present what has been accomplished so far and discuss the remaining open challenges and their possible solutions. Under (2) we present a design principle we have utilized successfully both for our...

  9. Development of X-TOOLSS: Preliminary Design of Space Systems Using Evolutionary Computation

    Science.gov (United States)

    Schnell, Andrew R.; Hull, Patrick V.; Turner, Mike L.; Dozier, Gerry; Alverson, Lauren; Garrett, Aaron; Reneau, Jarred

    2008-01-01

    Evolutionary computational (EC) techniques such as genetic algorithms (GA) have been identified as promising methods to explore the design space of mechanical and electrical systems at the earliest stages of design. In this paper the authors summarize their research in the use of evolutionary computation to develop preliminary designs for various space systems. An evolutionary computational solver developed over the course of the research, X-TOOLSS (Exploration Toolset for the Optimization of Launch and Space Systems) is discussed. With the success of early, low-fidelity example problems, an outline of work involving more computationally complex models is discussed.

  10. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

    Science.gov (United States)

    Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

    2017-10-01

    Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

  11. Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

    Science.gov (United States)

    Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

    2000-01-01

    This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

  12. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  13. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Legay, Axel

    2014-01-01

    timed automata and most recently hybrid systems using the tool Uppaal SMC. In this paper we enable the application of SMC to complex biological systems, by combining Uppaal SMC with ANIMO, a plugin of the tool Cytoscape used by biologists, as well as with SimBiology®, a plugin of Matlab to simulate...

  14. Evolutionary psychology from a developmental systems perspective: comment on Lickliter and Honeycutt (2003).

    Science.gov (United States)

    Bjorklund, David F

    2003-11-01

    Although agreeing with R. Lickliter and H. Honeycutt (2003) that evolutionary psychology lacks and should adopt a coherent developmental model to explain how evolved mechanisms become expressed in phenotypes, it is argued that adhering to the principles of developmental systems theory, despite enhancing evolutionary psychology, would not change appreciably its basic focus. The concepts of innateness and modularity, what is inherited and what evolves, as well as the possible role of developmental plasticity in the evolution of human cognition are discussed. It is proposed that evolutionary psychology can incorporate the developmental systems perspective into its theorizing, with the end result being a science that more closely reflects human nature.

  15. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

  16. Plant systems biology: insights, advances and challenges.

    Science.gov (United States)

    Sheth, Bhavisha P; Thaker, Vrinda S

    2014-07-01

    Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

  17. Effects of chronic stress on the auditory system and fear learning: an evolutionary approach.

    Science.gov (United States)

    Dagnino-Subiabre, Alexies

    2013-01-01

    Stress is a complex biological reaction common to all living organisms that allows them to adapt to their environments. Chronic stress alters the dendritic architecture and function of the limbic brain areas that affect memory, learning, and emotional processing. This review summarizes our research about chronic stress effects on the auditory system, providing the details of how we developed the main hypotheses that currently guide our research. The aims of our studies are to (1) determine how chronic stress impairs the dendritic morphology of the main nuclei of the rat auditory system, the inferior colliculus (auditory mesencephalon), the medial geniculate nucleus (auditory thalamus), and the primary auditory cortex; (2) correlate the anatomic alterations with the impairments of auditory fear learning; and (3) investigate how the stress-induced alterations in the rat limbic system may spread to nonlimbic areas, affecting specific sensory system, such as the auditory and olfactory systems, and complex cognitive functions, such as auditory attention. Finally, this article gives a new evolutionary approach to understanding the neurobiology of stress and the stress-related disorders.

  18. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  19. The EvoDevoCI: A Concept Inventory for Gauging Students' Understanding of Evolutionary Developmental Biology

    Science.gov (United States)

    Perez, Kathryn E.; Hiatt, Anna; Davis, Gregory K.; Trujillo, Caleb; French, Donald P.; Terry, Mark; Price, Rebecca M.

    2013-01-01

    The American Association for the Advancement of Science 2011 report "Vision and Change in Undergraduate Biology Education" encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary…

  20. Soft computing integrating evolutionary, neural, and fuzzy systems

    CERN Document Server

    Tettamanzi, Andrea

    2001-01-01

    Soft computing encompasses various computational methodologies, which, unlike conventional algorithms, are tolerant of imprecision, uncertainty, and partial truth. Soft computing technologies offer adaptability as a characteristic feature and thus permit the tracking of a problem through a changing environment. Besides some recent developments in areas like rough sets and probabilistic networks, fuzzy logic, evolutionary algorithms, and artificial neural networks are core ingredients of soft computing, which are all bio-inspired and can easily be combined synergetically. This book presents a well-balanced integration of fuzzy logic, evolutionary computing, and neural information processing. The three constituents are introduced to the reader systematically and brought together in differentiated combinations step by step. The text was developed from courses given by the authors and offers numerous illustrations as

  1. Assessing the prospects for a return of organisms in evolutionary biology.

    Science.gov (United States)

    Huneman, Philippe

    2010-01-01

    An argument has been raised from various perspectives against the Modern Synthesis (MS) in the past two decades: it has forgotten organisms. Niche construction theorists (Odling-Smee et al. 2003), developmental biologists like West-Eberhard (2003) and Evo-Devo elaborated various views which concur on a rehabilitation of the explanatory role of organisms, formerly neglected by an evolutionary science mostly centered on genes. This paper aims at assessing such criticisms by unraveling the specific arguments they use and evaluating how empirical findings may support them. In the first section, I review the usual critiques about the way MS treats organisms and show that the organisms-concerned critique is multifaceted, and I use the controversy about units of selection in order to show that purely conceptual and empirical arguments have been mixed up when organisms were concerned. In the second section, I consider successively the challenges raised to evolutionary MS by structuralist biologists and then the developmentalist challenge mostly raised by Evo-Devo. I distinguish what is purely conceptual among those criticisms and what mostly relies on recent empirical findings about genome activation, inheritance, and epigenetics. The last section discusses another program in MS, namely "evolutionary transitions" research, as enquiry into the emergence of organisms.

  2. How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

    Science.gov (United States)

    Marioni, John C; Arendt, Detlev

    2017-10-06

    The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells. We discuss recent insights into the evolution of stem cells and initial attempts to reconstruct the evolutionary cell type tree of the mammalian forebrain, for example, by the comparative analysis of neuron types in the mesencephalic floor. These studies illustrate the immense potential of single-cell genomics to open up a new era in developmental and evolutionary research.

  3. Evolutionary biology and anthropology suggest biome reconstitution as a necessary approach toward dealing with immune disorders.

    Science.gov (United States)

    Parker, William; Ollerton, Jeff

    2013-01-01

    Industrialized society currently faces a wide range of non-infectious, immune-related pandemics. These pandemics include a variety of autoimmune, inflammatory and allergic diseases that are often associated with common environmental triggers and with genetic predisposition, but that do not occur in developing societies. In this review, we briefly present the idea that these pandemics are due to a limited number of evolutionary mismatches, the most damaging being 'biome depletion'. This particular mismatch involves the loss of species from the ecosystem of the human body, the human biome, many of which have traditionally been classified as parasites, although some may actually be commensal or even mutualistic. This view, evolved from the 'hygiene hypothesis', encompasses a broad ecological and evolutionary perspective that considers host-symbiont relations as plastic, changing through ecological space and evolutionary time. Fortunately, this perspective provides a blueprint, termed 'biome reconstitution', for disease treatment and especially for disease prevention. Biome reconstitution includes the controlled and population-wide reintroduction (i.e. domestication) of selected species that have been all but eradicated from the human biome in industrialized society and holds great promise for the elimination of pandemics of allergic, inflammatory and autoimmune diseases.

  4. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...

  5. Towards design space exploration for biological systems

    NARCIS (Netherlands)

    Polstra, S.; Pronk, T.E.; Pimentel, A.D.; Breit, T.M.

    2008-01-01

    For both embedded systems and biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. Given the similarities between computers and cellular systems, methods and models of computation from the domain of

  6. Metabolic systems biology: a brief primer.

    Science.gov (United States)

    Edwards, Lindsay M

    2017-05-01

    In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

  7. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider......Spatial arrangements are very important for many biological systems. This thesis presents several different studies of biological systems, which are related to spatial arrangements at two different levels: one is the growth of biological macromolecules, here related to protein aggregation...... system and resembles a situation of chronic inflammation in the tissue. In Chapter 5 we consider inflammatory response in the islets of Langerhans, which are responsible for regulating the levels of blood sugar (by releasing insulin and glucagon) and which are located in the pancreas. Low-grade chronic...

  8. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  9. Carbon Nanotubes – Interactions with Biological Systems

    OpenAIRE

    Reis, Joana; Capela-Silva, Fernando; Potes, José; Fonseca, Alexandra; Oliveira, Mónica; Kanagaraj, Subramani; Marques, António Torres

    2011-01-01

    his book chapter discusses the prospective biomedical applications of carbon nanotubes based materials, the impact of carbon nanotubes properties in the interaction with biological systems. Protein adsorption, impact on cell viability and cytokine production are explored. Potential respiratory and dermal toxicity are reviewed, as the difficulties on studying the biological response. In face of recent studies, special attention is drawn upon promising orthopaedic use.

  10. NASA's Evolutionary Xenon Thruster: The NEXT Ion Propulsion System for Solar System Exploration

    Science.gov (United States)

    Pencil, Eric J.; Benson, Scott W.

    2008-01-01

    This viewgraph presentation reviews NASA s Evolutionary Xenon Thruster (NEXT) Ion Propulsion system. The NEXT project is developing a solar electric ion propulsion system. The NEXT project is advancing the capability of ion propulsion to meet NASA robotic science mission needs. The NEXT system is planned to significantly improve performance over the state of the art electric propulsion systems, such as NASA Solar Electric Propulsion Technology Application Readiness (NSTAR). The status of NEXT development is reviewed, including information on the NEXT Thruster, the power processing unit, the propellant management system (PMS), the digital control interface unit, and the gimbal. Block diagrams NEXT system are presented. Also a review of the lessons learned from the Dawn and NSTAR systems is provided. In summary the NEXT project activities through 2007 have brought next-generation ion propulsion technology to a sufficient maturity level.

  11. How do biological systems escape 'chaotic' state?

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    level property that can explain this quandary across multiple .... Math. Biosci. 257 104–110. Nijhout HF, Sadre-Marandi F, Best J and Reed MC 2017 Systems biology of phenotypic robustness and plasticity. Integr. Comput. Biol.

  12. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  13. Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology

    Science.gov (United States)

    Hiatt, Anna; Davis, Gregory K.; Trujillo, Caleb; Terry, Mark; French, Donald P.; Price, Rebecca M.; Perez, Kathryn E.

    2013-01-01

    To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we…

  14. "Evo in the News:" Understanding Evolution and Students' Attitudes toward the Relevance of Evolutionary Biology

    Science.gov (United States)

    Infanti, Lynn M.; Wiles, Jason R.

    2014-01-01

    This investigation evaluated the effects of exposure to the "Evo in the News" section of the "Understanding Evolution" website on students' attitudes toward biological evolution in undergraduates in a mixed-majors introductory biology course at Syracuse University. Students' attitudes toward evolution and changes therein were…

  15. Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare.

    Science.gov (United States)

    Tribe, Michael; Pritchard, Alan J.

    This five-chapter document (part of a series on biology and human welfare) focuses on biological systems as energy sources and on the teaching of this subject area. Chapter 1 discusses various topics related to energy and ecology, including biomass, photosynthesis and world energy balances, energy flow through ecosystems, and others. Chapter 2…

  16. In the beginning was the familiar voice: personally familiar voices in the evolutionary and contemporary biology of communication.

    Science.gov (United States)

    Sidtis, Diana; Kreiman, Jody

    2012-06-01

    The human voice is described in dialogic linguistics as an embodiment of self in a social context, contributing to expression, perception and mutual exchange of self, consciousness, inner life, and personhood. While these approaches are subjective and arise from phenomenological perspectives, scientific facts about personal vocal identity, and its role in biological development, support these views. It is our purpose to review studies of the biology of personal vocal identity-the familiar voice pattern-as providing an empirical foundation for the view that the human voice is an embodiment of self in the social context. Recent developments in the biology and evolution of communication are concordant with these notions, revealing that familiar voice recognition (also known as vocal identity recognition or individual vocal recognition) has contributed to survival in the earliest vocalizing species. Contemporary ethology documents the crucial role of familiar voices across animal species in signaling and perceiving internal states and personal identities. Neuropsychological studies of voice reveal multimodal cerebral associations arising across brain structures involved in memory, emotion, attention, and arousal in vocal perception and production, such that the voice represents the whole person. Although its roots are in evolutionary biology, human competence for processing layered social and personal meanings in the voice, as well as personal identity in a large repertory of familiar voice patterns, has achieved an immense sophistication.

  17. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    Aspergilli are widely used as cell factories for the production of food ingredients, enzymes and antibiotics. Traditionally, improvement of these cell factories has been done using classical methods, that is, random mutagenesis and screening; however, advances in methods for performing directed...... possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  18. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  19. Nonequilibrium Thermodynamics in Biological Systems

    Science.gov (United States)

    Aoki, I.

    2005-12-01

    1. Respiration Oxygen-uptake by respiration in organisms decomposes macromolecules such as carbohydrate, protein and lipid and liberates chemical energy of high quality, which is then used to chemical reactions and motions of matter in organisms to support lively order in structure and function in organisms. Finally, this chemical energy becomes heat energy of low quality and is discarded to the outside (dissipation function). Accompanying this heat energy, entropy production which inevitably occurs by irreversibility also is discarded to the outside. Dissipation function and entropy production are estimated from data of respiration. 2. Human body From the observed data of respiration (oxygen absorption), the entropy production in human body can be estimated. Entropy production from 0 to 75 years old human has been obtained, and extrapolated to fertilized egg (beginning of human life) and to 120 years old (maximum period of human life). Entropy production show characteristic behavior in human life span : early rapid increase in short growing phase and later slow decrease in long aging phase. It is proposed that this tendency is ubiquitous and constitutes a Principle of Organization in complex biotic systems. 3. Ecological communities From the data of respiration of eighteen aquatic communities, specific (i.e. per biomass) entropy productions are obtained. They show two phase character with respect to trophic diversity : early increase and later decrease with the increase of trophic diversity. The trophic diversity in these aquatic ecosystems is shown to be positively correlated with the degree of eutrophication, and the degree of eutrophication is an "arrow of time" in the hierarchy of aquatic ecosystems. Hence specific entropy production has the two phase: early increase and later decrease with time. 4. Entropy principle for living systems The Second Law of Thermodynamics has been expressed as follows. 1) In isolated systems, entropy increases with time and

  20. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

    Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  1. [System biology and synthetic biology modify drug discovery and development].

    Science.gov (United States)

    Haiech, Jacques; Ranjeva, Raoul; Kilhoffer, Marie-Claude

    2012-02-01

    Life Sciences are built on observations. Right now, a more systemic approach allowing to integrate the different organizational levels in Biology is emerging. Such an approach uses a set of technologies and strategies allowing to build models that appear to be more and more predictive (omics, bioinformatics, integrative biology, computational biology…). Those models accelerate the rational development of new therapies avoiding an engineering based only on trials and errors. This approach both holistic and predictive radically modifies the discovery and development modalities used today in health industries. Moreover, because of the apparition of new jobs at the interface of disciplines, of private and public sectors and of life sciences and engineering sciences, this implies to rethink the training programs in both their contents and their pedagogical tools. © 2012 médecine/sciences – Inserm / SRMS.

  2. Evolutionary Design of Both Topologies and Parameters of a Hybrid Dynamical System

    DEFF Research Database (Denmark)

    Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

    2012-01-01

    This paper investigates the issue of evolutionary design of open-ended plants for hybrid dynamical systems--i.e. both their topologies and parameters. Hybrid bond graphs are used to represent dynamical systems involving both continuous and discrete system dynamics. Genetic programming, with some...

  3. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  4. Evolutionary and biological implications of dental mesial drift in rodents: the case of the Ctenodactylidae (Rodentia, Mammalia.

    Directory of Open Access Journals (Sweden)

    Helder Gomes Rodrigues

    Full Text Available Dental characters are importantly used for reconstructing the evolutionary history of mammals, because teeth represent the most abundant material available for the fossil species. However, the characteristics of dental renewal are presently poorly used, probably because dental formulae are frequently not properly established, whereas they could be of high interest for evolutionary and developmental issues. One of the oldest rodent families, the Ctenodactylidae, is intriguing in having longstanding disputed dental formulae. Here, we investigated 70 skulls among all extant ctenodactylid genera (Ctenodactylus, Felovia, Massoutiera and Pectinator by using X-ray conventional and synchrotron microtomography in order to solve and discuss these dental issues. Our study clearly indicates that Massoutiera, Felovia and Ctenodactylus differ from Pectinator not only by a more derived dentition, but also by a more derived eruptive sequence. In addition to molars, their dentition only includes the fourth deciduous premolars, and no longer bears permanent premolars, conversely to Pectinator. Moreover, we found that these premolars are lost during adulthood, because of mesial drift of molars. Mesial drift is a striking mechanism involving migration of teeth allowed by both bone remodeling and dental resorption. This dental innovation is to date poorly known in rodents, since it is only the second report described. Interestingly, we noted that dental drift in rodents is always associated with high-crowned teeth favoring molar size enlargement. It can thus represent another adaptation to withstand high wear, inasmuch as these rodents inhabit desert environments where dust is abundant. A more accurate study of mesial drift in rodents would be very promising from evolutionary, biological and orthodontic points of view.

  5. Evolutionary and Biological Implications of Dental Mesial Drift in Rodents: The Case of the Ctenodactylidae (Rodentia, Mammalia)

    Science.gov (United States)

    Gomes Rodrigues, Helder; Solé, Floréal; Charles, Cyril; Tafforeau, Paul; Vianey-Liaud, Monique; Viriot, Laurent

    2012-01-01

    Dental characters are importantly used for reconstructing the evolutionary history of mammals, because teeth represent the most abundant material available for the fossil species. However, the characteristics of dental renewal are presently poorly used, probably because dental formulae are frequently not properly established, whereas they could be of high interest for evolutionary and developmental issues. One of the oldest rodent families, the Ctenodactylidae, is intriguing in having longstanding disputed dental formulae. Here, we investigated 70 skulls among all extant ctenodactylid genera (Ctenodactylus, Felovia, Massoutiera and Pectinator) by using X-ray conventional and synchrotron microtomography in order to solve and discuss these dental issues. Our study clearly indicates that Massoutiera, Felovia and Ctenodactylus differ from Pectinator not only by a more derived dentition, but also by a more derived eruptive sequence. In addition to molars, their dentition only includes the fourth deciduous premolars, and no longer bears permanent premolars, conversely to Pectinator. Moreover, we found that these premolars are lost during adulthood, because of mesial drift of molars. Mesial drift is a striking mechanism involving migration of teeth allowed by both bone remodeling and dental resorption. This dental innovation is to date poorly known in rodents, since it is only the second report described. Interestingly, we noted that dental drift in rodents is always associated with high-crowned teeth favoring molar size enlargement. It can thus represent another adaptation to withstand high wear, inasmuch as these rodents inhabit desert environments where dust is abundant. A more accurate study of mesial drift in rodents would be very promising from evolutionary, biological and orthodontic points of view. PMID:23185576

  6. Evolutionary cell biology: functional insight from “endless forms most beautiful”

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G.; Dacks, Joel B.

    2015-01-01

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. PMID:26668171

  7. Systems biology: leading the revolution in ecotoxicology.

    Science.gov (United States)

    Garcia-Reyero, Natàlia; Perkins, Edward J

    2011-02-01

    The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems. © 2010 SETAC.

  8. Optimal parameters of FACTS devices in electric power systems applying evolutionary strategies

    Energy Technology Data Exchange (ETDEWEB)

    Dominguez-Navarro, Jose A.; Bernal-Agustin, Jose L. [Electrical Engineering Department, University of Zaragoza, Calle Maria de Luna, 3, 50018 Zaragoza (Spain); Diaz, Alexis; Vargas, Emilio P. [Electrical Engineering Department, UNEXPO, Urbanizacion Villa Asia, Puerto Ordaz (Venezuela); Requena, Durlym [General Studies Department, Section of Physical Sciences, UNEXPO, Urbanizacion Villa Asia, Puerto Ordaz (Venezuela)

    2007-01-15

    This paper illustrates, for the first time, the use of an evolutionary strategy for the coordination of FACTS (flexible AC transmission systems). The main purpose of the current work involves the study of power systems with the use of FACTS controllers. FACTS controllers cannot only increase considerably power transmission capacity without having to invest on the production of new power lines-but they can also enhance stability in power systems. The task of searching and finding the optimal values of control variables for the FACTS controllers is a complex optimization problem which cannot be easily solved. The results achieved in this work suggest the effective use of evolutionary strategies in order to obtain the optimal values of control variables for the FACTS located on a power system. The illustrative example and final conclusions allow considering evolutionary strategies as one of the best alternatives for the coordination of FACTS. (author)

  9. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  10. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology.

    Science.gov (United States)

    Wideman, Jeremy G; Muñoz-Gómez, Sergio A

    2016-08-01

    The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. The Evolutionary Biology of Ourselves Unit Requirements and Organizational Change in United States History

    CERN Document Server

    Lipo, C; Lipo, Carl; Madsen, Mark

    1999-01-01

    Researchers have proposed that the distinction between so-called "simple" and "complex" societies can be expressed by an increase in the number of levels at which functional organization, interaction, and thus selection, operate. In spite of the obvious links between this suggestion and research into complex social organization amongst insects and other social animals, the levels of selection model has seen little use among anthropologists. We suggest that the primary reason for lack of research into the evolutionary causes of social complexity has been the lack of descriptive units with which we can examine phenotypic variation and heritability of social organization above the level of the organism. The goal of our paper, therefore, is to begin constructing descriptive units which map to meaningful models of multi-level selection. In order to demonstrate how these units are useful in a real dataset, we examine the functional changes involved in the United States economy over the last 100 years, a period of t...

  12. A systemic approach for modeling biological evolution using Parallel DEVS.

    Science.gov (United States)

    Heredia, Daniel; Sanz, Victorino; Urquia, Alfonso; Sandín, Máximo

    2015-08-01

    A new model for studying the evolution of living organisms is proposed in this manuscript. The proposed model is based on a non-neodarwinian systemic approach. The model is focused on considering several controversies and open discussions about modern evolutionary biology. Additionally, a simplification of the proposed model, named EvoDEVS, has been mathematically described using the Parallel DEVS formalism and implemented as a computer program using the DEVSLib Modelica library. EvoDEVS serves as an experimental platform to study different conditions and scenarios by means of computer simulations. Two preliminary case studies are presented to illustrate the behavior of the model and validate its results. EvoDEVS is freely available at http://www.euclides.dia.uned.es. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

  14. Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

    CERN Document Server

    Demirel, Yasar

    2014-01-01

    Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

  15. Monogonont rotifers as model systems for the study of micro-evolutionary adaptation and its eco-evolutionary implications

    NARCIS (Netherlands)

    Declerck, S.A.J.; Papakostas, S.

    2017-01-01

    A better understanding of the ability of organisms to adapt to local selection conditions is essential for a better insight in their ecological dynamics. The study of micro-evolutionary adaptation and its eco-evolutionary consequences is challenging for many reasons and the choice of a suitable

  16. Current advances in systems and integrative biology

    Directory of Open Access Journals (Sweden)

    Scott W. Robinson

    2014-08-01

    Full Text Available Systems biology has gained a tremendous amount of interest in the last few years. This is partly due to the realization that traditional approaches focusing only on a few molecules at a time cannot describe the impact of aberrant or modulated molecular environments across a whole system. Furthermore, a hypothesis-driven study aims to prove or disprove its postulations, whereas a hypothesis-free systems approach can yield an unbiased and novel testable hypothesis as an end-result. This latter approach foregoes assumptions which predict how a biological system should react to an altered microenvironment within a cellular context, across a tissue or impacting on distant organs. Additionally, re-use of existing data by systematic data mining and re-stratification, one of the cornerstones of integrative systems biology, is also gaining attention. While tremendous efforts using a systems methodology have already yielded excellent results, it is apparent that a lack of suitable analytic tools and purpose-built databases poses a major bottleneck in applying a systematic workflow. This review addresses the current approaches used in systems analysis and obstacles often encountered in large-scale data analysis and integration which tend to go unnoticed, but have a direct impact on the final outcome of a systems approach. Its wide applicability, ranging from basic research, disease descriptors, pharmacological studies, to personalized medicine, makes this emerging approach well suited to address biological and medical questions where conventional methods are not ideal.

  17. Systems Biology: The Next Frontier for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Vladimir A. Likić

    2010-01-01

    Full Text Available Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i mathematical and computational modeling; (ii the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems.

  18. Systematics and evolutionary biology: uneasy bedfellows? Sistemática y biología evolutiva: ¿compañeros incómodos?

    Directory of Open Access Journals (Sweden)

    Jeffrey H. Schwartz

    2011-03-01

    Full Text Available The history of systematics and evolutionary biology demonstrates how greatly the "modern evolutionary synthesis" instrumentally prevented, rather than facilitated, the intellectual growth and maturity of the diversity of evolutionary disciplines. In truth, the claim of the synthesis being synthetic is essentially without basis, indeed a myth. Instead, the "synthesis" had precisely the opposite effect: namely, squelching the arena of debate, disagreement, and diverse theorizing that had characterized the preceding decades. Although each of the 3 primary architects of the synthesis - Dobzhansky, Mayr, and Simpson - had his own agenda, they were united around the theme of population genetics and population thinking. When applied to systematics, especially by Mayr, the result can now be seen as confused at best. Perhaps this review will provoke a revival of earlier years of intellectual curiosity and fervor, and rekindle interest in systematic method and theory.La historia de la sistemática y de la biología evolutiva muestra el papel que tuvo la "síntesis evolutiva moderna" para impedir, en lugar de favorecer, el crecimiento intelectual y la maduración de la diversidad de disciplinas evolucionistas. En efecto, la pretensión de la "síntesis" de ser sintética carece de bases, y por ende, resulta un mito. En su lugar, la "síntesis" tuvo precisamente el efecto opuesto: suprimir escenarios de debate, acuerdos, y cancelar el desarrollo mismo de las teorías que caracterizaron las décadas precedentes. Aunque cada uno de los 3 estudiosos responsables de formular la síntesis -Dobzhansky, Mayr y Simpson- tenía su propia agenda, coincidían en torno al tema de la genética de poblaciones y el pensamiento poblacional. Sin embargo, el resultado del debate respecto a la sistemática, especialmente abordado por Mayr, es actualmente confuso en el mejor de los casos. Quizás esta revisión provoque un resurgimiento en el fervor y la curiosidad intelectual

  19. The Design and Transformation of Biofundamentals: A Nonsurvey Introductory Evolutionary and Molecular Biology Course

    Science.gov (United States)

    Klymkowsky, Michael W.; Rentsch, Jeremy D.; Begovic, Emina; Cooper, Melanie M.

    2016-01-01

    Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the…

  20. Using the Principles of SoTL to Redesign an Advanced Evolutionary Biology Course

    Science.gov (United States)

    deBraga, Michael; Boyd, Cleo; Abdulnour, Shahad

    2015-01-01

    A primary goal of university instruction is the students' demonstration of improved, highly developed critical thinking (CT) skills. However, how do faculty encourage CT and its potential concomitant increase in student workload without negatively impacting student perceptions of the course? In this investigation, an advanced biology course is…

  1. Evolutionary Design of a Robotic Material Defect Detection System

    Science.gov (United States)

    Ballard, Gary; Howsman, Tom; Craft, Mike; ONeil, Daniel; Steincamp, Jim; Howell, Joe T. (Technical Monitor)

    2002-01-01

    During the post-flight inspection of SSME engines, several inaccessible regions must be disassembled to inspect for defects such as cracks, scratches, gouges, etc. An improvement to the inspection process would be the design and development of very small robots capable of penetrating these inaccessible regions and detecting the defects. The goal of this research was to utilize an evolutionary design approach for the robotic detection of these types of defects. A simulation and visualization tool was developed prior to receiving the hardware as a development test bed. A small, commercial off-the-shelf (COTS) robot was selected from several candidates as the proof of concept robot. The basic approach to detect the defects was to utilize Cadmium Sulfide (CdS) sensors to detect changes in contrast of an illuminated surface. A neural network, optimally designed utilizing a genetic algorithm, was employed to detect the presence of the defects (cracks). By utilization of the COTS robot and US sensors, the research successfully demonstrated that an evolutionarily designed neural network can detect the presence of surface defects.

  2. Systems medicine: evolution of systems biology from bench to bedside.

    Science.gov (United States)

    Wang, Rui-Sheng; Maron, Bradley A; Loscalzo, Joseph

    2015-01-01

    High-throughput experimental techniques for generating genomes, transcriptomes, proteomes, metabolomes, and interactomes have provided unprecedented opportunities to interrogate biological systems and human diseases on a global level. Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties. Most human diseases are biological states caused by multiple components of perturbed pathways and regulatory networks rather than individual failing components. Systems biology not only facilitates basic biological research but also provides new avenues through which to understand human diseases, identify diagnostic biomarkers, and develop disease treatments. At the same time, systems biology seeks to assist in drug discovery, drug optimization, drug combinations, and drug repositioning by investigating the molecular mechanisms of action of drugs at a system's level. Indeed, systems biology is evolving to systems medicine as a new discipline that aims to offer new approaches for addressing the diagnosis and treatment of major human diseases uniquely, effectively, and with personalized precision. © 2015 Wiley Periodicals, Inc.

  3. International Conference on Artificial Intelligence and Evolutionary Algorithms in Engineering Systems

    CERN Document Server

    Dash, Subhransu; Panigrahi, Bijaya

    2015-01-01

      The book is a collection of high-quality peer-reviewed research papers presented in Proceedings of International Conference on Artificial Intelligence and Evolutionary Algorithms in Engineering Systems (ICAEES 2014) held at Noorul Islam Centre for Higher Education, Kumaracoil, India. These research papers provide the latest developments in the broad area of use of artificial intelligence and evolutionary algorithms in engineering systems. The book discusses wide variety of industrial, engineering and scientific applications of the emerging techniques. It presents invited papers from the inventors/originators of new applications and advanced technologies.

  4. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search....... However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally...... be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method...

  5. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  6. The Impact of Systems Biology on Bioprocessing

    DEFF Research Database (Denmark)

    Campbell, Kate; Xia, Jianye; Nielsen, Jens

    2017-01-01

    Bioprocessing offers a sustainable and green approach to the production of chemicals. However, a bottleneck in introducing bioprocesses is cell factory development, which is costly and time-consuming. A systems biology approach can expedite cell factory design by using genome-wide analyses...... and its regulation, which can be achieved using quantitative and integrated omic characterization, alongside more advanced analytical methods. We discuss here the current impact of systems biology and challenges of closing the gap between bioprocessing and more traditional methods of chemical production....

  7. An Evolutionary Approach to the Biological Management of Invasive Brown Treesnakes (Boiga irregularis) on Guam

    Science.gov (United States)

    2012-03-14

    of the most significant parasite afflictions of captive snakes and is highly contagious. These organisms cause extensive damage to the intestinal ...Wisniewski 2010). Estimates of the annual economic costs from the damages caused by the invasion of B. irregularis to the Hawaiian Islands from... Salmonella spp. for rodents (Singleton 1994 ) and numerous others. ‘Real world’ examples of successful biological management of vertebrate pests involve

  8. Examining Gender Differences in Written Assessment Tasks in Biology: A Case Study of Evolutionary Explanations.

    Science.gov (United States)

    Federer, Meghan Rector; Nehm, Ross H; Pearl, Dennis K

    2016-01-01

    Understanding sources of performance bias in science assessment provides important insights into whether science curricula and/or assessments are valid representations of student abilities. Research investigating assessment bias due to factors such as instrument structure, participant characteristics, and item types are well documented across a variety of disciplines. However, the relationships among these factors are unclear for tasks evaluating understanding through performance on scientific practices, such as explanation. Using item-response theory (Rasch analysis), we evaluated differences in performance by gender on a constructed-response (CR) assessment about natural selection (ACORNS). Three isomorphic item strands of the instrument were administered to a sample of undergraduate biology majors and nonmajors (Group 1: n = 662 [female = 51.6%]; G2: n = 184 [female = 55.9%]; G3: n = 642 [female = 55.1%]). Overall, our results identify relationships between item features and performance by gender; however, the effect is small in the majority of cases, suggesting that males and females tend to incorporate similar concepts into their CR explanations. These results highlight the importance of examining gender effects on performance in written assessment tasks in biology. © 2016 M. R. Federer 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).

  9. Systems Biology to Support Nanomaterial Grouping.

    Science.gov (United States)

    Riebeling, Christian; Jungnickel, Harald; Luch, Andreas; Haase, Andrea

    2017-01-01

    The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.

  10. Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract.

    Science.gov (United States)

    Mills, E N Clare; Jenkins, John A; Alcocer, Marcos J C; Shewry, Peter R

    2004-01-01

    The recently completed genome sequence of the model plant species Arabidopsis has been estimated to encode over 25,000 proteins, which, on the basis of their function, can be classified into structural and metabolic (the vast majority of plant proteins), protective proteins, which defend a plant against invasion by pathogens or feeding by pests, and storage proteins, which proved a nutrient store to support germination in seeds. It is now clear that almost all plant food allergens are either protective or storage proteins. It is also becoming evident that those proteins that trigger the development of an allergic response through the gastrointestinal tract belong primarily to two large protein superfamilies: (1) The cereal prolamin superfamily, comprising three major groups of plant food allergens, the 2S albumins, lipid transfer proteins, and cereal alpha-amylase/trypsin inhibitors, which have related structures, and are stable to thermal processing and proteolysis. They include major allergens from Brazil nut, peanuts, fruits, such as peaches, and cereals, such as rice and wheat; (2) The cupin superfamily, comprising the major globulin storage proteins from a number of plant species. The globulins have been found to be allergens in plant foods, such as peanuts, soya bean, and walnut; (3) The cyteine protease C1 family, comprising the papain-like proteases from microbes, plants, and animals. This family contains two notable allergens that sensitize via the GI tract, namely actinidin from kiwi fruit and the soybean allergen, Gly m Bd 30k/P34. This study describes the properties, structures, and evolutionary relationships of these protein families, the allergens that belong to them, and discusses them in relation to the role protein structure may play in determining protein allergenicity.

  11. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.

    Directory of Open Access Journals (Sweden)

    Yuan-Yuan Li

    2006-07-01

    Full Text Available Several "head-to-head" (or "bidirectional" gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural features, evolutionary conservation, expression correlation and functional association. Of the present 1,262, 1,071, and 491 head-to-head pairs identified in human, mouse, and rat genomes, respectively, pairs with 1- to 400-base pair distance between transcription start sites form the majority (62.36%, 64.15%, and 55.19% for human, mouse, and rat,respectively of each dataset, and the largest group is always the one with a transcription start site distance of 101 to 200 base pairs. The phylogenetic analysis among Fugu, chicken, and human indicates a negative selection on the separation of head-to-head genes across vertebrate evolution, and thus the ancestral existence of this gene organization. The expression analysis shows that most of the human head-to-head genes are significantly correlated,and the correlation could be positive, negative, or alternative depending on the experimental conditions. Finally, head to-head genes statistically tend to perform similar functions, and gene pairs associated with the significant cofunctions seem to have stronger expression correlations. The findings indicate that the head-to-head gene organization is ancient and conserved, which subjects functionally related genes to correlated transcriptional regulation and thus provides an exquisite mechanism of transcriptional regulation based on gene organization. These results have significantly expanded the knowledge about head-to-head gene organization. Supplementary materials for this study are available at http://www.scbit.org/h2h.

  12. Beyond fossil calibrations: Realities of molecular clock practices in evolutionary biology

    Directory of Open Access Journals (Sweden)

    Christy Anna Hipsley

    2014-05-01

    Full Text Available Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from previous analyses. To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over 600 articles published from 2007 to 2013. Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each. Vertebrate taxa were subjects of nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each. Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types. This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of phenotypic

  13. Where Did You Come From? Where Will You Go? Human Evolutionary Biology Education and American Students' Academic Interests and Achievements, Professional Goals, and Socioscientific Decision-Making

    Science.gov (United States)

    Schrein, Caitlin M.

    2014-01-01

    In the United States, there is a national agenda to increase the number of qualified science, technology, engineering, and maths (STEM) professionals and a movement to promote science literacy among the general public. This project explores the association between formal human evolutionary biology education (HEB) and high school science class…

  14. Discovery of Chemical Toxicity via Biological Networks and Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, Edward; Habib, Tanwir; Guan, Xin; Escalon, Barbara; Falciani, Francesco; Chipman, J.K.; Antczak, Philipp; Edwards, Stephen; Taylor, Ronald C.; Vulpe, Chris; Loguinov, Alexandre; Van Aggelen, Graham; Villeneuve, Daniel L.; Garcia-Reyero, Natalia

    2010-09-30

    Both soldiers and animals are exposed to many chemicals as the result of military activities. Tools are needed to understand the hazards and risks that chemicals and new materials pose to soldiers and the environment. We have investigated the potential of global gene regulatory networks in understanding the impact of chemicals on reproduction. We characterized effects of chemicals on ovaries of the model animal system, the Fathead minnow (Pimopheles promelas) connecting chemical impacts on gene expression to circulating blood levels of the hormones testosterone and estradiol in addition to the egg yolk protein vitellogenin. We describe the application of reverse engineering complex interaction networks from high dimensional gene expression data to characterize chemicals that disrupt the hypothalamus-pituitary-gonadal endocrine axis that governs reproduction in fathead minnows. The construction of global gene regulatory networks provides deep insights into how drugs and chemicals effect key organs and biological pathways.

  15. The ctenophore genome and the evolutionary origins of neural systems

    NARCIS (Netherlands)

    Moroz, Leonid L.; Kocot, Kevin M.; Citarella, Mathew R.; Dosung, Sohn; Norekian, Tigran P.; Povolotskaya, Inna S.; Grigorenko, Anastasia P.; Dailey, Christopher; Berezikov, Eugene; Buckley, Katherine M.; Ptitsyn, Andrey; Reshetov, Denis; Mukherjee, Krishanu; Moroz, Tatiana P.; Bobkova, Yelena; Yu, Fahong; Kapitonov, Vladimir V.; Jurka, Jerzy; Bobkov, Yuri V.; Swore, Joshua J.; Girardo, David O.; Fodor, Alexander; Gusev, Fedor; Sanford, Rachel; Bruders, Rebecca; Kittler, Ellen; Mills, Claudia E.; Rast, Jonathan P.; Derelle, Romain; Solovyev, Victor V.; Kondrashov, Fyodor A.; Swalla, Billie J.; Sweedler, Jonathan V.; Rogaev, Evgeny I.; Halanych, Kenneth M.; Kohn, Andrea B.

    2014-01-01

    The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we

  16. Fostering 21st-Century Evolutionary Reasoning: Teaching Tree Thinking to Introductory Biology Students.

    Science.gov (United States)

    Novick, Laura R; Catley, Kefyn M

    2016-01-01

    The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction. We found greater gains in tree-thinking abilities for the experimental instruction group than for the business-as-usual group, as measured by performance on our novel assessment instrument. This was a medium size effect. These gains were observed on an unannounced test that was administered ∼5-6 weeks after the primary instruction in tree thinking. The nature of students' postinstruction difficulties with tree thinking suggests that the critical underlying concept for acquiring expert-level competence in this area is understanding that any specific phylogenetic tree is a subset of the complete, unimaginably large ToL. © 2016 L. R. Novick and K. M. Catley. 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).

  17. Systems biology for organotypic cell cultures.

    Science.gov (United States)

    Grego, Sonia; Dougherty, Edward R; Alexander, Francis J; Auerbach, Scott S; Berridge, Brian R; Bittner, Michael L; Casey, Warren; Cooley, Philip C; Dash, Ajit; Ferguson, Stephen S; Fennell, Timothy R; Hawkins, Brian T; Hickey, Anthony J; Kleensang, Andre; Liebman, Michael N J; Martin, Florian; Maull, Elizabeth A; Paragas, Jason; Qiao, Guilin Gary; Ramaiahgari, Sreenivasa; Sumner, Susan J; Yoon, Miyoung

    2017-01-01

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, "organotypic" cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.

  18. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  19. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    philosophically interesting for their own sake. By pursuing ambitious aims such as the development of multiscale computational models and synthetic life forms, they uncover new ground for philosophical analysis. Systems and synthetic biology raise fundamental questions about how far research can be taken through...

  20. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  1. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the…

  2. Extended inclusive fitness theory: synergy and assortment drives the evolutionary dynamics in biology and economics.

    Science.gov (United States)

    Jaffe, Klaus

    2016-01-01

    W.D. Hamilton's Inclusive Fitness Theory explains the conditions that favor the emergence and maintenance of social cooperation. Today we know that these include direct and indirect benefits an agent obtains by its actions, and through interactions with kin and with genetically unrelated individuals. That is, in addition to kin-selection, assortation or homophily, and social synergies drive the evolution of cooperation. An Extended Inclusive Fitness Theory (EIFT) synthesizes the natural selection forces acting on biological evolution and on human economic interactions by assuming that natural selection driven by inclusive fitness produces agents with utility functions that exploit assortation and synergistic opportunities. This formulation allows to estimate sustainable cost/benefit threshold ratios of cooperation among organisms and/or economic agents, using existent analytical tools, illuminating our understanding of the dynamic nature of society, the evolution of cooperation among kin and non-kin, inter-specific cooperation, co-evolution, symbioses, division of labor and social synergies. EIFT helps to promote an interdisciplinary cross fertilization of the understanding of synergy by, for example, allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics. Another example is a bio-economic understanding of the motivations of terrorists, which identifies different forms of terrorism.

  3. Language Based Techniques for Systems Biology

    DEFF Research Database (Denmark)

    Pilegaard, Henrik

    calculi have similarly been used for the study of bio-chemical reactive systems. In this dissertation it is argued that techniques rooted in the theory and practice of programming languages, language based techniques if you will, constitute a strong basis for the investigation of models of biological...... on the π calculus fragment of BioAmbients. In both cases the analyses compute very precise estimates of the temporal structure of the underlying pathways; hence they are applicable across a family of widely used bio-ware languages that descend from Milner’s Calculus of Communicating Systems. The presented......Process calculus is the common denominator for a class of compact, idealised, domain-specific formalisms normally associated with the study of reactive concurrent systems within Computer Science. With the rise of the interactioncentred science of Systems Biology a number of bio-inspired process...

  4. Evolutionary morphology of the hemolymph vascular system of basal araneomorph spiders (Araneae: Araneomorphae).

    Science.gov (United States)

    Huckstorf, Katarina; Michalik, Peter; Ramírez, Martín; Wirkner, Christian S

    2015-11-01

    The superfamily Austrochiloidea (Austrochilidae and Gradungulidae) take a pivotal position in araneomorph spider phylogeny. In this discussion crevice weaver spiders (Filistatidae) are of equal interest. Especially data from these phylogenetically uncertain yet basal off branching groups can enlighten our understanding on the evolution of organ systems. In the course of a survey on the evolutionary morphology of the circulatory system in spiders we therefore investigated the hemolymph vascular system in two austrochiloid and one filistatid species. Additionally some data on a hypochilid and a gradungulid species are included. Using up-to-date morphological methods, the vascular systems in these spiders are visualized three dimensionally. Ground pattern features of the circulatory systems in austrochiloid spiders are presented and the data discussed along recent lines of phylogenetic hypotheses. Special topics highlighted are the intraspecific variability of the origins of some prosomal arteries and the evolutionary correlation of respiratory and circulatory systems in spiders. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Evolutionary-Simulative Methodology in the Management of Social and Economic Systems

    Directory of Open Access Journals (Sweden)

    Konyavskiy V.A.

    2017-01-01

    Full Text Available The article outlines the main provisions of the evolutionary-simulative methodology (ESM which is a methodology of mathematical modeling of equilibrium random processes (CPR, widely used in the economy. It discusses the basic directions of use of ESM solutions for social problems and economic management systems.

  6. Optimal routes scheduling for municipal waste disposal garbage trucks using evolutionary algorithm and artificial immune system

    Directory of Open Access Journals (Sweden)

    Bogna MRÓWCZYŃSKA

    2011-01-01

    Full Text Available This paper describes an application of an evolutionary algorithm and an artificial immune systems to solve a problem of scheduling an optimal route for waste disposal garbage trucks in its daily operation. Problem of an optimisation is formulated and solved using both methods. The results are presented for an area in one of the Polish cities.

  7. Models for Evolutionary Algorithms and Their Applications in System Identification and Control Optimization

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    In recent years, optimization algorithms have received increasing attention by the research community as well as the industry. In the area of evolutionary computation (EC), inspiration for optimization algorithms originates in Darwin’s ideas of evolution and survival of the fittest. Such algorithms...... simulate an evolutionary process where the goal is to evolve solutions by means of crossover, mutation, and selection based on their quality (fitness) with respect to the optimization problem at hand. Evolutionary algorithms (EAs) are highly relevant for industrial applications, because they are capable...... optimization. In addition to general investigations in these areas, I introduce a number of algorithms and demonstrate their potential on real-world problems in system identification and control. Furthermore, I investigate dynamic optimization problems in the context of the three fundamental areas as well...

  8. Systems biology and integrative physiological modelling.

    Science.gov (United States)

    Hester, Robert L; Iliescu, Radu; Summers, Richard; Coleman, Thomas G

    2011-03-01

    Over the last 10 years, 'Systems Biology' has focused on the integration of biology and medicine with information technology and computation. The current challenge is to use the discoveries of the last 20 years, such as genomics and proteomics, to develop targeted therapeutical strategies. These strategies are the result of understanding the aetiologies of complex diseases. Scientists predict the data will make personalized medicine rapidly available. However, the data need to be considered as a highly complex system comprising multiple inputs and feedback mechanisms. Translational medicine requires the functional and conceptual linkage of genetics to proteins, proteins to cells, cells to organs, organs to systems and systems to the organism. To help understand the complex integration of these systems, a mathematical model of the entire human body, which accurately links the functioning of all organs and systems together, could provide a framework for the development and testing of new hypotheses that will be important in clinical outcomes. There are several efforts to develop a 'Human Physiome', with the strengths and weaknesses of each being presented here. The development of a 'Human Model', with verification, documentation and validation of the underlying and integrative responses, is essential to provide a usable environment. Future development of a 'Human Model' requires integrative physiologists working in collaboration with other scientists, who have expertise in all areas of human biology, to develop the most accurate and usable human model.

  9. Evolutionary Dynamics While Trapped in Resonance: A Keplerian Binary System Perturbed by Gravitational Radiation

    OpenAIRE

    Chicone, Carmen; Mashhoon, Bahram; Retzloff, David

    1996-01-01

    The method of averaging is used to investigate the phenomenon of capture into resonance for a model that describes a Keplerian binary system influenced by radiation damping and external normally incident periodic gravitational radiation. The dynamical evolution of the binary orbit while trapped in resonance is elucidated using the second order partially averaged system. This method provides a theoretical framework that can be used to explain the main evolutionary dynamics of a physical system...

  10. Identifying the Evolutionary Building Blocks of the Cardiac Conduction System

    NARCIS (Netherlands)

    Jensen, Bjarke; Boukens, Bastiaan J. D.; Postma, Alex V.; Gunst, Quinn D.; van den Hoff, Maurice J. B.; Moorman, Antoon F. M.; Wang, Tobias; Christoffels, Vincent M.

    2012-01-01

    The endothermic state of mammals and birds requires high heart rates to accommodate the high rates of oxygen consumption. These high heart rates are driven by very similar conduction systems consisting of an atrioventricular node that slows the electrical impulse and a His-Purkinje system that

  11. B chromosomes: from cytogenetics to systems biology.

    Science.gov (United States)

    Valente, Guilherme T; Nakajima, Rafael T; Fantinatti, Bruno E A; Marques, Diego F; Almeida, Rodrigo O; Simões, Rafael P; Martins, Cesar

    2017-02-01

    Though hundreds to thousands of reports have described the distribution of B chromosomes among diverse eukaryote groups, a comprehensive theory of their biological role has not yet clearly emerged. B chromosomes are classically understood as a sea of repetitive DNA sequences that are poor in genes and are maintained by a parasitic-drive mechanism during cell division. Recent developments in high-throughput DNA/RNA analyses have increased the resolution of B chromosome biology beyond those of classical and molecular cytogenetic methods; B chromosomes contain many transcriptionally active sequences, including genes, and can modulate the activity of autosomal genes. Furthermore, the most recent knowledge obtained from omics analyses, which is associated with a systemic view, has demonstrated that B chromosomes can influence cell biology in a complex way, possibly favoring their own maintenance and perpetuation.

  12. Intelligent and Evolutionary Systems : the 20th Asia Pacific Symposium

    CERN Document Server

    Singh, Hemant; Elsayed, Saber

    2017-01-01

    Over the last two decades the field of Intelligent Systems delivered to human kind significant achievements, while also facing major transformations. 20 years ago, automation and knowledge-based AI were still the dominant paradigms fueling the efforts of both researchers and practitioners. Later, 10 years ago, statistical machine intelligence was on the rise, heavily supported by the digital computing, and led to the unprecedented advances in and dependence on digital technology. However, the resultant intelligent systems remained designer-based endeavors and thus, were limited in their true learning and development abilities. Today, the challenge is to have in place intelligent systems that can develop themselves on behalf of their creators, and gain abilities with no or limited supervision in the tasks they are meant to perform. Cognitive development systems, and the supporting cognitive computing are on the rise today, promising yet other significant achievements for the future of human kind. This book cap...

  13. Measuring cell identity in noisy biological systems

    Science.gov (United States)

    Birnbaum, Kenneth D.; Kussell, Edo

    2011-01-01

    Global gene expression measurements are increasingly obtained as a function of cell type, spatial position within a tissue and other biologically meaningful coordinates. Such data should enable quantitative analysis of the cell-type specificity of gene expression, but such analyses can often be confounded by the presence of noise. We introduce a specificity measure Spec that quantifies the information in a gene's complete expression profile regarding any given cell type, and an uncertainty measure dSpec, which measures the effect of noise on specificity. Using global gene expression data from the mouse brain, plant root and human white blood cells, we show that Spec identifies genes with variable expression levels that are nonetheless highly specific of particular cell types. When samples from different individuals are used, dSpec measures genes’ transcriptional plasticity in each cell type. Our approach is broadly applicable to mapped gene expression measurements in stem cell biology, developmental biology, cancer biology and biomarker identification. As an example of such applications, we show that Spec identifies a new class of biomarkers, which exhibit variable expression without compromising specificity. The approach provides a unifying theoretical framework for quantifying specificity in the presence of noise, which is widely applicable across diverse biological systems. PMID:21803789

  14. Why an extended evolutionary synthesis is necessary.

    Science.gov (United States)

    Müller, Gerd B

    2017-10-06

    Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the '-omics' revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.

  15. Using the Principles of SoTL to Redesign an Advanced Evolutionary Biology Course

    Directory of Open Access Journals (Sweden)

    Michael deBraga

    2015-03-01

    Full Text Available A primary goal of university instruction is the students’ demonstration of improved, highly developed critical thinking (CT skills. However, how do faculty encourage CT and its potential concomitant increase in student workload without negatively impacting student perceptions of the course? In this investigation, an advanced biology course is evaluated after structural changes (implemented in 2010 met with a poor student evaluation of the course and the instructor. This analysis first examines the steps used to transform a course to encourage CT and then explains how it can be assessed. To accomplish these goals, the instructor collaborated with an educational developer to redesign the course using a philosophy informed by SoTL. This approach, as we see it, represents a set of principles that demand transparency in the development and application of strategies whose aim is to encourage student learning. However, the SoTL approach would be insufficient to simply promote a set of strategies without some mechanism for evaluating its efficacy. Therefore, we designed a “Graded Response” (GR multiple-choice test to measure CT development and hence to properly evaluate whether the strategies embedded in our SoTL-informed course redesign have adequately met our goals.

  16. Effects of Pesticides on Biological Systems

    Directory of Open Access Journals (Sweden)

    Ergul Belge Kurutas

    2003-06-01

    Full Text Available The use of pesticid both in Turkey and other contries is widespread in order to combat against many pests which cause economical damages. However, pesticides in human pass through skin, respiratory or digestive systems and is metabolized by monooxygenase system dependent upon cytocrome P450 in liver. They also give rise to severe decreases cytochrome P450 and amount of "hem" enzyme activites of glucose-6-phosphatase, pyrophosphatase by stimulating lipid peroxidation on hepatic microsomes. In this study effects of pesticides on biological systems will be presented in genaral terms. [Archives Medical Review Journal 2003; 12(3.000: 215-228

  17. Image-based systems biology of infection.

    Science.gov (United States)

    Medyukhina, Anna; Timme, Sandra; Mokhtari, Zeinab; Figge, Marc Thilo

    2015-06-01

    The successful treatment of infectious diseases requires interdisciplinary studies of all aspects of infection processes. The overarching combination of experimental research and theoretical analysis in a systems biology approach can unravel mechanisms of complex interactions between pathogens and the human immune system. Taking into account spatial information is especially important in the context of infection, since the migratory behavior and spatial interactions of cells are often decisive for the outcome of the immune response. Spatial information is provided by image and video data that are acquired in microscopy experiments and that are at the heart of an image-based systems biology approach. This review demonstrates how image-based systems biology improves our understanding of infection processes. We discuss the three main steps of this approach--imaging, quantitative characterization, and modeling--and consider the application of these steps in the context of studying infection processes. After summarizing the most relevant microscopy and image analysis approaches, we discuss ways to quantify infection processes, and address a number of modeling techniques that exploit image-derived data to simulate host-pathogen interactions in silico. © 2015 International Society for Advancement of Cytometry.

  18. An updated evolutionary classification of CRISPR-Cas systems

    NARCIS (Netherlands)

    Makarova, K.S.; Wolf, Y.I.; Alkhnbashi, O.S.; Brouns, S.J.J.; Oost, Van Der John

    2015-01-01

    The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward

  19. Optimising software development policies for evolutionary system requirements

    NARCIS (Netherlands)

    Noppen, J.A.R.; Tekinerdogan, B.; Aksit, Mehmet; Glandrup, Maurice; Nicola, V.F.

    2002-01-01

    Anticipating future software requirements might support the evolution of software systems and as such reduce the cost of development and maintenance in due time. Unfortunately identifying the right set of evolution scenarios is difficult due to the uncertainty of occurrence of future requirements.

  20. The ctenophore genome and the evolutionary origins of neural systems.

    Science.gov (United States)

    Moroz, Leonid L; Kocot, Kevin M; Citarella, Mathew R; Dosung, Sohn; Norekian, Tigran P; Povolotskaya, Inna S; Grigorenko, Anastasia P; Dailey, Christopher; Berezikov, Eugene; Buckley, Katherine M; Ptitsyn, Andrey; Reshetov, Denis; Mukherjee, Krishanu; Moroz, Tatiana P; Bobkova, Yelena; Yu, Fahong; Kapitonov, Vladimir V; Jurka, Jerzy; Bobkov, Yuri V; Swore, Joshua J; Girardo, David O; Fodor, Alexander; Gusev, Fedor; Sanford, Rachel; Bruders, Rebecca; Kittler, Ellen; Mills, Claudia E; Rast, Jonathan P; Derelle, Romain; Solovyev, Victor V; Kondrashov, Fyodor A; Swalla, Billie J; Sweedler, Jonathan V; Rogaev, Evgeny I; Halanych, Kenneth M; Kohn, Andrea B

    2014-06-05

    The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.

  1. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  2. Developmental biology, the stem cell of biological disciplines.

    Science.gov (United States)

    Gilbert, Scott F

    2017-12-01

    Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

  3. Primary Emotional Systems and Personality: An Evolutionary Perspective

    OpenAIRE

    Montag, Christian; Panksepp, Jaak

    2017-01-01

    The present article highlights important concepts of personality including stability issues from the perspective of situational demands and stability over the life-course. Following this more introductory section, we argue why individual differences in primary emotional systems may represent the phylogenetically oldest parts of human personality. Our argumentation leads to the need to increasingly consider individual differences in the raw affects/emotions of people to understand human person...

  4. From growth physiology to systems biology.

    Science.gov (United States)

    Schaechter, Moselio

    2006-09-01

    As it focuses on the integrated behavior of the entire cell, systems biology is a powerful extension of growth physiology. Here, I briefly trace some of the origins of modern-day bacterial growth physiology and its relevance to systems biology. I describe how growth physiology emerged from the foggy picture of the growth curve as a self-contained entity. For this insight, we can thank Henrici, Hershey, Monod, Maaløe, and others. As a result of their work, growth rate is understood to be the unitary manifestation of the response to nutritional conditions and to the control condition for studies on the effect of environmental stresses. For this response to be usefully reproducible, cultures must be in the steady state known as balanced growth. I point out that present-day experimenters are not always aware of this imperative and thus do not always use conditions that ensure the balanced growth of their control cultures.

  5. The Impact of Systems Biology on Bioprocessing.

    Science.gov (United States)

    Campbell, Kate; Xia, Jianye; Nielsen, Jens

    2017-12-01

    Bioprocessing offers a sustainable and green approach to the production of chemicals. However, a bottleneck in introducing bioprocesses is cell factory development, which is costly and time-consuming. A systems biology approach can expedite cell factory design by using genome-wide analyses alongside mathematical modeling to characterize and predict cellular physiology. This approach can drive cycles of design, build, test, and learn implemented by metabolic engineers to optimize the cell factory performance. Streamlining of the design phase requires a clearer understanding of metabolism and its regulation, which can be achieved using quantitative and integrated omic characterization, alongside more advanced analytical methods. We discuss here the current impact of systems biology and challenges of closing the gap between bioprocessing and more traditional methods of chemical production. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Single molecule interactions in biological systems

    CERN Document Server

    Tessmer, I

    2002-01-01

    The interactions of biological molecules are traditionally investigated using ensemble techniques. These provide information on the molecular behaviour based on averaged data resulting from collective ensemble properties. While this has enabled the resolution of structure and function of many proteins and other biomolecules, an understanding of how and why the molecules go about structural changes and modulate inter- and intra-molecular interactions is difficult to gain using these approaches. More recently, single molecule techniques have evolved. These allow us to follow the behaviour of the individual molecules over time and/or under changing conditions. From such data, subtle molecular changes can be resolved without the need to synchronise the system. Further, variations within a biological system can be detected which would be lost using the ensemble techniques, due to the concomitant averaging procedures. This is exploited to help understand the molecular procedures involved. In this thesis, the applic...

  7. Erziehung in einer biologisch determinierten Welt--Herausforderung fur die Theoriebildung einer Evolutionaren Padagogik aus Biologischer Perspektive (Education in a Biologically Determined World--A Challenge for a Theory of Evolutionary Pedagogics from a Biological Point of View).

    Science.gov (United States)

    Voland, Eckart; Voland, Renate

    2002-01-01

    Designates four challenges for a theory of evolutionary pedagogics which result from the theoretical progress made in biological science: (1) subjectively perceived autonomy; (2) teachability; (3) preparation for future life; and (4) the reality norm dilemma. Argues that these confrontations are the theoretical challenges for the further…

  8. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    Science.gov (United States)

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  9. The Emergence of Modularity in Biological Systems

    Science.gov (United States)

    Lorenz, Dirk M.; Jeng, Alice; Deem, Michael W.

    2015-01-01

    In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks. There once were two watchmakers, named Hora and Tempus, who manufactured very fine watches. Both of them were highly regarded, and the phones in their workshops rang frequently — new customers were constantly calling them. However, Hora prospered, while Tempus became poorer and poorer and finally lost his shop. What was the reason? The watches the men made consisted of about 1,000 parts each. Tempus had so constructed his that if he had one partly assembled and had to put it down — to answer the phone say— it immediately fell to pieces and had to be reassembled from the elements. The better the customers liked his watches, the more they phoned him, the more difficult it became for him to find enough uninterrupted time to finish a watch. The watches that Hora made were no less complex than those of Tempus. But he had designed them so that he could put together subassemblies of about ten elements each. Ten of these subassemblies, again, could be put together into a larger subassembly; and a system of ten of the latter sub

  10. Topological sensitivity analysis for systems biology.

    Science.gov (United States)

    Babtie, Ann C; Kirk, Paul; Stumpf, Michael P H

    2014-12-30

    Mathematical models of natural systems are abstractions of much more complicated processes. Developing informative and realistic models of such systems typically involves suitable statistical inference methods, domain expertise, and a modicum of luck. Except for cases where physical principles provide sufficient guidance, it will also be generally possible to come up with a large number of potential models that are compatible with a given natural system and any finite amount of data generated from experiments on that system. Here we develop a computational framework to systematically evaluate potentially vast sets of candidate differential equation models in light of experimental and prior knowledge about biological systems. This topological sensitivity analysis enables us to evaluate quantitatively the dependence of model inferences and predictions on the assumed model structures. Failure to consider the impact of structural uncertainty introduces biases into the analysis and potentially gives rise to misleading conclusions.

  11. An Encoding Technique for Multiobjective Evolutionary Algorithms Applied to Power Distribution System Reconfiguration

    Directory of Open Access Journals (Sweden)

    J. L. Guardado

    2014-01-01

    Full Text Available Network reconfiguration is an alternative to reduce power losses and optimize the operation of power distribution systems. In this paper, an encoding scheme for evolutionary algorithms is proposed in order to search efficiently for the Pareto-optimal solutions during the reconfiguration of power distribution systems considering multiobjective optimization. The encoding scheme is based on the edge window decoder (EWD technique, which was embedded in the Strength Pareto Evolutionary Algorithm 2 (SPEA2 and the Nondominated Sorting Genetic Algorithm II (NSGA-II. The effectiveness of the encoding scheme was proved by solving a test problem for which the true Pareto-optimal solutions are known in advance. In order to prove the practicability of the encoding scheme, a real distribution system was used to find the near Pareto-optimal solutions for different objective functions to optimize.

  12. Fundamentals of computational intelligence neural networks, fuzzy systems, and evolutionary computation

    CERN Document Server

    Keller, James M; Fogel, David B

    2016-01-01

    This book covers the three fundamental topics that form the basis of computational intelligence: neural networks, fuzzy systems, and evolutionary computation. The text focuses on inspiration, design, theory, and practical aspects of implementing procedures to solve real-world problems. While other books in the three fields that comprise computational intelligence are written by specialists in one discipline, this book is co-written by current former Editor-in-Chief of IEEE Transactions on Neural Networks and Learning Systems, a former Editor-in-Chief of IEEE Transactions on Fuzzy Systems, and the founding Editor-in-Chief of IEEE Transactions on Evolutionary Computation. The coverage across the three topics is both uniform and consistent in style and notation. Discusses single-layer and multilayer neural networks, radial-basi function networks, and recurrent neural networks Covers fuzzy set theory, fuzzy relations, fuzzy logic interference, fuzzy clustering and classification, fuzzy measures and fuzz...

  13. EVOLUTIONARY MODELING PROBLEMS IN STRUCTURAL SYNTHESIS OF INFORMATION NETWORKS OF AUTOMATED CONTROL SYSTEMS

    Directory of Open Access Journals (Sweden)

    N.R.Yusupbekov

    2014-07-01

    Full Text Available This paper provides a new approach for solving a problem of modeling and structural syntheses of information networks of automated control systems by applying fuzzy sets theory, fuzzy logic and genetic algorithms. The procedure of formalizing structural syntheses of multi-level dispersed information networks of automated control systems is proposed. Also, the paper proposes a conceptual model of evolutionary syntheses based on genetic algorithms, which do not require additional information about the characteristics and features of target function. Modified genetic operators of crossover, mutation and algorithms of evolutionary syntheses of information networks systems are developed. Finally, the results of computational experiments on researching the influence of probability of the use of crossover and mutation operators, method of choosing parental pairs, and the size of initial population on the speed and precision of final results are provided.

  14. Development of an evolutionary simulator and an overall control system for intelligent wheelchair

    Science.gov (United States)

    Imai, Makoto; Kawato, Koji; Hamagami, Tomoki; Hirata, Hironori

    The goal of this research is to develop an intelligent wheelchair (IWC) system which aids an indoor safe mobility for elderly and disabled people with a new conceptual architecture which realizes autonomy, cooperativeness, and a collaboration behavior. In order to develop the IWC system in real environment, we need design-tools and flexible architecture. In particular, as more significant ones, this paper describes two key techniques which are an evolutionary simulation and an overall control mechanism. The evolutionary simulation technique corrects the error between the virtual environment in a simulator and real one in during the learning of an IWC agent, and coevolves with the agent. The overall control mechanism is implemented with subsumption architecture which is employed in an autonomous robot controller. By using these techniques in both simulations and experiments, we confirm that our IWC system acquires autonomy, cooperativeness, and a collaboration behavior efficiently.

  15. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  16. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  17. Systems biology of the structural proteome.

    Science.gov (United States)

    Brunk, Elizabeth; Mih, Nathan; Monk, Jonathan; Zhang, Zhen; O'Brien, Edward J; Bliven, Spencer E; Chen, Ke; Chang, Roger L; Bourne, Philip E; Palsson, Bernhard O

    2016-03-11

    The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM

  18. Biological information systems: Evolution as cognition-based information management.

    Science.gov (United States)

    Miller, William B

    2017-11-22

    An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Bergmann's Rule, Adaptation, and Thermoregulation in Arctic Animals: Conflicting Perspectives from Physiology, Evolutionary Biology, and Physical Anthropology After World War II.

    Science.gov (United States)

    Hagen, Joel B

    2017-05-01

    Bergmann's rule and Allen's rule played important roles in mid-twentieth century discussions of adaptation, variation, and geographical distribution. Although inherited from the nineteenth-century natural history tradition these rules gained significance during the consolidation of the modern synthesis as evolutionary theorists focused attention on populations as units of evolution. For systematists, the rules provided a compelling rationale for identifying geographical races or subspecies, a function that was also picked up by some physical anthropologists. More generally, the rules provided strong evidence for adaptation by natural selection. Supporters of the rules tacitly, or often explicitly, assumed that the clines described by the rules reflected adaptations for thermoregulation. This assumption was challenged by the physiologists Laurence Irving and Per Scholander based on their arctic research conducted after World War II. Their critique spurred a controversy played out in a series of articles in Evolution, in Ernst Mayr's Animal Species and Evolution, and in the writings of other prominent evolutionary biologists and physical anthropologists. Considering this episode highlights the complexity and ambiguity of important biological concepts such as adaptation, homeostasis, and self-regulation. It also demonstrates how different disciplinary orientations and styles of scientific research influenced evolutionary explanations, and the consequent difficulties of constructing a truly synthetic evolutionary biology in the decades immediately following World War II.

  20. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  1. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  2. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  3. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  4. Evolutionary Computation for the Identification of Emergent Behavior in Autonomous Systems

    Science.gov (United States)

    Terrile, Richard J.; Guillaume, Alexandre

    2009-01-01

    Over the past several years the Center for Evolutionary Computation and Automated Design at the Jet Propulsion Laboratory has developed a technique based on Evolutionary Computational Methods (ECM) that allows for the automated optimization of complex computationally modeled systems. An important application of this technique is for the identification of emergent behaviors in autonomous systems. Mobility platforms such as rovers or airborne vehicles are now being designed with autonomous mission controllers that can find trajectories over a solution space that is larger than can reasonably be tested. It is critical to identify control behaviors that are not predicted and can have surprising results (both good and bad). These emergent behaviors need to be identified, characterized and either incorporated into or isolated from the acceptable range of control characteristics. We use cluster analysis of automatically retrieved solutions to identify isolated populations of solutions with divergent behaviors.

  5. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  6. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  7. The female gametophyte: an emerging model for cell type-specific systems biology in plant development

    Directory of Open Access Journals (Sweden)

    Marc William Schmid

    2015-11-01

    Full Text Available Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods (omics now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis. Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.

  8. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  9. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  10. The evolutionary conformation from traditional lecture to active learning in an undergraduate biology course and its effects on student achievement

    Science.gov (United States)

    Diederich, Kirsten Bakke

    In response to the declining number of students in the United States entering into the STEM (science, technology, engineering, and math) disciplines, there has been an attempt to retain student interest in the sciences through the implementation of more active learning in the classroom. Active learning is defined as any instructional method that requires students do something in the classroom rather than simply listen to a lecture (Herreid, 2006). These student centered approaches provide the students with the opportunity to work cooperatively while developing the skills required for critical inquiry. They also help the students make the connections between what is being taught and how it can be applied in a real world setting. Science education researchers have attempted to analyze the efficacy of active learning. Although they find it difficult to compare the data, they state unequivocally that "Active learning is a better strategy for learning than the traditional didactic lecture format" (Prince, 2004). However, even though research supports the efficacy of active learning, instructors find it difficult to adopt this pedagogy into their classrooms due to concerns such as loss of content knowledge and student resistance. This three year qualitative and quantitative study addressed the level of student learning and satisfaction in an introductory vertebrate biology class at a small liberal arts college. The courses were taught by the same instructor using three pedagogical methods; traditional lecture (TL), problem-based learning (PBL), and case-based learning (CBL). Student grades and levels of assessment were compared between the TL and PBL, while student attrition rates, course satisfaction and views of active and group learning were analyzed across all three sections. The evolutionary confirmations from TL to PBL and ultimately the adoption of CBL as the method of choice are discussed from the view of both the faculty member and the students.

  11. Biological Diversity in the Patent System

    Science.gov (United States)

    Oldham, Paul; Hall, Stephen; Forero, Oscar

    2013-01-01

    Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual

  12. Biological diversity in the patent system.

    Science.gov (United States)

    Oldham, Paul; Hall, Stephen; Forero, Oscar

    2013-01-01

    Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual

  13. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  14. Live cell imaging and systems biology

    Science.gov (United States)

    Sung, Myong-Hee; McNally, James G

    2010-01-01

    Much of the experimental data used to construct mathematical models of molecular networks are derived from in vitro measurements. However, there is increasing evidence that in vitro measurements fail to capture both the complexity and the individuality found in single, living cells. These limitations can be overcome by live cell microscopy which is evolving to enable in vivo biochemistry. Here we survey the current capabilities of live cell microscopy and illustrate how a number of different imaging approaches could be applied to analyze a specific molecular network. We argue that incorporation of such quantitative live cell imaging methods is critical for the progress of systems biology. PMID:20730797

  15. Nutritional Systems Biology: Definitions and Approaches

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Nielsen, Jens

    2009-01-01

    will benefit most from, or be placed at risk by, intervention strategies. More accurate assessment of the inputs to human health and the consequences of those inputs measured as accurate transcriptomic, proteomic, and metabolomic analyses would bring personalized health/diet to practice far faster than would...... waiting for a predictive knowledge of genetic variation. It is widely recognized that systems and network biology has the potential to increase our understanding of how nutrition influences metabolic pathways and homeostasis, how this regulation is disturbed in a diet-related disease, and to what extent...

  16. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    He also enjoys music. (especially .... and, especially in ancient civilizations, the detailed classifica- tion of plants and animals was often based on their significance to humans. However, there was widespread recognition that the. I. , _ .___ l . ..... particular behaviour or morphological trait has evolved in that group of taxa.

  17. The Biosphere as a Living System. On Peculiarities of the Evolutionary Process on the Biosphere Level

    Directory of Open Access Journals (Sweden)

    Alexej Yablokov

    2016-10-01

    ; spontaneity and non-directional changes of the development programs; securing successful changes by natural selection; geometrical progression of reproduction as a “spring” of life. There are four basic levels of organization of life: molecular-genetics, ontogenetics, species-populational, ecosystemic. Among the main features of the evolution of the biosphere: spreading of life on the planet; the uprising of the biosphere’ turnover of matters on the basis of the use of solar energy; increasing of the closeness of this turnover; strengthening the energy flow through the biosphere; the increase in mass of organic matter involved in this cycle; the emergence of the genetic code; the emergence of eukaryotes; increasing of the structural and functional diversity of the biosphere. Among the major achievements of evolution in the plant world: improving the chemical mechanisms of photosynthesis, plants access to land (the appearance of vascular and root systems; the growth of the photosynthetic capacity of terrestrial plant communities. Among the main achievements of evolution in the animal world: the appearance of the skeleton, hemoglobin; increasing the independence from the external factors (growth of a homeostasis; the emergence of the nervous system and sociality. Among the patterns of evolution of organs and functions in different groups of living organisms: the intensification of functions; intensification of the multifunctionality and duplications of biological systems components; supplementation (rather than substitution of new functions to the old. Chorologically (spatially biosphere is composed of ecosystems of all sizes, including biogeocoenoses (which are the ecosystems within the boundaries of the phytocenosis. Biogeocoenoses are minimal spatial unit of biosphere with its own evolutionary destiny (but not "one more" name of an ecosystem, is as usual treated in the western literature. The Biosphere as whole is not only the largest Earth’ ecosystem, but also

  18. Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

    OpenAIRE

    David M Bryson; Charles Ofria

    2013-01-01

    We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad...

  19. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  20. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  1. Synthesis of porous-acoustic absorbing systems by an evolutionary optimization method

    Science.gov (United States)

    Silva, F. I.; Pavanello, R.

    2010-10-01

    Topology optimization is frequently used to design structures and acoustic systems in a large range of engineering applications. In this work, a method is proposed for maximizing the absorbing performance of acoustic panels by using a coupled finite element model and evolutionary strategies. The goal is to find the best distribution of porous material for sound absorbing panels. The absorbing performance of the porous material samples in a Kundt tube is simulated using a coupled porous-acoustic finite element model. The equivalent fluid model is used to represent the foam material. The porous material model is coupled to a wave guide using a modal superposition technique. A sensitivity number indicating the optimum locations for porous material to be removed is derived and used in a numerical hard kill scheme. The sensitivity number is used to form an evolutionary porous material optimization algorithm which is verified through examples.

  2. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  3. Microphysiologic systems in female reproductive biology.

    Science.gov (United States)

    Young, Alexandria N; Moyle-Heyrman, Georgette; Kim, J Julie; Burdette, Joanna E

    2017-11-01

    Microphysiologic systems (MPS), including new organ-on-a-chip technologies, recapitulate tissue microenvironments by employing specially designed tissue or cell culturing techniques and microfluidic flow. Such systems are designed to incorporate physiologic factors that conventional 2D or even 3D systems cannot, such as the multicellular dynamics of a tissue-tissue interface or physical forces like fluid sheer stress. The female reproductive system is a series of interconnected organs that are necessary to produce eggs, support embryo development and female health, and impact the functioning of non-reproductive tissues throughout the body. Despite its importance, the human reproductive tract has received less attention than other organ systems, such as the liver and kidney, in terms of modeling with MPS. In this review, we discuss current gaps in the field and areas for technological advancement through the application of MPS. We explore current MPS research in female reproductive biology, including fertilization, pregnancy, and female reproductive tract diseases, with a focus on their clinical applications. Impact statement This review discusses existing microphysiologic systems technology that may be applied to study of the female reproductive tract, and those currently in development to specifically investigate gametes, fertilization, embryo development, pregnancy, and diseases of the female reproductive tract. We focus on the clinical applicability of these new technologies in fields such as assisted reproductive technologies, drug testing, disease diagnostics, and personalized medicine.

  4. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  5. Parallel stochastic systems biology in the cloud.

    Science.gov (United States)

    Aldinucci, Marco; Torquati, Massimo; Spampinato, Concetto; Drocco, Maurizio; Misale, Claudia; Calcagno, Cristina; Coppo, Mario

    2014-09-01

    The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in bioinformatics. The simulation-analysis workflow may result computationally expensive reducing the interactivity required in the model tuning. In this work, we advocate the high-level software design as a vehicle for building efficient and portable parallel simulators for the cloud. In particular, the Calculus of Wrapped Components (CWC) simulator for systems biology, which is designed according to the FastFlow pattern-based approach, is presented and discussed. Thanks to the FastFlow framework, the CWC simulator is designed as a high-level workflow that can simulate CWC models, merge simulation results and statistically analyse them in a single parallel workflow in the cloud. To improve interactivity, successive phases are pipelined in such a way that the workflow begins to output a stream of analysis results immediately after simulation is started. Performance and effectiveness of the CWC simulator are validated on the Amazon Elastic Compute Cloud. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  6. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  7. Evolutionary perspectives on human personality. Comment on "Personality from a cognitive-biological perspective" by Y. Neuman

    Science.gov (United States)

    Southard, Ashton C.; Zeigler-Hill, Virgil; Shackelford, Todd K.

    2014-12-01

    Yair Neuman [6] presents many provocative ideas in his interdisciplinary approach to human personality. In this commentary, we focus on his ideas regarding (1) the evolutionary basis of personality and (2) human sperm competition.

  8. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  9. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  10. Microbial stress tolerance for biofuels. Systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

    2012-07-01

    The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

  11. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.

    Science.gov (United States)

    Zheng, W Jim; Ruan, Jianhua; Xu, Hua; Zhao, Zhongming; Liu, Zhangdong

    2017-10-03

    Between December 8-10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics in 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics and systems biology. Systems biology has been a main theme in ICIBM 2016, with exciting advances were presented in many areas of systems biology. Here, we selected seven high quality papers to be published in BMC Systems Biology.

  12. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-04-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the study: special lessons designed to promote systems thinking, a computer-simulated scenario on the topic "ecosystem forest," and a combination of both special lessons and the computer simulation. These groups were then compared to a control group. A questionnaire was used to assess systems thinking skills of 424 sixth-grade students of secondary schools in Germany. The assessment differentiated between a conceptual understanding (measured as achievement score) and a reflexive justification (measured as justification score) of systems thinking. The following control variables were used: logical thinking, grades in school, memory span, and motivational goal orientation. Based on the pretest-posttest control group design, only those students who received both special instruction and worked with the computer simulation showed a significant increase in their achievement scores. The justification score increased in the computer simulation condition as well as in the combination of computer simulation and lesson condition. The possibilities and limits of promoting various forms of systems thinking by using realistic computer simulations are discussed.

  13. A Comprehensive Systems Biology Approach to Studying Zika Virus.

    Directory of Open Access Journals (Sweden)

    Meghan May

    Full Text Available Zika virus (ZIKV is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an 'omics' approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05 for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a. The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b. further divergence at specific sites is predictable as endemnicity is established in the Americas.

  14. Evolutionary theory and teleology.

    Science.gov (United States)

    O'Grady, R T

    1984-04-21

    The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

  15. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  16. Inflated impact factors? The true impact of evolutionary papers in non-evolutionary journals.

    Directory of Open Access Journals (Sweden)

    Erik Postma

    Full Text Available Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal's overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field

  17. Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

    Science.gov (United States)

    Louridas, George E; Lourida, Katerina G

    2017-02-21

    Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

  18. Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases

    Directory of Open Access Journals (Sweden)

    George E. Louridas

    2017-02-01

    Full Text Available Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction and emergence (upward biological direction could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

  19. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    Science.gov (United States)

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  20. Computational Fluid Dynamic Approach for Biological System Modeling

    OpenAIRE

    Huang, Weidong; Wu, Chundu; Xiao, Bingjia; Xia, Weidong

    2005-01-01

    Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper, it is found that the enzymatic reaction and multi-order reaction rate is often controlled by the transport of the reactants in biological systems. A Computational Fluid Dynamic (CFD) approach, which is based on transport of the components and kinetics of b...

  1. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  2. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2017-01-01

    The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research...... of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... complexity....

  3. Systems biology of energy homeostasis in yeast.

    Science.gov (United States)

    Zhang, Jie; Vemuri, Goutham; Nielsen, Jens

    2010-06-01

    The yeast Saccharomyces cerevisiae attains energy homeostasis through complex regulatory events that are predominantly controlled by the Snf1 kinase. This master regulator senses the stress and energy starvation and activates the metabolic processes to produce ATP and inhibits biosynthesis. In doing so, Snf1 controls the switch between catabolism and anabolism accordingly, and regulates the cellular growth and development in coordination with other signaling pathways. Since its mammalian ortholog AMPK, a drug target for obesity and type II diabetes, also exerts analogous control of metabolism, there has been extensive interest recently to understand the chemical and biological aspects of Snf1 activation and regulation in yeast to expedite human disease studies as well as fundamental understanding of yeast. This review will focus on how Snf1 regulates lipid metabolism based on the cellular energy status in yeast and drawing parallels with the mammalian system. Copyright 2010 Elsevier Ltd. All rights reserved.

  4. The start of systems biology in Ukraine

    Directory of Open Access Journals (Sweden)

    Obolenskaya M. Yu.

    2014-01-01

    Full Text Available The first laboratory of Systems Biology in Ukraine (IMBIG NASU represents a track record of its scientific results. They include the pioneered development of a web-based tool for genome-wide surveys of eukaryotic promoters for the presence of transcription factors binding sites (COTRASIF; the deciphered mechanisms of the fine-tuned and balanced response of primary hepatocytes to interferon alpha levels recorded after partial hepatectomy; the elaboration of a novel method of gene regulatory network inference compatible with GRID environment and the development of a stoichiometric model of folate-related one carbon unit metabolism in human placenta and its application for the characteristics of the system’s behavior as a whole at different human pathologies.

  5. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    Humans are exposed to various chemical agents through food, cosmetics, pharmaceuticals and other sources. Exposure to chemicals is suspected of playing a main role in the development of some adverse health effects in humans. Additionally, European regulatory authorities have recognized the risk...... associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... projects three different approaches to using computational toxicology to aid classical toxicological investigations. In project I, we predicted human health effects of five pesticides using publicly available data. We obtained a grouping of the chemical according to their potential human health effects...

  6. Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection.

    Directory of Open Access Journals (Sweden)

    Helena Barroso

    Full Text Available BACKGROUND: Unlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection. METHODOLOGY/PRINCIPAL FINDINGS: We performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2 or V3 (HIV-1. The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature. CONCLUSIONS/SIGNIFICANCE: We identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of

  7. Expert systems guide biological phosphorus removal

    Energy Technology Data Exchange (ETDEWEB)

    Krichten, D.J.; Wilson, K.D.; Tracy, K.D. (Air Products and Chemicals, Inc., Allentown, PA (United States))

    1991-10-01

    There is a large body of knowledge regarding optimum control strategies for new secondary wastewater treatment technology using an anaerobic selector to provide biological phosphorus removal. However, because the selector technology is new and the concepts differ somewhat from those used in conventional activated sludge wastewater treatment, a method of communicating this knowledge to plant operators is needed. Traditional methods such as classroom training and operating manuals are of limited effectiveness. The commonplace availability and low cost of the personal computer (PC) makes it practical to use a computer program to communicate the type of information required to control a wastewater treatment plant. Knowledge-based systems technology, commonly referred to as expert systems (ES) technology, is easy to use, provides useful information regarding a consistent control strategy, relieves the anxiety associated with learning a new process,' and provides instruction for inexperienced personnel. ES technology does not require special formatted input and is therefore easily accessible. All information required by the program is readily available through routine laboratory analysis, common plant instrumentation, or direct user observation. The program was designed for all levels of computer users and will run on all IBM-compatible or Apple MacIntosh systems.

  8. Biological Robustness: Paradigms, Mechanisms, and Systems Principles

    Directory of Open Access Journals (Sweden)

    James Michael Whitacre

    2012-05-01

    Full Text Available Robustness has been studied through the analysis of data sets, simulations, and a variety of experimental techniques that each have their own limitations but together confirm the ubiquity of biological robustness. Recent trends suggest that different types of perturbation (e.g. mutational, environmental are commonly stabilized by similar mechanisms, and system sensitivities often display a long-tailed distribution with relatively few perturbations representing the majority of sensitivities. Conceptual paradigms from network theory, control theory, complexity science, and natural selection have been used to understand robustness, however each paradigm has a limited scope of applicability and there has been little discussion of the conditions that determine this scope or the relationships between paradigms. Systems properties such as modularity, bow-tie architectures, degeneracy, and other topological features are often positively associated with robust traits, however common underlying mechanisms are rarely mentioned. For instance, many system properties support robustness through functional redundancy or through response diversity with responses regulated by competitive exclusion and cooperative facilitation. Moreover, few studies compare and contrast alternative strategies for achieving robustness such as homeostasis, adaptive plasticity, environment shaping, and environment tracking. These strategies share similarities in their utilization of adaptive and self-organization processes that are not well appreciated yet might be suggestive of reusable building blocks for generating robust behavior.

  9. Evolutionary Theories in Environmental and Resource Economics: Approaches and Applications

    NARCIS (Netherlands)

    van den Bergh, J.C.J.M.; Gowdy, J.M.

    2000-01-01

    Recent advances in evolutionary theory have important implications for environmental economics. A short overview is offered of evolutionary thinking in economics. Subsequently, major concepts and approaches in evolutionary biology and evolutionary economics are presented and compared. Attention is

  10. Computational optimization for S-type biological systems: cockroach genetic algorithm.

    Science.gov (United States)

    Wu, Shinq-Jen; Wu, Cheng-Tao

    2013-10-01

    S-type biological systems (S-systems) are demonstrated to be universal approximations of continuous biological systems. S-systems are easy to be generalized to large systems. The systems are identified through data-driven identification techniques (cluster-based algorithms or computational methods). However, S-systems' identification is challenging because multiple attractors exist in such highly nonlinear systems. Moreover, in some biological systems the interactive effect cannot be neglected even the interaction order is small. Therefore, learning should be focused on increasing the gap between the true and redundant interaction. In addition, a wide searching space is necessary because no prior information is provided. The used technologies should have the ability to achieve convergence enhancement and diversity preservation. Cockroaches live in nearly all habitats and survive for more than 300 million years. In this paper, we mimic cockroaches' competitive swarm behavior and integrated it with advanced evolutionary operations. The proposed cockroach genetic algorithm (CGA) possesses strong snatching-food ability to rush forward to a target and high migration ability to escape from local minimum. CGA was tested with three small-scale systems, a twenty-state medium-scale system and a thirty-state large-scale system. A wide search space ([0,100] for rate constants and [-100,100] for kinetic orders) with random or bad initial starts are used to show the high exploration performance. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Is floral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae).

    Science.gov (United States)

    Tripp, Erin A; Manos, Paul S

    2008-07-01

    Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the large genus Ruellia. Phylogenetic analyses, morphological ordinations, ancestral state reconstructions, and a character mapping simulation were conducted to reveal key patterns in the direction and lability of floral characters associated with pollination. We found significant floral morphological differences among species that were generally associated with different groups of floral visitors. Floral evolution has been highly labile and also directional. Some specialized systems such as hawkmoth or bat pollination are likely evolutionary dead-ends. In contrast, specialized pollination by hummingbirds is clearly not a dead-end. We found evidence for multiple reverse transitions from presumed ancestral hummingbird pollination to more derived bee or insect pollination. These repeated origins of insect pollination from hummingbird-pollinated ancestors have not evolved without historical baggage. Flowers of insect-pollinated species derived from hummingbird-pollinated ancestors are morphologically more similar to hummingbird flowers than they are to other more distantly related insect-pollinated flowers. Finally, some pollinator switches were concomitant with changes in floral morphology that are associated with those pollinators. These observations are consistent with the hypothesis that some transitions have been adaptive in the evolution of Ruellia.

  12. Microbial systems biology: New frontiers open to predictive microbiology

    NARCIS (Netherlands)

    Brul, S.; Mensonides, F.I.C.; Hellingwerf, K.J.; Teixeira De Mattos, M.J.

    2008-01-01

    The field of Systems Biology is a rapidly evolving area of research. It follows on from the previous experimental and theoretical ‘omics’ revolution in biology. Now that we have through the use of these tools many ‘indices’ of biological systems available the next step is to actually start composing

  13. Systems biology in practice: concepts, implementation and application

    National Research Council Canada - National Science Library

    Klipp, E

    2005-01-01

    ... approaching systems biology from a different discipline. We see the origin and the methodological foundations for systems biology (1) in the accumulation of detailed biological knowledge with the prospect of utilization in biotechnology and health care, (2) in the emergence of new experimental techniques in genomics and proteomics, (3) in the traditio...

  14. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

  15. An Evolutionary Complex Systems Decision-Support Tool for the Management of Operations

    Science.gov (United States)

    Baldwin, J. S.; Allen, P. M.; Ridgway, K.

    2011-12-01

    This research aimed to add both to the development of complex systems thinking in the subject area of Operations and Production Management and to the limited number of applications of computational models and simulations from the science of complex systems. The latter potentially offer helpful decision-support tools for operations and production managers. A mechanical engineering firm was used as a case study where a combined qualitative and quantitative methodological approach was employed to extract the required data from four senior managers. Company performance measures as well as firm technologies, practices and policies, and their relation and interaction with one another, were elicited. The data were subjected to an evolutionary complex systems model resulting in a series of simulations. The findings included both reassuring and some unexpected results. The simulation based on the CEO's opinions led the most cohesive and synergistic collection of practices describing the firm, closely followed by the Marketing and R&D Managers. The Manufacturing Manager's responses led to the most extreme evolutionary trajectory where the integrity of the entire firm came into question particularly when considering how employees were utilised. By drawing directly from the opinions and views of managers rather than from logical 'if-then' rules and averaged mathematical representations of agents that characterise agent-based and other self-organisational models, this work builds on previous applications by capturing a micro-level description of diversity and a learning effect that has been problematical not only in terms of theory but also in application. This approach can be used as a decision-support tool for operations and other managers providing a forum with which to explore a) the strengths, weaknesses and consequences of different decision-making capacities within the firm; b) the introduction of new manufacturing technologies, practices and policies; and, c) the

  16. International Conference on Artificial Intelligence and Evolutionary Computations in Engineering Systems

    CERN Document Server

    Bhaskar, M; Panigrahi, Bijaya; Das, Swagatam

    2016-01-01

    The book is a collection of high-quality peer-reviewed research papers presented in the first International Conference on International Conference on Artificial Intelligence and Evolutionary Computations in Engineering Systems (ICAIECES -2015) held at Velammal Engineering College (VEC), Chennai, India during 22 – 23 April 2015. The book discusses wide variety of industrial, engineering and scientific applications of the emerging techniques. Researchers from academic and industry present their original work and exchange ideas, information, techniques and applications in the field of Communication, Computing and Power Technologies.

  17. Evolutionary approach for spatial architecture layout design enhanced by an agent-based topology finding system

    Directory of Open Access Journals (Sweden)

    Zifeng Guo

    2017-03-01

    Full Text Available This paper presents a method for the automatic generation of a spatial architectural layout from a user-specified architectural program. The proposed approach binds a multi-agent topology finding system and an evolutionary optimization process. The former generates topology satisfied layouts for further optimization, while the latter focuses on refining the layouts to achieve predefined architectural criteria. The topology finding process narrows the search space and increases the performance in subsequent optimization. Results imply that the spatial layout modeling and the multi-floor topology are handled.

  18. International Conference on Artificial Intelligence and Evolutionary Computations in Engineering Systems

    CERN Document Server

    Vijayakumar, K; Panigrahi, Bijaya; Das, Swagatam

    2017-01-01

    The volume is a collection of high-quality peer-reviewed research papers presented in the International Conference on Artificial Intelligence and Evolutionary Computation in Engineering Systems (ICAIECES 2016) held at SRM University, Chennai, Tamilnadu, India. This conference is an international forum for industry professionals and researchers to deliberate and state their research findings, discuss the latest advancements and explore the future directions in the emerging areas of engineering and technology. The book presents original work and novel ideas, information, techniques and applications in the field of communication, computing and power technologies.

  19. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

    Full Text Available Many  authors have proposed  that contextualization of reality  is necessary  to teach  Biology, empha- sizing students´ social and  economic realities.   However, contextualization means  more than  this;  it is related  to working with  different kinds of phenomena  and/or objects  which enable  the  expression of scientific concepts.  Thus,  contextualization allows the integration of different contents.  Under this perspective,  the  objectives  of this  work were to articulate different  biology concepts  in order  to de- velop a systemic vision of biology; to establish  relationships with other areas of knowledge and to make concrete the  cell molecular  structure and organization as well as their  implications  on living beings´ environment, using  contextualization.  The  methodology  adopted  in this  work  was based  on three aspects:  interdisciplinarity, contextualization and development of competences,  using energy:  its flux and transformations as a thematic axis and  an approach  which allowed the  interconnection between different situations involving  these  concepts.   The  activities developed  were:  1.   dialectic exercise, involving a movement around  micro and macroscopic aspects,  by using questions  and activities,  sup- ported  by the use of alternative material  (as springs, candles on the energy, its forms, transformations and  implications  in the  biological way (microscopic  concepts;  2, Construction of molecular  models, approaching the concepts of atom,  chemical bonds and bond energy in molecules; 3. Observations de- veloped in Manguezal¨(mangrove swamp  ecosystem (Itapissuma, PE  were used to work macroscopic concepts  (as  diversity  and  classification  of plants  and  animals,  concerning  to  energy  flow through food chains and webs. A photograph register of all activities  along the course plus texts

  20. Remotely Sensed Predictions and In Situ Observations of Lower Congo River Dynamics in Support of Fish Evolutionary Biology

    Science.gov (United States)

    Gardiner, N.; Bjerklie, D. M.

    2011-12-01

    Ongoing research into the evolution of fishes in the lower Congo River suggests a close tie between diversity and hydraulic complexity of flow in the channel. For example, fish populations on each side of the rapids at the head of the lower Congo are within 1.5 km of one another, a distance normally allowing for interbreeding in river systems of comparable size, yet these fish populations show about 5% divergence in their mitochondrial DNA signatures. The proximal reason for this divergence is hydraulic complexity: the speed and turbulence of water moving through the thalweg is a barrier to dispersal for these fishes. Further examination of fish diversity suggests additional correlations of evolutionary divergence of fish clades in association with geomorphic and hydraulic features such as deep pools, extensive systems of rapids, alternating sections of fast and slow current, and recurring whirlpools. Due to prohibitive travel costs, limited field time, and the large geographic domain (approximately 400 river km) of the study area, we undertook a nested set of remote sensing analyses to extract habitat features, geomorphic descriptors, and hydraulic parameters including channel forming velocity, depth, channel roughness, slope, and shear stress. Each of these estimated parameters is mapped for each 1 km segment of the river from the rapids described above to below Inga Falls, a massive cataract where several endemic fish species have been identified. To validate remote sensing estimates, we collected depth and velocity data within the river using gps-enabled sonar measurements from a kayak and Doppler profiling from a motor-driven dugout canoe. Observations corroborate remote sensing estimates of geomorphic parameters. Remote sensing-based estimates of channel-forming velocity and depth were less than the observed maximum channel depth but correlated well with channel properties within 1 km reach segments. This correspondence is notable. The empirical models used