Estimating the change in asymptotic direction due to secular changes in the geomagnetic field

NASA Technical Reports Server (NTRS)

Flueckiger, E. O.; Smart, D. F.; Shea, M. A.; Gentile, L. C.; Bathurat, A. A.

1985-01-01

The concept of geomagnetic optics, as described by the asymptotic directions of approach, is extremely useful in the analysis of cosmic radiation data. However, when changes in cutoff occur as a result of evolution in the geomagnetic field, there are corresponding changes in the asymptotic cones of acceptance. A method is introduced of estimating the change in the asymptotic direction of approach for vertically incident cosmic ray particles from a reference set of directions at a specific epoch by considering the change in the geomagnetic cutoff.

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems.

PubMed

Acevedo-Rocha, Carlos G; Agudo, Ruben; Reetz, Manfred T

2014-12-10

Directed evolution of stereoselective enzymes provides a means to generate useful biocatalysts for asymmetric transformations in organic chemistry and biotechnology. Almost all of the numerous examples reported in the literature utilize high-throughput screening systems based on suitable analytical techniques. Since the screening step is the bottleneck of the overall procedure, researchers have considered the use of genetic selection systems as an alternative to screening. In principle, selection would be the most elegant and efficient approach because it is based on growth advantage of host cells harboring stereoselective mutants, but devising such selection systems is very challenging. They must be designed so that the host organism profits from the presence of an enantioselective variant. Progress in this intriguing research area is summarized in this review, which also includes some examples of display systems designed for enantioselectivity as assayed by fluorescence-activated cell sorting (FACS). Although the combination of display systems and FACS is a powerful approach, we also envision innovative ideas combining metabolic engineering and genetic selection systems with protein directed evolution for the development of highly selective and efficient biocatalysts. Copyright © 2014 Elsevier B.V. All rights reserved.

Directional selection in the evolution of elongated upper canines in clouded leopards and sabre-toothed cats.

PubMed

Harano, Tomohiro; Kutsukake, Nobuyuki

2018-06-14

Extremely developed or specialised traits such as the elongated upper canines of extinct sabre-toothed cats are often not analogous to those of any extant species, which limits our understanding of their evolutionary cause. However, an extant species may have undergone directional selection for a similar extreme phenotype. Among living felids, the clouded leopard, Neofelis nebulosa, has exceptionally long upper canines for its body size. We hypothesised that directional selection generated the elongated upper canines of clouded leopards in a manner similar to the process in extinct sabre-toothed cats. To test this, we developed an approach that compared the effect of directional selection among lineages in a phylogeny using a simulation of trait evolution and approximate Bayesian computation. This approach was applied to analyse the evolution of upper canine length in the Felidae phylogeny. Our analyses consistently showed directional selection favouring longer upper canines in the clouded leopard lineage and a lineage leading to the sabre-toothed cat with the longest upper canines, Smilodon. Most of our analyses detected an effect of directional selection for longer upper canines in the lineage leading to another sabre-toothed cat, Homotherium, although this selection may have occurred exclusively in the primitive species. In all the analyses, the clouded leopard and Smilodon lineages showed comparable directional selection. This implies that clouded leopards share a selection advantage with sabre-toothed cats in having elongated upper canines. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation.

PubMed

Weaver, Timothy D; Gunz, Philipp

2018-04-01

Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

PubMed

Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

2016-01-01

In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution.

PubMed

Wedge, David C; Rowe, William; Kell, Douglas B; Knowles, Joshua

2009-03-07

We model the process of directed evolution (DE) in silico using genetic algorithms. Making use of the NK fitness landscape model, we analyse the effects of mutation rate, crossover and selection pressure on the performance of DE. A range of values of K, the epistatic interaction of the landscape, are considered, and high- and low-throughput modes of evolution are compared. Our findings suggest that for runs of or around ten generations' duration-as is typical in DE-there is little difference between the way in which DE needs to be configured in the high- and low-throughput regimes, nor across different degrees of landscape epistasis. In all cases, a high selection pressure (but not an extreme one) combined with a moderately high mutation rate works best, while crossover provides some benefit but only on the less rugged landscapes. These genetic algorithms were also compared with a "model-based approach" from the literature, which uses sequential fixing of the problem parameters based on fitting a linear model. Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes.

A Metal-Organic Framework Approach toward Highly Nitrogen-Doped Graphitic Carbon as a Metal-Free Photocatalyst for Hydrogen Evolution.

PubMed

Zhao, Xiuxia; Yang, Hao; Jing, Peng; Shi, Wei; Yang, Guangming; Cheng, Peng

2017-03-01

Zeolitic imidazolate framework-8 (ZIF-8)-derived N-doped graphene analogous polyhedrons (ZNGs) obtained via the direct carbonation of ZIF-8 are applied to photocatalytic hydrogen evolution for the first time. The contents of different types of nitrogen atoms in ZNGs can be fine-tuned via the calcination temperature, which significantly influences the hydrogen evolution rate of the ZNGs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Million-body star cluster simulations: comparisons between Monte Carlo and direct N-body

NASA Astrophysics Data System (ADS)

Rodriguez, Carl L.; Morscher, Meagan; Wang, Long; Chatterjee, Sourav; Rasio, Frederic A.; Spurzem, Rainer

2016-12-01

We present the first detailed comparison between million-body globular cluster simulations computed with a Hénon-type Monte Carlo code, CMC, and a direct N-body code, NBODY6++GPU. Both simulations start from an identical cluster model with 106 particles, and include all of the relevant physics needed to treat the system in a highly realistic way. With the two codes `frozen' (no fine-tuning of any free parameters or internal algorithms of the codes) we find good agreement in the overall evolution of the two models. Furthermore, we find that in both models, large numbers of stellar-mass black holes (>1000) are retained for 12 Gyr. Thus, the very accurate direct N-body approach confirms recent predictions that black holes can be retained in present-day, old globular clusters. We find only minor disagreements between the two models and attribute these to the small-N dynamics driving the evolution of the cluster core for which the Monte Carlo assumptions are less ideal. Based on the overwhelming general agreement between the two models computed using these vastly different techniques, we conclude that our Monte Carlo approach, which is more approximate, but dramatically faster compared to the direct N-body, is capable of producing an accurate description of the long-term evolution of massive globular clusters even when the clusters contain large populations of stellar-mass black holes.

Research program for a search of the origin of Darwinian evolution. Research program for a vesicle-based model of the origin of Darwinian evolution on prebiotic early Earth

NASA Astrophysics Data System (ADS)

Tessera, Marc

2017-03-01

The search for origin of `life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

Research program for a search of the origin of Darwinian evolution : Research program for a vesicle-based model of the origin of Darwinian evolution on prebiotic early Earth.

PubMed

Tessera, Marc

2017-03-01

The search for origin of 'life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

Imitative and Direct Learning as Interacting Factors in Life History Evolution.

PubMed

Bullinaria, John A

2017-01-01

The idea that lifetime learning can have a significant effect on life history evolution has recently been explored using a series of artificial life simulations. These involved populations of competing individuals evolving by natural selection to learn to perform well on simplified abstract tasks, with the learning consisting of identifying regularities in their environment. In reality, there is more to learning than that type of direct individual experience, because it often includes a substantial degree of social learning that involves various forms of imitation of what other individuals have learned before them. This article rectifies that omission by incorporating memes and imitative learning into revised versions of the previous approach. To do this reliably requires formulating and testing a general framework for meme-based simulations that will enable more complete investigations of learning as a factor in any life history evolution scenarios. It does that by simulating imitative information transfer in terms of memes being passed between individuals, and developing a process for merging that information with the (possibly inconsistent) information acquired by direct experience, leading to a consistent overall body of learning. The proposed framework is tested on a range of learning variations and a representative set of life history factors to confirm the robustness of the approach. The simulations presented illustrate the types of interactions and tradeoffs that can emerge, and indicate the kinds of species-specific models that could be developed with this approach in the future.

Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution.

PubMed

Shivange, Amol V; Roccatano, Danilo; Schwaneberg, Ulrich

2016-01-01

Bacterial phytases have attracted industrial interest as animal feed supplement due to their high activity and sufficient thermostability (required for feed pelleting). We devised an approach named KeySIDE,  an iterative Key-residues interrogation of the wild type with Substitutions Identified in Directed Evolution for improving Yersinia mollaretii phytase (Ymphytase) thermostability by combining key beneficial substitutions and elucidating their individual roles. Directed evolution yielded in a discovery of nine positions in Ymphytase and combined iteratively to identify key positions. The "best" combination (M6: T77K, Q154H, G187S, and K289Q) resulted in significantly improved thermal resistance; the residual activity improved from 35 % (wild type) to 89 % (M6) at 58 °C and 20-min incubation. Melting temperature increased by 3 °C in M6 without a loss of specific activity. Molecular dynamics simulation studies revealed reduced flexibility in the loops located next to helices (B, F, and K) which possess substitutions (Helix-B: T77K, Helix-F: G187S, and Helix-K: K289E/Q). Reduced flexibility in the loops might be caused by strengthened hydrogen bonding network (e.g., G187S and K289E/K289Q) and a salt bridge (T77K). Our results demonstrate a promising approach to design phytases in food research, and we hope that the KeySIDE might become an attractive approach for understanding of structure-function relationships of enzymes.

Vector Design Tour de Force: Integrating Combinatorial and Rational Approaches to Derive Novel Adeno-associated Virus Variants

PubMed Central

Marsic, Damien; Govindasamy, Lakshmanan; Currlin, Seth; Markusic, David M; Tseng, Yu-Shan; Herzog, Roland W; Agbandje-McKenna, Mavis; Zolotukhin, Sergei

2014-01-01

Methodologies to improve existing adeno-associated virus (AAV) vectors for gene therapy include either rational approaches or directed evolution to derive capsid variants characterized by superior transduction efficiencies in targeted tissues. Here, we integrated both approaches in one unified design strategy of “virtual family shuffling” to derive a combinatorial capsid library whereby only variable regions on the surface of the capsid are modified. Individual sublibraries were first assembled in order to preselect compatible amino acid residues within restricted surface-exposed regions to minimize the generation of dead-end variants. Subsequently, the successful families were interbred to derive a combined library of ~8 × 105 complexity. Next-generation sequencing of the packaged viral DNA revealed capsid surface areas susceptible to directed evolution, thus providing guidance for future designs. We demonstrated the utility of the library by deriving an AAV2-based vector characterized by a 20-fold higher transduction efficiency in murine liver, now equivalent to that of AAV8. PMID:25048217

Unified anomaly suppression and boundary extraction in laser radar range imagery based on a joint curve-evolution and expectation-maximization algorithm.

PubMed

Feng, Haihua; Karl, William Clem; Castañon, David A

2008-05-01

In this paper, we develop a new unified approach for laser radar range anomaly suppression, range profiling, and segmentation. This approach combines an object-based hybrid scene model for representing the range distribution of the field and a statistical mixture model for the range data measurement noise. The image segmentation problem is formulated as a minimization problem which jointly estimates the target boundary together with the target region range variation and background range variation directly from the noisy and anomaly-filled range data. This formulation allows direct incorporation of prior information concerning the target boundary, target ranges, and background ranges into an optimal reconstruction process. Curve evolution techniques and a generalized expectation-maximization algorithm are jointly employed as an efficient solver for minimizing the objective energy, resulting in a coupled pair of object and intensity optimization tasks. The method directly and optimally extracts the target boundary, avoiding a suboptimal two-step process involving image smoothing followed by boundary extraction. Experiments are presented demonstrating that the proposed approach is robust to anomalous pixels (missing data) and capable of producing accurate estimation of the target boundary and range values from noisy data.

Directed Evolution of a Cyclized Peptoid-Peptide Chimera against a Cell-Free Expressed Protein and Proteomic Profiling of the Interacting Proteins to Create a Protein-Protein Interaction Inhibitor.

PubMed

Kawakami, Takashi; Ogawa, Koji; Hatta, Tomohisa; Goshima, Naoki; Natsume, Tohru

2016-06-17

N-alkyl amino acids are useful building blocks for the in vitro display evolution of ribosomally synthesized peptides because they can increase the proteolytic stability and cell permeability of these peptides. However, the translation initiation substrate specificity of nonproteinogenic N-alkyl amino acids has not been investigated. In this study, we screened various N-alkyl amino acids and nonamino carboxylic acids for translation initiation with an Escherichia coli reconstituted cell-free translation system (PURE system) and identified those that efficiently initiated translation. Using seven of these efficiently initiating acids, we next performed in vitro display evolution of cyclized peptidomimetics against an arbitrarily chosen model human protein (β-catenin) cell-free expressed from its cloned cDNA (HUPEX) and identified a novel β-catenin-binding cyclized peptoid-peptide chimera. Furthermore, by a proteomic approach using direct nanoflow liquid chromatography-tandem mass spectrometry (DNLC-MS/MS), we successfully identified which protein-β-catenin interaction is inhibited by the chimera. The combination of in vitro display evolution of cyclized N-alkyl peptidomimetics and in vitro expression of human proteins would be a powerful approach for the high-speed discovery of diverse human protein-targeted cyclized N-alkyl peptidomimetics.

Macroscopic dielectric function within time-dependent density functional theory—Real time evolution versus the Casida approach

NASA Astrophysics Data System (ADS)

Sander, Tobias; Kresse, Georg

2017-02-01

Linear optical properties can be calculated by solving the time-dependent density functional theory equations. Linearization of the equation of motion around the ground state orbitals results in the so-called Casida equation, which is formally very similar to the Bethe-Salpeter equation. Alternatively one can determine the spectral functions by applying an infinitely short electric field in time and then following the evolution of the electron orbitals and the evolution of the dipole moments. The long wavelength response function is then given by the Fourier transformation of the evolution of the dipole moments in time. In this work, we compare the results and performance of these two approaches for the projector augmented wave method. To allow for large time steps and still rely on a simple difference scheme to solve the differential equation, we correct for the errors in the frequency domain, using a simple analytic equation. In general, we find that both approaches yield virtually indistinguishable results. For standard density functionals, the time evolution approach is, with respect to the computational performance, clearly superior compared to the solution of the Casida equation. However, for functionals including nonlocal exchange, the direct solution of the Casida equation is usually much more efficient, even though it scales less beneficial with the system size. We relate this to the large computational prefactors in evaluating the nonlocal exchange, which renders the time evolution algorithm fairly inefficient.

Directional cultural change by modification and replacement of memes.

PubMed

Cardoso, Gonçalo C; Atwell, Jonathan W

2011-01-01

Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations--modification of memes--to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered an urban habitat. Many songbirds have higher minimum song frequency in cities, to alleviate masking by low-frequency noise. We estimated that the input of meme modifications in an urban songbird population explains about half the extent of the population divergence in song frequency. This contribution of cultural mutations is large, but insufficient to explain the entire population divergence. The remaining divergence is due to selection of memes or creation of new memes. We conclude that the input of cultural mutations can be quantitatively important, unlike in genetic evolution, and that it operates together with other mechanisms of cultural evolution. For this and other traits, in which the input of cultural mutations might be important, quantitative studies of cultural mutation are necessary to calibrate realistic models of cultural evolution. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

From crater functions to partial differential equations: a new approach to ion bombardment induced nonequilibrium pattern formation.

PubMed

Norris, Scott A; Brenner, Michael P; Aziz, Michael J

2009-06-03

We develop a methodology for deriving continuum partial differential equations for the evolution of large-scale surface morphology directly from molecular dynamics simulations of the craters formed from individual ion impacts. Our formalism relies on the separation between the length scale of ion impact and the characteristic scale of pattern formation, and expresses the surface evolution in terms of the moments of the crater function. We demonstrate that the formalism reproduces the classical Bradley-Harper results, as well as ballistic atomic drift, under the appropriate simplifying assumptions. Given an actual set of converged molecular dynamics moments and their derivatives with respect to the incidence angle, our approach can be applied directly to predict the presence and absence of surface morphological instabilities. This analysis represents the first work systematically connecting molecular dynamics simulations of ion bombardment to partial differential equations that govern topographic pattern-forming instabilities.

Low rank alternating direction method of multipliers reconstruction for MR fingerprinting.

PubMed

Assländer, Jakob; Cloos, Martijn A; Knoll, Florian; Sodickson, Daniel K; Hennig, Jürgen; Lattanzi, Riccardo

2018-01-01

The proposed reconstruction framework addresses the reconstruction accuracy, noise propagation and computation time for magnetic resonance fingerprinting. Based on a singular value decomposition of the signal evolution, magnetic resonance fingerprinting is formulated as a low rank (LR) inverse problem in which one image is reconstructed for each singular value under consideration. This LR approximation of the signal evolution reduces the computational burden by reducing the number of Fourier transformations. Also, the LR approximation improves the conditioning of the problem, which is further improved by extending the LR inverse problem to an augmented Lagrangian that is solved by the alternating direction method of multipliers. The root mean square error and the noise propagation are analyzed in simulations. For verification, in vivo examples are provided. The proposed LR alternating direction method of multipliers approach shows a reduced root mean square error compared to the original fingerprinting reconstruction, to a LR approximation alone and to an alternating direction method of multipliers approach without a LR approximation. Incorporating sensitivity encoding allows for further artifact reduction. The proposed reconstruction provides robust convergence, reduced computational burden and improved image quality compared to other magnetic resonance fingerprinting reconstruction approaches evaluated in this study. Magn Reson Med 79:83-96, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

PubMed Central

Currin, Andrew; Swainston, Neil; Day, Philip J.

2015-01-01

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust. PMID:25503938

CryoTEM as an Advanced Analytical Tool for Materials Chemists.

PubMed

Patterson, Joseph P; Xu, Yifei; Moradi, Mohammad-Amin; Sommerdijk, Nico A J M; Friedrich, Heiner

2017-07-18

Morphology plays an essential role in chemistry through the segregation of atoms and/or molecules into different phases, delineated by interfaces. This is a general process in materials synthesis and exploited in many fields including colloid chemistry, heterogeneous catalysis, and functional molecular systems. To rationally design complex materials, we must understand and control morphology evolution. Toward this goal, we utilize cryogenic transmission electron microscopy (cryoTEM), which can track the structural evolution of materials in solution with nanometer spatial resolution and a temporal resolution of <1 s. In this Account, we review examples of our own research where direct observations by cryoTEM have been essential to understanding morphology evolution in macromolecular self-assembly, inorganic nucleation and growth, and the cooperative evolution of hybrid materials. These three different research areas are at the heart of our approach to materials chemistry where we take inspiration from the myriad examples of complex materials in Nature. Biological materials are formed using a limited number of chemical components and under ambient conditions, and their formation pathways were refined during biological evolution by enormous trial and error approaches to self-organization and biomineralization. By combining the information on what is possible in nature and by focusing on a limited number of chemical components, we aim to provide an essential insight into the role of structure evolution in materials synthesis. Bone, for example, is a hierarchical and hybrid material which is lightweight, yet strong and hard. It is formed by the hierarchical self-assembly of collagen into a macromolecular template with nano- and microscale structure. This template then directs the nucleation and growth of oriented, nanoscale calcium phosphate crystals to form the composite material. Fundamental insight into controlling these structuring processes will eventually allow us to design such complex materials with predetermined and potentially unique properties.

Design issues for directional coupler- and MMI-based optical microring resonator filters on InP

NASA Astrophysics Data System (ADS)

Themistos, Christos; Kalli, Kyriacos; Komodromos, Michalis; Rajarajan, Muttukrishnan; Rahman, B. M. A.; Grattan, Kenneth T. V.

2004-08-01

The characterization and optimization of optical microring resonator-based optical filters on deeply etched GaInAsP-Inp waveguides, using the finite element-based beam propagation approach is presented here. Design issues for directional coupler- and multimode interference coupler-based devices, such as field evolution, optical power, phase, fabrication tolerance and wavelength dependence have been investigated.

Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication.

PubMed

Brödel, Andreas K; Jaramillo, Alfonso; Isalan, Mark

2017-09-01

Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.

Compartmentalized partnered replication for the directed evolution of genetic parts and circuits.

PubMed

Abil, Zhanar; Ellefson, Jared W; Gollihar, Jimmy D; Watkins, Ella; Ellington, Andrew D

2017-12-01

Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production. Individual cells are then trapped in water-in-oil emulsion droplets in the presence of primers and dNTPs, followed by the recovery of the partner genes via emulsion PCR. In this step, droplets with cells expressing partner proteins that promote polymerase production will produce higher copy numbers of the improved partner gene. The resulting partner genes can subsequently be recloned for the next round of selection. Here, we present a step-by-step guideline for the procedure by providing examples of (i) selection of T7 RNA polymerases that recognize orthogonal promoters and (ii) selection of tRNA for enhanced amber codon suppression. A single round of CPR should take ∼3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency.

Lithium-sulfur batteries: Making the invisible visible

NASA Astrophysics Data System (ADS)

Johansson, Patrik

2017-06-01

The presence of polysulfides in Li-S batteries significantly affects battery operation, but their presence and reaction mechanisms are not well understood. Now, an operando X-ray diffraction approach is used to directly observe these polysulfides, offering insights on their formation and evolution.

Nested Tracking Graphs

DOE PAGES

Lukasczyk, Jonas; Weber, Gunther; Maciejewski, Ross; ...

2017-06-01

Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to eachmore » other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We show the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.« less

Darwinism and the cultural evolution of sports.

PubMed

De Block, Andreas; Dewitte, Siegfried

2009-01-01

This article outlines a Darwinian approach to sports that takes into account its profoundly cultural character and thereby overcomes the traditional nature-culture dichotomies in the sociology of sport. We argue that there are good reasons to view sports as culturally evolved signaling systems that serve a function similar to (biological) courtship rituals in other animals. Our approach combines the insights of evolutionary psychology, which states that biological adaptations determine the boundaries for the types of sport that are possible, and pure cultural theories, which describe the mechanism of cultural evolution without referring to sport's biological bases. Several biological and cultural factors may moderate the direct effect that signaling value has on a sport's viability or popularity. Social learning underlies many aspects of the cultural control of sports, and sports have evolved new cultural functions more-or-less unrelated to mate choice as cultural evolution itself became important in humans.

Dinosaur evolution. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds.

PubMed

Lee, Michael S Y; Cau, Andrea; Naish, Darren; Dyke, Gareth J

2014-08-01

Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains. Copyright © 2014, American Association for the Advancement of Science.

The modern temperature-accelerated dynamics approach

DOE PAGES

Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny; ...

2016-06-01

Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, thesemore » enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. Here, we review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD.« less

Multi-Model approach to reconstruct the Mediterranean Freshwater Evolution

NASA Astrophysics Data System (ADS)

Simon, Dirk; Marzocchi, Alice; Flecker, Rachel; Lunt, Dan; Hilgen, Frits; Meijer, Paul

2016-04-01

Today the Mediterranean Sea is isolated from the global ocean by the Strait of Gibraltar. This restricted nature causes the Mediterranean basin to react more sensitively to climatic and tectonic related phenomena than the global ocean. Not just eustatic sea-level and regional river run-off, but also gateway tectonics and connectivity between sub-basins are leaving an enhanced fingerprint in its geological record. To understand its evolution, it is crucial to understand how these different effects are coupled. The Miocene-Pliocene sedimentary record of the Mediterranean shows alternations in composition and colour and has been astronomically tuned. Around the Miocene-Pliocene Boundary the most extreme changes occur in the Mediterranean Sea. About 6% of the salt in the global ocean deposited in the Mediterranean Region, forming an approximately 2 km thick salt layer, which is still present today. This extreme event is named the Messinian Salinity Crisis (MSC, 5.97-5.33 Ma). The gateway and climate evolution is not well constrained for this time, which makes it difficult to distinguish which of the above mentioned drivers might have triggered the MSC. We, therefore, decided to tackle this problem via a multi-model approach: (1) We calculate the Mediterranean freshwater evolution via 30 atmosphere-ocean-vegetation simulations (using HadCM3L), to which we fitted to a function, using a regression model. This allows us to directly relate the orbital curves to evaporation, precipitation and run off. The resulting freshwater evolution can be directly correlated to other sedimentary and proxy records in the late Miocene. (2) By feeding the new freshwater evolution curve into a box/budget model we can predict the salinity and strontium evolution of the Mediterranean for a certain Atlantic-Mediterranean gateway. (3) By comparing these results to the known salinity thresholds of gypsum and halite saturation of sea water, but also to the late Miocene Mediterranean strontium record, we can infer how the connectivity between global ocean and the Mediterranean must have changed through time in order to cause the MSC. (4) Such a connectivity evolution will give us the basis to understand the interplay between eustatic sea-level and regional tectonic changes in the Gibraltar region. Here we present the detailed method, the results and the applications of this multi-model approach.

Research on Capturing of Customer Requirements Based on Innovation Theory

NASA Astrophysics Data System (ADS)

junwu, Ding; dongtao, Yang; zhenqiang, Bao

To exactly and effectively capture customer requirements information, a new customer requirements capturing modeling method was proposed. Based on the analysis of function requirement models of previous products and the application of technology system evolution laws of the Theory of Innovative Problem Solving (TRIZ), the customer requirements could be evolved from existing product designs, through modifying the functional requirement unit and confirming the direction of evolution design. Finally, a case study was provided to illustrate the feasibility of the proposed approach.

Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search.

PubMed

Porter, Joanne L; Boon, Priscilla L S; Murray, Tracy P; Huber, Thomas; Collyer, Charles A; Ollis, David L

2015-02-20

The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a powerful tool for engineering enzymes with improved physical and catalytic properties and can be used to evolve enzymes where lack of structural information may thwart the use of rational design. In this study, we take the versatile and diverse α/β hydrolase fold framework, in the form of dienelactone hydrolase, and evolve it over three unique sequential evolutions with a total of 14 rounds of screening to generate a series of enzyme variants. The native enzyme has a low level of promiscuous activity toward p-nitrophenyl acetate but almost undetectable activity toward larger p-nitrophenyl esters. Using p-nitrophenyl acetate as an evolutionary intermediate, we have generated variants with altered specificity and catalytic activity up to 3 orders of magnitude higher than the native enzyme toward the larger nonphysiological p-nitrophenyl ester substrates. Several variants also possess increased stability resulting from the multidimensional approach to screening. Crystal structure analysis and substrate docking show how the enzyme active site changes over the course of the evolutions as either a direct or an indirect result of mutations.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Directional Darwinian Selection in proteins.

PubMed

McClellan, David A

2013-01-01

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

Automating Microbial Directed Evolution For Bioengineering Applications

NASA Astrophysics Data System (ADS)

Lee, A.; Demachkie, I. S.; Sardesh, N.; Arismendi, D.; Ouandji, C.; Wang, J.; Blaich, J.; Gentry, D.

2016-12-01

From a micro-biology perspective, directed evolution is a technique that uses controlled environmental pressures to select for a desired phenotype. Directed evolution has the distinct advantage over rational design of not needing extensive knowledge of the genome or pathways associated with a microorganism to induce phenotypes. However, there are currently limitations to the applicability of this technique including being time-consuming, error-prone, and dependent on existing assays that may lack selectivity for the given phenotype. The AADEC (Autonomous Adaptive Directed Evolution Chamber) system is a proof-of-concept instrument to automate and improve the technique such that directed evolution can be used more effectively as a general bioengineering tool. A series of tests using the automated system and comparable by-hand survival assay measurements have been carried out using UV-C radiation and Escherichia coli cultures in order to demonstrate the advantages of the AADEC versus traditional implementations of directed evolution such as random mutagenesis. AADEC uses UV-C exposure as both a source of environmental stress and mutagenesis, so in order to evaluate the UV-C tolerance obtained from the cultures, a manual UV-C exposure survival assay was developed alongside the device to compare the survival fractions at a fixed dosage. This survival assay involves exposing E.coli to UV-C radiation using a custom-designed exposure hood to control the flux and dose. Surviving cells are counted then transferred to the next iteration and so on for several iterations to calculate the survival fractions for each exposure iteration. This survival assay primarily serves as a baseline for the AADEC device, allowing quantification of the differences between the AADEC system over the manual approach. The primary data of comparison is survival fractions; this is obtained by optical density and plate counts in the manual assay and by optical density growth curve fits pre- and post-exposure in the automated case. This data can then be compiled to calculate trends over the iterations to characterize increasing UV-C resistance of the E.coli strains. The observed trends are statistically indistinguishable through several iterations from both sources.

Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover

PubMed Central

Parreiras, Lucas S.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman; Higbee, Alan J.; La Reau, Alex; Tremaine, Mary; Qin, Li; Willis, Laura B.; Bice, Benjamin D.; Bonfert, Brandi L.; Pinhancos, Rebeca C.; Balloon, Allison J.; Uppugundla, Nirmal; Liu, Tongjun; Li, Chenlin; Tanjore, Deepti; Ong, Irene M.; Li, Haibo; Pohlmann, Edward L.; Serate, Jose; Withers, Sydnor T.; Simmons, Blake A.; Hodge, David B.; Westphall, Michael S.; Coon, Joshua J.; Dale, Bruce E.; Balan, Venkatesh; Keating, David H.; Zhang, Yaoping; Landick, Robert; Gasch, Audrey P.; Sato, Trey K.

2014-01-01

The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH. PMID:25222864

Pechukas-Yukawa approach to the evolution of the quantum state of a parametrically perturbed system

NASA Astrophysics Data System (ADS)

Qureshi, Mumnuna A.; Zhong, Johnny; Qureshi, Zihad; Mason, Peter; Betouras, Joseph J.; Zagoskin, Alexandre M.

2018-03-01

We consider the evolution of the quantum states of a Hamiltonian that is parametrically perturbed via a term proportional to the adiabatic parameter λ (t ) . Starting with the Pechukas-Yukawa mapping of the energy eigenvalue evolution in a generalized Calogero-Sutherland model of a one-dimensional classical gas, we consider the adiabatic approximation with two different expansions of the quantum state in powers of d λ /d t and compare them with a direct numerical simulation. We show that one of these expansions (Magnus series) is especially convenient for the description of nonadiabatic evolution of the system. Applying the expansion to the exact cover 3-satisfiability problem, we obtain the occupation dynamics, which provides insight into the population of states and sources of decoherence in a quantum system.

Validation of an LES Model for Soot Evolution against DNS Data in Turbulent Jet Flames

NASA Astrophysics Data System (ADS)

Mueller, Michael

2012-11-01

An integrated modeling approach for soot evolution in turbulent reacting flows is validated against three-dimensional Direct Numerical Simulation (DNS) data in a set of n-heptane nonpremixed temporal jet flames. As in the DNS study, the evolution of the soot population is described statistically with the Hybrid Method of Moments (HMOM). The oxidation of the fuel and formation of soot precursors are described with the Radiation Flamelet/Progress Variable (RFPV) model that includes an additional transport equation for Polycyclic Aromatic Hydrocarbons (PAH) to account for the slow chemistry governing these species. In addition, the small-scale interactions between soot, chemistry, and turbulence are described with a presumed subfilter PDF approach that accounts for the very large spatial intermittency characterizing soot in turbulent reacting flows. The DNS dataset includes flames at three different Damköhler numbers to study the influence of global mixing rates on the evolution of PAH and soot. In this work, the ability of the model to capture these trends quantitatively as Damköhler number varies is investigated. In order to reliably assess the LES approach, the LES is initialized from the filtered DNS data after an initial transitional period in an effort to minimize the hydrodynamic differences between the DNS and the LES.

Directed evolution of an extremely stable fluorescent protein.

PubMed

Kiss, Csaba; Temirov, Jamshid; Chasteen, Leslie; Waldo, Geoffrey S; Bradbury, Andrew R M

2009-05-01

In this paper we describe the evolution of eCGP123, an extremely stable green fluorescent protein based on a previously described fluorescent protein created by consensus engineering (CGP: consensus green protein). eCGP123 could not be denatured by a standard thermal melt, preserved almost full fluorescence after overnight incubation at 80 degrees C and possessed a free energy of denaturation of 12.4 kcal/mol. It was created from CGP by a recursive process involving the sequential introduction of three destabilizing heterologous inserts, evolution to overcome the destabilization and finally 'removal' of the destabilizing insert by gene synthesis. We believe that this approach may be generally applicable to the stabilization of other proteins.

Linking adverse outcome pathways and population models: Current state of the science and future directions

EPA Science Inventory

Analysis of population impacts of chemical stressors through the use of modeling provides a linkage between endpoints observed in the individual and ecological risk to the population as a whole. In this presentation, we describe the evolution of an approach developed in our labor...

Direct reconstruction of the two-dimensional pair distribution function in partially ordered systems with angular correlations.

PubMed

Zaluzhnyy, I A; Kurta, R P; Menushenkov, A P; Ostrovskii, B I; Vartanyants, I A

2016-09-01

An x-ray scattering approach to determine the two-dimensional (2D) pair distribution function (PDF) in partially ordered 2D systems is proposed. We derive relations between the structure factor and PDF that enable quantitative studies of positional and bond-orientational (BO) order in real space. We apply this approach in the x-ray study of a liquid crystal (LC) film undergoing the smectic-A-hexatic-B phase transition, to analyze the interplay between the positional and BO order during the temperature evolution of the LC film. We analyze the positional correlation length in different directions in real space.

Temperature-dependent evolution of the wetting layer thickness during Ge deposition on Si(001).

PubMed

Bergamaschini, R; Brehm, M; Grydlik, M; Fromherz, T; Bauer, G; Montalenti, F

2011-07-15

The evolution of the wetting layer (WL) thickness during Ge deposition on Si(001) is analyzed with the help of a rate-equation approach. The combined role of thickness, island volume and shape-dependent chemical potentials is considered. Several experimental observations, such as WL thinning following the pyramid-to-dome transformation, are captured by the model, as directly demonstrated by a close comparison with photoluminescence measurements (PL) on samples grown at three different temperatures. The limitations of the model in describing late stages of growth are critically addressed.

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning.

PubMed

Davatzikos, Christos

2016-10-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. Copyright © 2016. Published by Elsevier B.V.

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning

PubMed Central

Davatzikos, Christos

2017-01-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. PMID:27514582

The Evolution of Mutual Mate Choice under Direct Benefits.

PubMed

Courtiol, Alexandre; Etienne, Loïc; Feron, Romain; Godelle, Bernard; Rousset, François

2016-11-01

In nature, the intensity of mate choice (i.e., choosiness) is highly variable within and between sexes. Despite growing empirical evidence of male and/or mutual mate choice, theoretical investigations of the joint evolution of female and male choosiness are few. In addition, previous approaches have often assumed an absence of trade-off between the direct benefits per mating and the lower mating rate that results from being choosy. Here we model the joint evolution of female and male choosiness when it is solely ruled by this fundamental trade-off. We show that this trade-off can generate a diversity of stable combinations of choosiness. Mutual mate choice can evolve only if both females and males exhibit long latency after mating. Furthermore, we show that an increase in choosiness in one sex does not necessarily prevent the evolution of mutual mate choice; the outcome depends on details shaping the trade-off: the life history, the decision rule for mate choice, and how the fecundity of a pair is shaped by the quality of both individuals. Last, we discuss the power of the sensitivity of the relative searching time (i.e., of the proportion of a lifetime spent searching for mates) as a predictor of the joint evolution of choosiness.

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift.

PubMed

Johnson, Norman A; Porter, Adam H

2007-01-01

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

On the kinematics of scalar iso-surfaces in turbulent flow

NASA Astrophysics Data System (ADS)

Blakeley, Brandon C.; Riley, James J.; Storti, Duane W.; Wang, Weirong

2017-11-01

The behavior of scalar iso-surfaces in turbulent flows is of fundamental interest and importance in a number of problems, e.g., the stoichiometric surface in non-premixed reactions, and the turbulent/non-turbulent interface in localized turbulent shear flows. Of particular interest here is the behavior of the average surface area per unit volume, Σ. We report on the use of direct numerical simulations and sophisticated surface tracking techniques to directly compute Σ and model its evolution. We consider two different scalar configurations in decaying, isotropic turbulence: first, the iso-surface is initially homogenous and isotropic in space, second, the iso-surface is initially planar. A novel method of computing integral properties from regularly-sampled values of a scalar function is leveraged to provide accurate estimates of Σ. Guided by simulation results, modeling is introduced from two perspectives. The first approach models the various terms in the evolution equation for Σ, while the second uses Rice's theorem to model Σ directly. In particular, the two principal effects on the evolution of Σ, i.e., the growth of the surface area due to local surface stretching, and the ultimate decay due to molecular destruction, are addressed.

DIRECTIONAL CULTURAL CHANGE BY MODIFICATION AND REPLACEMENT OF MEMES

PubMed Central

Cardoso, Gonçalo C.; Atwell, Jonathan W.

2017-01-01

Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations—modification of memes—to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered an urban habitat. Many songbirds have higher minimum song frequency in cities, to alleviate masking by low-frequency noise. We estimated that the input of meme modifications in an urban songbird population explains about half the extent of the population divergence in song frequency. This contribution of cultural mutations is large, but insufficient to explain the entire population divergence. The remaining divergence is due to selection of memes or creation of new memes. We conclude that the input of cultural mutations can be quantitatively important, unlike in genetic evolution, and that it operates together with other mechanisms of cultural evolution. For this and other traits, in which the input of cultural mutations might be important, quantitative studies of cultural mutation are necessary to calibrate realistic models of cultural evolution. PMID:20722726

Isolating Escherichia coli strains for recombinant protein production.

PubMed

Schlegel, Susan; Genevaux, Pierre; de Gier, Jan-Willem

2017-03-01

Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.

Boundary-Layer Receptivity and Integrated Transition Prediction

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Choudhari, Meelan

2005-01-01

The adjoint parabold stability equations (PSE) formulation is used to calculate the boundary layer receptivity to localized surface roughness and suction for compressible boundary layers. Receptivity efficiency functions predicted by the adjoint PSE approach agree well with results based on other nonparallel methods including linearized Navier-Stokes equations for both Tollmien-Schlichting waves and crossflow instability in swept wing boundary layers. The receptivity efficiency function can be regarded as the Green's function to the disturbance amplitude evolution in a nonparallel (growing) boundary layer. Given the Fourier transformed geometry factor distribution along the chordwise direction, the linear disturbance amplitude evolution for a finite size, distributed nonuniformity can be computed by evaluating the integral effects of both disturbance generation and linear amplification. The synergistic approach via the linear adjoint PSE for receptivity and nonlinear PSE for disturbance evolution downstream of the leading edge forms the basis for an integrated transition prediction tool. Eventually, such physics-based, high fidelity prediction methods could simulate the transition process from the disturbance generation through the nonlinear breakdown in a holistic manner.

An ecological and behavioural approach to hominin evolution during the Pliocene

NASA Astrophysics Data System (ADS)

Macho, Gabriele A.

2014-07-01

The study considers the turnover in hominins, together with carnivorans and other primates, at 3.5 Ma against an environmental backdrop. Communalities are identified between evolving guilds that may directly inform hominin evolution. These are the evolution of (a) dietary generalists and (b) evidence for sociality in carnivores, baboons and hominins. Sociality and behavioural flexibility are regarded advantageous for the procurement of resources while, at the same time, reducing intraspecific competition; in primates it may initially also have served to reduce predation risk. Behavioural flexibility explains the evolutionary success of Panthera leo, Papio and Homo. Viewed within a wider palaeoecological and environmental context, it is possible that sociality in hominins, including allocare, were triggered by abiotic changes at about 3.5 Ma. If confirmed in future studies, this would mark the beginning of hominin life history evolution.

Early Evolution of the Toxicity Identification Evaluation Process: Contributions from the USEPA Effluent Testing Program

EPA Science Inventory

As part of its whole effluent testing program, the USEPA developed an effects-directed analysis (EDA) approach to identifying the cause of toxicity in toxic effluents or ambient waters, an EDA process termed a “Toxicity Identification Evaluation” (TIE), which is the focus of this...

Integral Education: New Directions for Higher Learning. SUNY Series in Integral Theory

ERIC Educational Resources Information Center

Esbjorn-Hargens, Sean, Ed.; Reams, Jonathan, Ed.; Gunnlaugson, Olen, Ed.

2010-01-01

The educational challenges faced today are driving us toward a new step in the evolution of educational theory and practice. Educators are called to go beyond simply presenting alternatives, to integrating the best of mainstream and alternative approaches and taking them to the next level. "Integral Education" accomplishes this by…

Creating Special Events

ERIC Educational Resources Information Center

deLisle, Lee

2009-01-01

"Creating Special Events" is organized as a systematic approach to festivals and events for students who seek a career in event management. This book looks at the evolution and history of festivals and events and proceeds to the nuts and bolts of event management. The book presents event management as the means of planning, organizing, directing,…

Exploring New Directions: Title I in the Year 2000.

ERIC Educational Resources Information Center

Puma, Michael J.; Drury, Darrel W.

This report takes stock of the present Title I program, identifies the most promising approaches to educating the nation's disadvantaged children, and offers guidance to policymakers seeking to improve Title I's effectiveness. The report draws upon hundreds of studies, evaluations, and other documents, and details the evolution of the Title I…

Engineering Cellulases for Biorefinery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2010-06-27

Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitutionmore » of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Thermostable Cellulases: Why & How?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2010-04-19

Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitutionmore » of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Evolution of bacterial virulence.

PubMed

Diard, Médéric; Hardt, Wolf-Dietrich

2017-09-01

Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population. We review both approaches and discuss how they can complement each other in order to obtain a comprehensive understanding of bacterial virulence, its emergence, maintenance and evolution. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships.

PubMed

Baier, F; Copp, J N; Tokuriki, N

2016-11-22

The sequence and functional diversity of enzyme superfamilies have expanded through billions of years of evolution from a common ancestor. Understanding how protein sequence and functional "space" have expanded, at both the evolutionary and molecular level, is central to biochemistry, molecular biology, and evolutionary biology. Integrative approaches that examine protein sequence, structure, and function have begun to provide comprehensive views of the functional diversity and evolutionary relationships within enzyme superfamilies. In this review, we outline the recent advances in our understanding of enzyme evolution and superfamily functional diversity. We describe the tools that have been used to comprehensively analyze sequence relationships and to characterize sequence and function relationships. We also highlight recent large-scale experimental approaches that systematically determine the activity profiles across enzyme superfamilies. We identify several intriguing insights from this recent body of work. First, promiscuous activities are prevalent among extant enzymes. Second, many divergent proteins retain "function connectivity" via enzyme promiscuity, which can be used to probe the evolutionary potential and history of enzyme superfamilies. Finally, we discuss open questions regarding the intricacies of enzyme divergence, as well as potential research directions that will deepen our understanding of enzyme superfamily evolution.

Laughter as an approach to vocal evolution: The bipedal theory.

PubMed

Provine, Robert R

2017-02-01

Laughter is a simple, stereotyped, innate, human play vocalization that is ideal for the study of vocal evolution. The basic approach of describing the act of laughter and when we do it has revealed a variety of phenomena of social, linguistic, and neurological significance. Findings include the acoustic structure of laughter, the minimal voluntary control of laughter, the punctuation effect (which describes the placement of laughter in conversation and indicates the dominance of speech over laughter), and the role of laughter in human matching and mating. Especially notable is the use of laughter to discover why humans can speak and other apes cannot. Quadrupeds, including our primate ancestors, have a 1:1 relation between breathing and stride because their thorax must absorb forelimb impacts during running. The direct link between breathing and locomotion limits vocalizations to short, simple utterances, such as the characteristic panting chimpanzee laugh (one sound per inward or outward breath). The evolution of bipedal locomotion freed the respiration system of its support function during running, permitting greater breath control and the selection for human-type laughter (a parsed exhalation), and subsequently the virtuosic, sustained, expiratory vocalization of speech. This is the basis of the bipedal theory of speech evolution.

Development of efficient time-evolution method based on three-term recurrence relation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akama, Tomoko, E-mail: a.tomo---s-b-l-r@suou.waseda.jp; Kobayashi, Osamu; Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp

The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function.more » Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.« less

The polarization evolution of electromagnetic waves as a diagnostic method for a motional plasma

NASA Astrophysics Data System (ADS)

Shahrokhi, Alireza; Mehdian, Hassan; Hajisharifi, Kamal; Hasanbeigi, Ali

2017-12-01

The polarization evolution of electromagnetic (EM) radiation propagating through an electron beam-ion channel system is studied in the presence of self-magnetic field. Solving the fluid-Maxwell equations to obtain the medium dielectric tensor, the Stokes vector-Mueller matrix approach is employed to determine the polarization of the launched EM wave at any point in the propagation direction, applying the space-dependent Mueller matrix on the initial polarization vector of the wave at the plasma-vacuum interface. Results show that the polarization evolution of the wave is periodic in space along the beam axis with the specified polarization wavelength. Using the obtained results, a novel diagnostic method based on the polarization evolution of the EM waves is proposed to evaluate the electron beam density and velocity. Moreover, to use the mentioned plasma system as a polarizer, the fraction of the output radiation power transmitted through a motional plasma crossed with the input polarization is calculated. The results of the present investigation will greatly contribute to design a new EM amplifier with fixed polarization or EM polarizer, as well as a new diagnostic approach for the electron beam system where the polarimetric method is employed.

Direct handling of sharp interfacial energy for microstructural evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernández–Rivera, Efraín; Tikare, Veena; Noirot, Laurence

In this study, we introduce a simplification to the previously demonstrated hybrid Potts–phase field (hPPF), which relates interfacial energies to microstructural sharp interfaces. The model defines interfacial energy by a Potts-like discrete interface approach of counting unlike neighbors, which we use to compute local curvature. The model is compared to the hPPF by studying interfacial characteristics and grain growth behavior. The models give virtually identical results, while the new model allows the simulator more direct control of interfacial energy.

Nonlinear techniques for forecasting solar activity directly from its time series

NASA Technical Reports Server (NTRS)

Ashrafi, S.; Roszman, L.; Cooley, J.

1992-01-01

Numerical techniques for constructing nonlinear predictive models to forecast solar flux directly from its time series are presented. This approach makes it possible to extract dynamical invariants of our system without reference to any underlying solar physics. We consider the dynamical evolution of solar activity in a reconstructed phase space that captures the attractor (strange), given a procedure for constructing a predictor of future solar activity, and discuss extraction of dynamical invariants such as Lyapunov exponents and attractor dimension.

Nonlinear techniques for forecasting solar activity directly from its time series

NASA Technical Reports Server (NTRS)

Ashrafi, S.; Roszman, L.; Cooley, J.

1993-01-01

This paper presents numerical techniques for constructing nonlinear predictive models to forecast solar flux directly from its time series. This approach makes it possible to extract dynamical in variants of our system without reference to any underlying solar physics. We consider the dynamical evolution of solar activity in a reconstructed phase space that captures the attractor (strange), give a procedure for constructing a predictor of future solar activity, and discuss extraction of dynamical invariants such as Lyapunov exponents and attractor dimension.

Direct handling of sharp interfacial energy for microstructural evolution

DOE PAGES

Hernández–Rivera, Efraín; Tikare, Veena; Noirot, Laurence; ...

2014-08-24

In this study, we introduce a simplification to the previously demonstrated hybrid Potts–phase field (hPPF), which relates interfacial energies to microstructural sharp interfaces. The model defines interfacial energy by a Potts-like discrete interface approach of counting unlike neighbors, which we use to compute local curvature. The model is compared to the hPPF by studying interfacial characteristics and grain growth behavior. The models give virtually identical results, while the new model allows the simulator more direct control of interfacial energy.

Programming cells by multiplex genome engineering and accelerated evolution.

PubMed

Wang, Harris H; Isaacs, Farren J; Carr, Peter A; Sun, Zachary Z; Xu, George; Forest, Craig R; Church, George M

2009-08-13

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

Novel Random Mutagenesis Method for Directed Evolution.

PubMed

Feng, Hong; Wang, Hai-Yan; Zhao, Hong-Yan

2017-01-01

Directed evolution is a powerful strategy for gene mutagenesis, and has been used for protein engineering both in scientific research and in the biotechnology industry. The routine method for directed evolution was developed by Stemmer in 1994 (Stemmer, Proc Natl Acad Sci USA 91, 10747-10751, 1994; Stemmer, Nature 370, 389-391, 1994). Since then, various methods have been introduced, each of which has advantages and limitations depending upon the targeted genes and procedure. In this chapter, a novel alternative directed evolution method which combines mutagenesis PCR with dITP and fragmentation by endonuclease V is described. The kanamycin resistance gene is used as a reporter gene to verify the novel method for directed evolution. This method for directed evolution has been demonstrated to be efficient, reproducible, and easy to manipulate in practice.

Modelling the bow–shock evolution along the DSO/G2 orbit in the Galactic centre

NASA Astrophysics Data System (ADS)

Štofanová, Lýdia; Zajaček, Michal; Kunneriath, Devaky; Eckart, Andreas; Karas, Vladimír

2017-12-01

A radially directed flow of gaseous environment from a supermassive black hole affects the evolution of a bow–shock that develops along the orbit of an object passing through the pericentre. The bow–shock exhibits asymmetry between the approaching and receding phases, as can be seen in calculations of the bow-shock size, the velocity profile along the shocked layer, and the surface density of the bow–shock, and by emission-measure maps. We discuss these effects in the context of the recent pericentre transit of DSO/G2 near Sagittarius A*.

Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion

DOE PAGES

Wang, Peng; Chang, Angela Y.; Novosad, Valentyn; ...

2017-06-11

We report on entirely man-made nanobio hybrid fabricated through assembly of cell-free expressed transmembrane proton pump and semiconductor nanoparticles as an efficient nanocatalysis for photocatalytic H 2 evolution. The system produces H 2 at a turnover rate of 239 (μmole protein) -1 h -1 under green and 17742 (μmole protein) -1 h -1 under white light at ambient conditions, in water at neutral pH with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allows for systemic manipulation at nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.

Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Peng; Chang, Angela Y.; Novosad, Valentyn

We report on entirely man-made nanobio hybrid fabricated through assembly of cell-free expressed transmembrane proton pump and semiconductor nanoparticles as an efficient nanocatalysis for photocatalytic H 2 evolution. The system produces H 2 at a turnover rate of 239 (μmole protein) -1 h -1 under green and 17742 (μmole protein) -1 h -1 under white light at ambient conditions, in water at neutral pH with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allows for systemic manipulation at nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.

Complex and changing patterns of natural selection explain the evolution of the human hip.

PubMed

Grabowski, Mark; Roseman, Charles C

2015-08-01

Causal explanations for the dramatic changes that occurred during the evolution of the human hip focus largely on selection for bipedal function and locomotor efficiency. These hypotheses rest on two critical assumptions. The first-that these anatomical changes served functional roles in bipedalism-has been supported in numerous analyses showing how postcranial changes likely affected locomotion. The second-that morphological changes that did play functional roles in bipedalism were the result of selection for that behavior-has not been previously explored and represents a major gap in our understanding of hominin hip evolution. Here we use evolutionary quantitative genetic models to test the hypothesis that strong directional selection on many individual aspects of morphology was responsible for the large differences observed across a sample of fossil hominin hips spanning the Plio-Pleistocene. Our approach uses covariance among traits and the differences between relatively complete fossils to estimate the net selection pressures that drove the major transitions in hominin hip evolution. Our findings show a complex and changing pattern of natural selection drove hominin hip evolution, and that many, but not all, traits hypothesized to play functional roles in bipedalism evolved as a direct result of natural selection. While the rate of evolutionary change for all transitions explored here does not exceed the amount expected if evolution was occurring solely through neutral processes, it was far above rates of evolution for morphological traits in other mammalian groups. Given that stasis is the norm in the mammalian fossil record, our results suggest that large shifts in the adaptive landscape drove hominin evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modelling language evolution: Examples and predictions

NASA Astrophysics Data System (ADS)

Gong, Tao; Shuai, Lan; Zhang, Menghan

2014-06-01

We survey recent computer modelling research of language evolution, focusing on a rule-based model simulating the lexicon-syntax coevolution and an equation-based model quantifying the language competition dynamics. We discuss four predictions of these models: (a) correlation between domain-general abilities (e.g. sequential learning) and language-specific mechanisms (e.g. word order processing); (b) coevolution of language and relevant competences (e.g. joint attention); (c) effects of cultural transmission and social structure on linguistic understandability; and (d) commonalities between linguistic, biological, and physical phenomena. All these contribute significantly to our understanding of the evolutions of language structures, individual learning mechanisms, and relevant biological and socio-cultural factors. We conclude the survey by highlighting three future directions of modelling studies of language evolution: (a) adopting experimental approaches for model evaluation; (b) consolidating empirical foundations of models; and (c) multi-disciplinary collaboration among modelling, linguistics, and other relevant disciplines.

Kinetic Rate Kernels via Hierarchical Liouville-Space Projection Operator Approach.

PubMed

Zhang, Hou-Dao; Yan, YiJing

2016-05-19

Kinetic rate kernels in general multisite systems are formulated on the basis of a nonperturbative quantum dissipation theory, the hierarchical equations of motion (HEOM) formalism, together with the Nakajima-Zwanzig projection operator technique. The present approach exploits the HEOM-space linear algebra. The quantum non-Markovian site-to-site transfer rate can be faithfully evaluated via projected HEOM dynamics. The developed method is exact, as evident by the comparison to the direct HEOM evaluation results on the population evolution.

Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

NASA Technical Reports Server (NTRS)

He, Guowei; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

A Research and Development Approach to the Delivery of Comprehensive Functional Education and Literacy in the Philippines.

ERIC Educational Resources Information Center

Doronila, Maria Luisa C.

In the Philippines, introduction of a formal education system, new written language, and the knowledge encoded in it have been part of a colonization process and not the result of direct evolution from informal education. The discontinuities between formal and informal education--abstraction, systematization, and specialization--are greater and…

Making Time for Instructional Leadership. Volume 1: The Evolution of the SAM Process

ERIC Educational Resources Information Center

Goldring, Ellen; Grissom, Jason A.; Neumerski, Christine M.; Murphy, Joseph; Blissett, Richard; Porter, Andy

2015-01-01

This three-volume report describes the "SAM (School Administration Manager) process," an approach that about 700 schools around the nation are using to direct more of principals' time and effort to improve teaching and learning in classrooms. Research has shown that a principal's instructional leadership is second only to teaching among…

On the application of ENO scheme with subcell resolution to conservation laws with stiff source terms

NASA Technical Reports Server (NTRS)

Chang, Shih-Hung

1991-01-01

Two approaches are used to extend the essentially non-oscillatory (ENO) schemes to treat conservation laws with stiff source terms. One approach is the application of the Strang time-splitting method. Here the basic ENO scheme and the Harten modification using subcell resolution (SR), ENO/SR scheme, are extended this way. The other approach is a direct method and a modification of the ENO/SR. Here the technique of ENO reconstruction with subcell resolution is used to locate the discontinuity within a cell and the time evolution is then accomplished by solving the differential equation along characteristics locally and advancing in the characteristic direction. This scheme is denoted ENO/SRCD (subcell resolution - characteristic direction). All the schemes are tested on the equation of LeVeque and Yee (NASA-TM-100075, 1988) modeling reacting flow problems. Numerical results show that these schemes handle this intriguing model problem very well, especially with ENO/SRCD which produces perfect resolution at the discontinuity.

Controlling the enantioselectivity of enzymes by directed evolution: Practical and theoretical ramifications

PubMed Central

Reetz, Manfred T.

2004-01-01

A fundamentally new approach to asymmetric catalysis in organic chemistry is described based on the in vitro evolution of enantioselective enzymes. It comprises the appropriate combination of gene mutagenesis and expression coupled with an efficient high-throughput screening system for evaluating enantioselectivity (enantiomeric excess assay). Several such cycles lead to a “Darwinistic” process, which is independent of any knowledge concerning the structure or the mechanism of the enzyme being evolved. The challenge is to choose the optimal mutagenesis methods to navigate efficiently in protein sequence space. As a first example, the combination of error-prone mutagenesis, saturation mutagenesis, and DNA-shuffling led to a dramatic enhancement of enantioselectivity of a lipase acting as a catalyst in the kinetic resolution of a chiral ester. Mutations at positions remote from the catalytically active center were identified, a surprising finding, which was explained on the basis of a novel relay mechanism. The scope and limitations of the method are discussed, including the prospect of directed evolution of stereoselective hybrid catalysts composed of robust protein hosts in which transition metal centers have been implanted. PMID:15079053

Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

PubMed

Bailey, Susan F; Bataillon, Thomas

2016-01-01

There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Directed evolution of artificial metalloenzymes for in vivo metathesis

NASA Astrophysics Data System (ADS)

Jeschek, Markus; Reuter, Raphael; Heinisch, Tillmann; Trindler, Christian; Klehr, Juliane; Panke, Sven; Ward, Thomas R.

2016-09-01

The field of biocatalysis has advanced from harnessing natural enzymes to using directed evolution to obtain new biocatalysts with tailor-made functions. Several tools have recently been developed to expand the natural enzymatic repertoire with abiotic reactions. For example, artificial metalloenzymes, which combine the versatile reaction scope of transition metals with the beneficial catalytic features of enzymes, offer an attractive means to engineer new reactions. Three complementary strategies exist: repurposing natural metalloenzymes for abiotic transformations; in silico metalloenzyme (re-)design; and incorporation of abiotic cofactors into proteins. The third strategy offers the opportunity to design a wide variety of artificial metalloenzymes for non-natural reactions. However, many metal cofactors are inhibited by cellular components and therefore require purification of the scaffold protein. This limits the throughput of genetic optimization schemes applied to artificial metalloenzymes and their applicability in vivo to expand natural metabolism. Here we report the compartmentalization and in vivo evolution of an artificial metalloenzyme for olefin metathesis, which represents an archetypal organometallic reaction without equivalent in nature. Building on previous work on an artificial metallohydrolase, we exploit the periplasm of Escherichia coli as a reaction compartment for the ‘metathase’ because it offers an auspicious environment for artificial metalloenzymes, mainly owing to low concentrations of inhibitors such as glutathione, which has recently been identified as a major inhibitor. This strategy facilitated the assembly of a functional metathase in vivo and its directed evolution with substantially increased throughput compared to conventional approaches that rely on purified protein variants. The evolved metathase compares favourably with commercial catalysts, shows activity for different metathesis substrates and can be further evolved in different directions by adjusting the workflow. Our results represent the systematic implementation and evolution of an artificial metalloenzyme that catalyses an abiotic reaction in vivo, with potential applications in, for example, non-natural metabolism.

Emergence, reductionism and landscape response to climate change

NASA Astrophysics Data System (ADS)

Harrison, Stephan; Mighall, Tim

2010-05-01

Predicting landscape response to external forcing is hampered by the non-linear, stochastic and contingent (ie dominated by historical accidents) forcings inherent in landscape evolution. Using examples from research carried out in southwest Ireland we suggest that non-linearity in landform evolution is likely to be a strong control making regional predictions of landscape response to climate change very difficult. While uncertainties in GCM projections have been widely explored in climate science much less attention has been directed by geomorphologists to the uncertainties in landform evolution under conditions of climate change and this problem may be viewed within the context of philosophical approaches to reductionsim and emergence. Understanding the present and future trajectory of landform change may also guide us to provide an enhanced appreciation of how landforms evolved in the past.

Regulatory mechanisms link phenotypic plasticity to evolvability

PubMed Central

van Gestel, Jordi; Weissing, Franz J.

2016-01-01

Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question – the optimal timing of bacterial sporulation – we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations. PMID:27087393

Bell-polynomial approach and Wronskian determinant solutions for three sets of differential-difference nonlinear evolution equations with symbolic computation

NASA Astrophysics Data System (ADS)

Qin, Bo; Tian, Bo; Wang, Yu-Feng; Shen, Yu-Jia; Wang, Ming

2017-10-01

Under investigation in this paper are the Belov-Chaltikian (BC), Leznov and Blaszak-Marciniak (BM) lattice equations, which are associated with the conformal field theory, UToda(m_1,m_2) system and r-matrix, respectively. With symbolic computation, the Bell-polynomial approach is developed to directly bilinearize those three sets of differential-difference nonlinear evolution equations (NLEEs). This Bell-polynomial approach does not rely on any dependent variable transformation, which constitutes the key step and main difficulty of the Hirota bilinear method, and thus has the advantage in the bilinearization of the differential-difference NLEEs. Based on the bilinear forms obtained, the N-soliton solutions are constructed in terms of the N × N Wronskian determinant. Graphic illustrations demonstrate that those solutions, more general than the existing results, permit some new properties, such as the solitonic propagation and interactions for the BC lattice equations, and the nonnegative dark solitons for the BM lattice equations.

Social cognitive evolution in captive foxes is a correlated by-product of experimental domestication.

PubMed

Hare, Brian; Plyusnina, Irene; Ignacio, Natalie; Schepina, Olesya; Stepika, Anna; Wrangham, Richard; Trut, Lyudmila

2005-02-08

Dogs have an unusual ability for reading human communicative gestures (e.g., pointing) in comparison to either nonhuman primates (including chimpanzees) or wolves . Although this unusual communicative ability seems to have evolved during domestication , it is unclear whether this evolution occurred as a result of direct selection for this ability, as previously hypothesized , or as a correlated by-product of selection against fear and aggression toward humans--as is the case with a number of morphological and physiological changes associated with domestication . We show here that fox kits from an experimental population selectively bred over 45 years to approach humans fearlessly and nonaggressively (i.e., experimentally domesticated) are not only as skillful as dog puppies in using human gestures but are also more skilled than fox kits from a second, control population not bred for tame behavior (critically, neither population of foxes was ever bred or tested for their ability to use human gestures) . These results suggest that sociocognitive evolution has occurred in the experimental foxes, and possibly domestic dogs, as a correlated by-product of selection on systems mediating fear and aggression, and it is likely the observed social cognitive evolution did not require direct selection for improved social cognitive ability.

Correlated evolution of migration and sexual dichromatism in the New World orioles (icterus).

PubMed

Friedman, Nicholas R; Hofmann, Christopher M; Kondo, Beatrice; Omland, Kevin E

2009-12-01

The evolution of sexual dimorphism has long been attributed to sexual selection, specifically as it would drive repeated gains of elaborate male traits. In contrast to this pattern, New World oriole species all exhibit elaborate male plumage, and the repeated gains of sexual dichromatism observed in the genus are due to losses of female elaboration. Interestingly, most sexually dichromatic orioles belong to migratory or temperate-breeding clades. Using character scoring and ancestral state reconstructions from two recent studies in Icterus, we tested a hypothesis of correlated evolution between migration and sexual dichromatism. We employed two discrete phylogenetic comparative approaches: the concentrated changes test and Pagel's discrete likelihood test. Our results show that the evolution of these traits is significantly correlated (CCT: uncorrected P < 0.05; ML: LRT = 12.470, P < 0.005). Indeed, our best model of character evolution suggests that gains of sexual dichromatism are 23 times more likely to occur in migratory taxa. This study demonstrates that a life-history trait with no direct relationship with sexual selection has a strong influence on the evolution of sexual dichromatism. We recommend that researchers further investigate the role of selection on elaborate female traits in the evolution of sexual dimorphism.

Probabilistic models of eukaryotic evolution: time for integration

PubMed Central

Lartillot, Nicolas

2015-01-01

In spite of substantial work and recent progress, a global and fully resolved picture of the macroevolutionary history of eukaryotes is still under construction. This concerns not only the phylogenetic relations among major groups, but also the general characteristics of the underlying macroevolutionary processes, including the patterns of gene family evolution associated with endosymbioses, as well as their impact on the sequence evolutionary process. All these questions raise formidable methodological challenges, calling for a more powerful statistical paradigm. In this direction, model-based probabilistic approaches have played an increasingly important role. In particular, improved models of sequence evolution accounting for heterogeneities across sites and across lineages have led to significant, although insufficient, improvement in phylogenetic accuracy. More recently, one main trend has been to move away from simple parametric models and stepwise approaches, towards integrative models explicitly considering the intricate interplay between multiple levels of macroevolutionary processes. Such integrative models are in their infancy, and their application to the phylogeny of eukaryotes still requires substantial improvement of the underlying models, as well as additional computational developments. PMID:26323768

Protein Engineering Approaches in the Post-Genomic Era.

PubMed

Singh, Raushan K; Lee, Jung-Kul; Selvaraj, Chandrabose; Singh, Ranjitha; Li, Jinglin; Kim, Sang-Yong; Kalia, Vipin C

2018-01-01

Proteins are one of the most multifaceted macromolecules in living systems. Proteins have evolved to function under physiological conditions and, therefore, are not usually tolerant of harsh experimental and environmental conditions. The growing use of proteins in industrial processes as a greener alternative to chemical catalysts often demands constant innovation to improve their performance. Protein engineering aims to design new proteins or modify the sequence of a protein to create proteins with new or desirable functions. With the emergence of structural and functional genomics, protein engineering has been invigorated in the post-genomic era. The three-dimensional structures of proteins with known functions facilitate protein engineering approaches to design variants with desired properties. There are three major approaches of protein engineering research, namely, directed evolution, rational design, and de novo design. Rational design is an effective method of protein engineering when the threedimensional structure and mechanism of the protein is well known. In contrast, directed evolution does not require extensive information and a three-dimensional structure of the protein of interest. Instead, it involves random mutagenesis and selection to screen enzymes with desired properties. De novo design uses computational protein design algorithms to tailor synthetic proteins by using the three-dimensional structures of natural proteins and their folding rules. The present review highlights and summarizes recent protein engineering approaches, and their challenges and limitations in the post-genomic era. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Toward Evolvable Hardware Chips: Experiments with a Programmable Transistor Array

NASA Technical Reports Server (NTRS)

Stoica, Adrian

1998-01-01

Evolvable Hardware is reconfigurable hardware that self-configures under the control of an evolutionary algorithm. We search for a hardware configuration can be performed using software models or, faster and more accurate, directly in reconfigurable hardware. Several experiments have demonstrated the possibility to automatically synthesize both digital and analog circuits. The paper introduces an approach to automated synthesis of CMOS circuits, based on evolution on a Programmable Transistor Array (PTA). The approach is illustrated with a software experiment showing evolutionary synthesis of a circuit with a desired DC characteristic. A hardware implementation of a test PTA chip is then described, and the same evolutionary experiment is performed on the chip demonstrating circuit synthesis/self-configuration directly in hardware.

A generalization of Hamilton's rule--love others how much?

PubMed

Alger, Ingela; Weibull, Jörgen W

2012-04-21

According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Efficient discovery of bioactive scaffolds by activity-directed synthesis

NASA Astrophysics Data System (ADS)

Karageorgis, George; Warriner, Stuart; Nelson, Adam

2014-10-01

The structures and biological activities of natural products have often provided inspiration in drug discovery. The functional benefits of natural products to the host organism steers the evolution of their biosynthetic pathways. Here, we describe a discovery approach—which we term activity-directed synthesis—in which reactions with alternative outcomes are steered towards functional products. Arrays of catalysed reactions of α-diazo amides, whose outcome was critically dependent on the specific conditions used, were performed. The products were assayed at increasingly low concentration, with the results informing the design of a subsequent reaction array. Finally, promising reactions were scaled up and, after purification, submicromolar ligands based on two scaffolds with no previous annotated activity against the androgen receptor were discovered. The approach enables the discovery, in tandem, of both bioactive small molecules and associated synthetic routes, analogous to the evolution of biosynthetic pathways to yield natural products.

Transmission dynamics: critical questions and challenges

PubMed Central

2017-01-01

This article overviews the dynamics of disease transmission in one-host–one-parasite systems. Transmission is the result of interacting host and pathogen processes, encapsulated with the environment in a ‘transmission triangle’. Multiple transmission modes and their epidemiological consequences are often not understood because the direct measurement of transmission is difficult. However, its different components can be analysed using nonlinear transmission functions, contact matrices and networks. A particular challenge is to develop such functions for spatially extended systems. This is illustrated for vector transmission where a ‘perception kernel’ approach is developed that incorporates vector behaviour in response to host spacing. A major challenge is understanding the relative merits of the large number of approaches to quantifying transmission. The evolution of transmission mode itself has been a rather neglected topic, but is important in the context of understanding disease emergence and genetic variation in pathogens. Disease impacts many biological processes such as community stability, the evolution of sex and speciation, yet the importance of different transmission modes in these processes is not understood. Broader approaches and ideas to disease transmission are important in the public health realm for combating newly emerging infections. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289255

RELATIVISTIC HEAVY ION PHYSICS: A THEORETICAL OVERVIEW.

DOE Office of Scientific and Technical Information (OSTI.GOV)

KHARZEEV,D.

2004-03-28

This is a mini-review of recent theoretical work in the field of relativistic heavy ion physics. The following topics are discussed initial conditions and the Color Glass Condensate; approach to thermalization and the hydrodynamic evolution; hard probes and the properties of the Quark-Gluon Plasma. Some of the unsolved problems and potentially promising directions for future research are listed as well.

An integrative method for testing form–function linkages and reconstructed evolutionary pathways of masticatory specialization

PubMed Central

Tseng, Z. Jack; Flynn, John J.

2015-01-01

Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form–function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways. PMID:25994295

Integrated cellulosic enzymes hydrolysis and fermentative advanced yeast bioconversion solution ready for biomass biorefineries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2011-05-04

These are slides from this conference. Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme,more » as well as on the reconstitution of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Thermostable Cellulases: Why & How?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2010-03-24

These are a set of slides from the conference. Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for eachmore » cellulase component enzyme, as well as on the reconstitution of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Development of a Commerical Enzyme System for Lignocellulosic Biomass Saccharification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2011-02-14

Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitutionmore » of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Highly Efficient Thermostable DSM Cellulases: Why & How?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2011-04-26

These are the slides from this presentation. Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase componentmore » enzyme, as well as on the reconstitution of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Fully Integrated Lignocellulosic Biorefinery with Onsite Production of Enzymes and Yeast

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2010-06-14

Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for each cellulase component enzyme, as well as on the reconstitutionmore » of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Color pattern evolution in Vanessa butterflies (Nymphalidae: Nymphalini): non-eyespot characters.

PubMed

Abbasi, Roohollah; Marcus, Jeffrey M

2015-01-01

A phylogenetic approach was used to study color pattern evolution in Vanessa butterflies. Twenty-four color pattern elements from the Nymphalid ground plan were identified on the dorsal and ventral surfaces of the fore- and hind wings. Eyespot characters were excluded and will be examined elsewhere. The evolution of each character was traced over a Bayesian phylogeny of Vanessa reconstructed from 7750 DNA base pairs from 10 genes. Generally, the correspondence between character states on the same surface of the two wings is stronger on the ventral side compared to the dorsal side. The evolution of character states on both sides of a wing correspond with each other in most extant species, but the correspondence between dorsal and ventral character states is much stronger in the forewing than in the hindwing. The dorsal hindwing of many species of Vanessa is covered with an extended Basal Symmetry System and the Discalis I pattern element is highly variable between species, making this wing surface dissimilar to the other wing surfaces. The Basal Symmetry System and Discalis I may contribute to behavioral thermoregulation in Vanessa. Overall, interspecific directional character state evolution of non-eyespot color patterns is relatively rare in Vanessa, with a majority of color pattern elements showing non-variable, non-directional, or ambiguous character state evolution. The ease with which the development of color patterns can be modified, including character state reversals, has likely made important contributions to the production of color pattern diversity in Vanessa and other butterfly groups. © 2014 Wiley Periodicals, Inc.

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution.

PubMed

Skinner, Michael K

2015-04-26

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The role of experiments in understanding fishery-induced evolution

PubMed Central

Conover, David O; Baumann, Hannes

2009-01-01

Evidence of fishery-induced evolution has been accumulating rapidly from various avenues of investigation. Here we review the knowledge gained from experimental approaches. The strength of experiments is in their ability to disentangle genetic from environmental differences. Common garden experiments have provided direct evidence of adaptive divergence in the wild and therefore the evolvability of various traits that influence production in numerous species. Most of these cases involve countergradient variation in physiological, life history, and behavioral traits. Selection experiments have provided examples of rapid life history evolution and, more importantly, that fishery-induced selection pressures cause simultaneous divergence of not one but a cluster of genetically and phenotypically correlated traits that include physiology, behavior, reproduction, and other life history characters. The drawbacks of experiments are uncertainties in the scale-up from small, simple environments to larger and more complex systems; the concern that taxons with short life cycles used for experimental research are atypical of those of harvested species; and the difficulty of adequately simulating selection due to fishing. Despite these limitations, experiments have contributed greatly to our understanding of fishery-induced evolution on both empirical and theoretical levels. Future advances will depend on integrating knowledge from experiments with those from modeling, field studies, and molecular genetic approaches. PMID:25567880

Head and Neck Cancer: An Evolving Treatment Paradigm

PubMed Central

Cognetti, David M.; Weber, Randal S.; Lai, Stephen Y.

2009-01-01

Since the inception of this journal in 1948, the understanding of etiologic factors that contribute to and the treatment of head and neck cancer has evolved dramatically. Advances in surgery, radiation therapy, and chemotherapy have improved locoregional control, survival, and quality of life. The outcomes of these treatment modalities have shifted the focus of curative efforts from radical ablation to preservation and restoration of function. This evolution has been documented in the pages of Cancer for the past 6 decades. This review focuses on the evolution of treatment approaches for head and neck cancer and future directions while recognizing the historic contributions recorded within this journal. PMID:18798532

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.

PubMed

Havird, Justin C; Whitehill, Nicholas S; Snow, Christopher D; Sloan, Daniel B

2015-12-01

Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Stochastic modelling of microstructure formation in solidification processes

NASA Astrophysics Data System (ADS)

Nastac, Laurentiu; Stefanescu, Doru M.

1997-07-01

To relax many of the assumptions used in continuum approaches, a general stochastic model has been developed. The stochastic model can be used not only for an accurate description of the fraction of solid evolution, and therefore accurate cooling curves, but also for simulation of microstructure formation in castings. The advantage of using the stochastic approach is to give a time- and space-dependent description of solidification processes. Time- and space-dependent processes can also be described by partial differential equations. Unlike a differential formulation which, in most cases, has to be transformed into a difference equation and solved numerically, the stochastic approach is essentially a direct numerical algorithm. The stochastic model is comprehensive, since the competition between various phases is considered. Furthermore, grain impingement is directly included through the structure of the model. In the present research, all grain morphologies are simulated with this procedure. The relevance of the stochastic approach is that the simulated microstructures can be directly compared with microstructures obtained from experiments. The computer becomes a `dynamic metallographic microscope'. A comparison between deterministic and stochastic approaches has been performed. An important objective of this research was to answer the following general questions: (1) `Would fully deterministic approaches continue to be useful in solidification modelling?' and (2) `Would stochastic algorithms be capable of entirely replacing purely deterministic models?'

The skeletal ontogeny of Astatotilapia burtoni - a direct-developing model system for the evolution and development of the teleost body plan.

PubMed

Woltering, Joost M; Holzem, Michaela; Schneider, Ralf F; Nanos, Vasilios; Meyer, Axel

2018-04-03

The experimental approach to the evolution and development of the vertebrate skeleton has to a large extent relied on "direct-developing" amniote model organisms, such as the mouse and the chicken. These organisms can however only be partially informative where it concerns secondarily lost features or anatomical novelties not present in their lineages. The widely used anamniotes Xenopus and zebrafish are "indirect-developing" organisms that proceed through an extended time as free-living larvae, before adopting many aspects of their adult morphology, complicating experiments at these stages, and increasing the risk for lethal pleiotropic effects using genetic strategies. Here, we provide a detailed description of the development of the osteology of the African mouthbrooding cichlid Astatotilapia burtoni, primarily focusing on the trunk (spinal column, ribs and epicentrals) and the appendicular skeleton (pectoral, pelvic, dorsal, anal, caudal fins and scales), and to a lesser extent on the cranium. We show that this species has an extremely "direct" mode of development, attains an adult body plan within 2 weeks after fertilization while living off its yolk supply only, and does not pass through a prolonged larval period. As husbandry of this species is easy, generation time is short, and the species is amenable to genetic targeting strategies through microinjection, we suggest that the use of this direct-developing cichlid will provide a valuable model system for the study of the vertebrate body plan, particularly where it concerns the evolution and development of fish or teleost specific traits. Based on our results we comment on the development of the homocercal caudal fin, on shared ontogenetic patterns between pectoral and pelvic girdles, and on the evolution of fin spines as novelty in acanthomorph fishes. We discuss the differences between "direct" and "indirect" developing actinopterygians using a comparison between zebrafish and A. burtoni development.

Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach.

PubMed

Garcia-Seisdedos, Hector; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

2012-01-01

Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity, its fundamental connection with molecular evolution and also because of its biotechnological applications. Current views on the relation between primary and promiscuous protein activities stem largely from laboratory evolution experiments aimed at increasing promiscuous activity levels. Here, on the other hand, we attempt to assess the main features of the simultaneous modulation of the primary and promiscuous functions during the course of natural evolution. The computational/experimental approach we propose for this task involves the following steps: a function-targeted, statistical coupling analysis of evolutionary data is used to determine a set of positions likely linked to the recruitment of a promiscuous activity for a new function; a combinatorial library of mutations on this set of positions is prepared and screened for both, the primary and the promiscuous activities; a partial-least-squares reconstruction of the full combinatorial space is carried out; finally, an approximation to the Pareto set of variants with optimal primary/promiscuous activities is derived. Application of the approach to the emergence of folding catalysis in thioredoxin scaffolds reveals an unanticipated scenario: diverse patterns of primary/promiscuous activity modulation are possible, including a moderate (but likely significant in a biological context) simultaneous enhancement of both activities. We show that this scenario can be most simply explained on the basis of the conformational diversity hypothesis, although alternative interpretations cannot be ruled out. Overall, the results reported may help clarify the mechanisms of the evolution of new functions. From a different viewpoint, the partial-least-squares-reconstruction/Pareto-set-prediction approach we have introduced provides the computational basis for an efficient directed-evolution protocol aimed at the simultaneous enhancement of several protein features and should therefore open new possibilities in the engineering of multi-functional enzymes.

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

PubMed Central

Garcia-Seisdedos, Hector; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

2012-01-01

Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity, its fundamental connection with molecular evolution and also because of its biotechnological applications. Current views on the relation between primary and promiscuous protein activities stem largely from laboratory evolution experiments aimed at increasing promiscuous activity levels. Here, on the other hand, we attempt to assess the main features of the simultaneous modulation of the primary and promiscuous functions during the course of natural evolution. The computational/experimental approach we propose for this task involves the following steps: a function-targeted, statistical coupling analysis of evolutionary data is used to determine a set of positions likely linked to the recruitment of a promiscuous activity for a new function; a combinatorial library of mutations on this set of positions is prepared and screened for both, the primary and the promiscuous activities; a partial-least-squares reconstruction of the full combinatorial space is carried out; finally, an approximation to the Pareto set of variants with optimal primary/promiscuous activities is derived. Application of the approach to the emergence of folding catalysis in thioredoxin scaffolds reveals an unanticipated scenario: diverse patterns of primary/promiscuous activity modulation are possible, including a moderate (but likely significant in a biological context) simultaneous enhancement of both activities. We show that this scenario can be most simply explained on the basis of the conformational diversity hypothesis, although alternative interpretations cannot be ruled out. Overall, the results reported may help clarify the mechanisms of the evolution of new functions. From a different viewpoint, the partial-least-squares-reconstruction/Pareto-set-prediction approach we have introduced provides the computational basis for an efficient directed-evolution protocol aimed at the simultaneous enhancement of several protein features and should therefore open new possibilities in the engineering of multi-functional enzymes. PMID:22719242

Inferring the photometric and size evolution of galaxies from image simulations. I. Method

NASA Astrophysics Data System (ADS)

Carassou, Sébastien; de Lapparent, Valérie; Bertin, Emmanuel; Le Borgne, Damien

2017-09-01

Context. Current constraints on models of galaxy evolution rely on morphometric catalogs extracted from multi-band photometric surveys. However, these catalogs are altered by selection effects that are difficult to model, that correlate in non trivial ways, and that can lead to contradictory predictions if not taken into account carefully. Aims: To address this issue, we have developed a new approach combining parametric Bayesian indirect likelihood (pBIL) techniques and empirical modeling with realistic image simulations that reproduce a large fraction of these selection effects. This allows us to perform a direct comparison between observed and simulated images and to infer robust constraints on model parameters. Methods: We use a semi-empirical forward model to generate a distribution of mock galaxies from a set of physical parameters. These galaxies are passed through an image simulator reproducing the instrumental characteristics of any survey and are then extracted in the same way as the observed data. The discrepancy between the simulated and observed data is quantified, and minimized with a custom sampling process based on adaptive Markov chain Monte Carlo methods. Results: Using synthetic data matching most of the properties of a Canada-France-Hawaii Telescope Legacy Survey Deep field, we demonstrate the robustness and internal consistency of our approach by inferring the parameters governing the size and luminosity functions and their evolutions for different realistic populations of galaxies. We also compare the results of our approach with those obtained from the classical spectral energy distribution fitting and photometric redshift approach. Conclusions: Our pipeline infers efficiently the luminosity and size distribution and evolution parameters with a very limited number of observables (three photometric bands). When compared to SED fitting based on the same set of observables, our method yields results that are more accurate and free from systematic biases.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Complex-envelope alternating-direction-implicit FDTD method for simulating active photonic devices with semiconductor/solid-state media.

PubMed

Singh, Gurpreet; Ravi, Koustuban; Wang, Qian; Ho, Seng-Tiong

2012-06-15

A complex-envelope (CE) alternating-direction-implicit (ADI) finite-difference time-domain (FDTD) approach to treat light-matter interaction self-consistently with electromagnetic field evolution for efficient simulations of active photonic devices is presented for the first time (to our best knowledge). The active medium (AM) is modeled using an efficient multilevel system of carrier rate equations to yield the correct carrier distributions, suitable for modeling semiconductor/solid-state media accurately. To include the AM in the CE-ADI-FDTD method, a first-order differential system involving CE fields in the AM is first set up. The system matrix that includes AM parameters is then split into two time-dependent submatrices that are then used in an efficient ADI splitting formula. The proposed CE-ADI-FDTD approach with AM takes 22% of the time as the approach of the corresponding explicit FDTD, as validated by semiconductor microdisk laser simulations.

Computational evolution: taking liberties.

PubMed

Correia, Luís

2010-09-01

Evolution has, for a long time, inspired computer scientists to produce computer models mimicking its behavior. Evolutionary algorithm (EA) is one of the areas where this approach has flourished. EAs have been used to model and study evolution, but they have been especially developed for their aptitude as optimization tools for engineering. Developed models are quite simple in comparison with their natural sources of inspiration. However, since EAs run on computers, we have the freedom, especially in optimization models, to test approaches both realistic and outright speculative, from the biological point of view. In this article, we discuss different common evolutionary algorithm models, and then present some alternatives of interest. These include biologically inspired models, such as co-evolution and, in particular, symbiogenetics and outright artificial operators and representations. In each case, the advantages of the modifications to the standard model are identified. The other area of computational evolution, which has allowed us to study basic principles of evolution and ecology dynamics, is the development of artificial life platforms for open-ended evolution of artificial organisms. With these platforms, biologists can test theories by directly manipulating individuals and operators, observing the resulting effects in a realistic way. An overview of the most prominent of such environments is also presented. If instead of artificial platforms we use the real world for evolving artificial life, then we are dealing with evolutionary robotics (ERs). A brief description of this area is presented, analyzing its relations to biology. Finally, we present the conclusions and identify future research avenues in the frontier of computation and biology. Hopefully, this will help to draw the attention of more biologists and computer scientists to the benefits of such interdisciplinary research.

Combinatorial evolution of site- and enantioselective catalysts for polyene epoxidation

NASA Astrophysics Data System (ADS)

Lichtor, Phillip A.; Miller, Scott J.

2012-12-01

Selectivity in the catalytic functionalization of complex molecules is a major challenge in chemical synthesis. The problem is magnified when there are several possible stereochemical outcomes and when similar functional groups occur repeatedly within the same molecule. Selective polyene oxidation provides an archetypical example of this challenge. Historically, enzymatic catalysis has provided the only precedents. Although non-enzymatic catalysts that meet some of these challenges became known, a comprehensive solution has remained elusive. Here, we describe low molecular weight peptide-based catalysts, discovered through a combinatorial synthesis and screening protocol, that exhibit site- and enantioselective oxidation of certain positions of various isoprenols. This diversity-based approach, which exhibits features reminiscent of the directed evolution of enzymes, delivers catalysts that compare favourably to the state-of-the-art for the asymmetric oxidation of these compounds. Moreover, the approach culminated in catalysts that exhibit alternative-site selectivity in comparison to oxidation catalysts previously described.

Adaptive array technique for differential-phase reflectometry in QUEST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idei, H., E-mail: idei@triam.kyushu-u.ac.jp; Hanada, K.; Zushi, H.

2014-11-15

A Phased Array Antenna (PAA) was considered as launching and receiving antennae in reflectometry to attain good directivity in its applied microwave range. A well-focused beam was obtained in a launching antenna application, and differential-phase evolution was properly measured by using a metal reflector plate in the proof-of-principle experiment at low power test facilities. Differential-phase evolution was also evaluated by using the PAA in the Q-shu University Experiment with Steady State Spherical Tokamak (QUEST). A beam-forming technique was applied in receiving phased-array antenna measurements. In the QUEST device that should be considered as a large oversized cavity, standing wave effectmore » was significantly observed with perturbed phase evolution. A new approach using derivative of measured field on propagating wavenumber was proposed to eliminate the standing wave effect.« less

An innovative approach to developing the reflective skills of medical students

PubMed Central

Henderson, Penny; Johnson, Martin H

2002-01-01

Background Development of the reflective skills of medical students is an acknowledged objective of medical education. Description Description of an educational exercise which uses an email-based process for developing the reflective skills of undergraduate medical students. Student quotations illustrate learning outcomes qualitatively. Discussion The process described is immediate, direct, linked to learning objectives, enables rapid responses to be given to the students individually, and is followed by group sharing of learning. It provides a rigorous and robust feedback loop for students. It is relatively economic for teachers and incidentally benefits curriculum design and evolution. The approach supports development of a reflective approach to learning. PMID:12003640

An analysis of microsystems development at Sandia National Laboratories

NASA Astrophysics Data System (ADS)

Herrera, Gilbert V.; Myers, David R.

2011-06-01

While Sandia initially was motivated to investigate emergent microsystem technology to miniaturize existing macroscale structures, present designs embody innovative approaches that directly exploit the fundamentally different material properties of a new technology at the micro- and nano-scale. Direct, hands-on experience with the emerging technology gave Sandia engineers insights that not only guided the evolution of the technology but also enabled them to address new applications that enlarged the customer base for the new technology. Sandia's early commitment to develop complex microsystems demonstrated the advantages that early adopters gain by developing an extensive design and process tool kit and a shared awareness of multiple approaches to achieve the multiple goals. As with any emergent technology, Sandia's program benefited from interactions with the larger technical community. However, custom development followed a spiral path of direct trial-and-error experience, analysis, quantification of materials properties at the micro- and nano-scale, evolution of design tools and process recipes, and an understanding of reliability factors and failure mechanisms even in extreme environments. The microsystems capability at Sandia relied on three key elements. The first was people: a mix of mechanical and semiconductor engineers, chemists, physical scientists, designers, and numerical analysts. The second was a unique facility that enabled the development of custom technologies without contaminating mainline product deliveries. The third was the arrival of specialized equipment as part of a Cooperative Research And Development Agreement (CRADA) enabled by the National Competitiveness Technology Transfer Act of 1989. Underpinning all these, the program was guided and sustained through the research and development phases by accomplishing intermediate milestones addressing direct mission needs.

The Molecular Basis of Human Brain Evolution.

PubMed

Enard, Wolfgang

2016-10-24

Humans are a remarkable species, especially because of the remarkable properties of their brain. Since the split from the chimpanzee lineage, the human brain has increased three-fold in size and has acquired abilities for vocal learning, language and intense cooperation. To better understand the molecular basis of these changes is of great biological and biomedical interest. However, all the about 16 million fixed genetic changes that occurred during human evolution are fully correlated with all molecular, cellular, anatomical and behavioral changes that occurred during this time. Hence, as humans and chimpanzees cannot be crossed or genetically manipulated, no direct evidence for linking particular genetic and molecular changes to human brain evolution can be obtained. Here, I sketch a framework how indirect evidence can be obtained and review findings related to the molecular basis of human cognition, vocal learning and brain size. In particular, I discuss how a comprehensive comparative approach, leveraging cellular systems and genomic technologies, could inform the evolution of our brain in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae).

PubMed

Sherratt, Emma; Alejandrino, Alvin; Kraemer, Andrew C; Serb, Jeanne M; Adams, Dean C

2016-09-01

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.

PubMed

Yang, Jin Kuk; Park, Min S; Waldo, Geoffrey S; Suh, Se Won

2003-01-21

One of the serious bottlenecks in structural genomics projects is overexpression of the target proteins in soluble form. We have applied the directed evolution technique and prepared soluble mutants of the Mycobacterium tuberculosis Rv2002 gene product, the wild type of which had been expressed as inclusion bodies in Escherichia coli. A triple mutant I6TV47MT69K (Rv2002-M3) was chosen for structural and functional characterizations. Enzymatic assays indicate that the Rv2002-M3 protein has a high catalytic activity as a NADH-dependent 3alpha, 20beta-hydroxysteroid dehydrogenase. We have determined the crystal structures of a binary complex with NAD(+) and a ternary complex with androsterone and NADH. The structure reveals that Asp-38 determines the cofactor specificity. The catalytic site includes the triad Ser-140Tyr-153Lys-157. Additionally, it has an unusual feature, Glu-142. Enzymatic assays of the E142A mutant of Rv2002-M3 indicate that Glu-142 reverses the effect of Lys-157 in influencing the pKa of Tyr-153. This study suggests that the Rv2002 gene product is a unique member of the SDR family and is likely to be involved in steroid metabolism in M. tuberculosis. Our work demonstrates the power of the directed evolution technique as a general way of overcoming the difficulties in overexpressing the target proteins in soluble form.

Reduced genetic variance among high fitness individuals: inferring stabilizing selection on male sexual displays in Drosophila serrata.

PubMed

Sztepanacz, Jacqueline L; Rundle, Howard D

2012-10-01

Directional selection is prevalent in nature, yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. However, the genetic basis of this limit is unresolved. Given widespread pleiotropy, opposing selection on a trait may arise from the effects of the underlying alleles on other traits under selection, generating net stabilizing selection on trait genetic variance. These pleiotropic costs of trait exaggeration may arise through any number of other traits, making them hard to detect in phenotypic analyses. Stabilizing selection can be inferred, however, if genetic variance is greater among low- compared to high-fitness individuals. We extend a recently suggested approach to provide a direct test of a difference in genetic variance for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on these traits, genetic variance differed between high- and low-fitness individuals and was greater among the low-fitness males for seven of eight CHCs, significantly more than expected by chance. Univariate tests of a difference in genetic variance were nonsignificant but likely have low power. Our results suggest that further CHC exaggeration in D. serrata in response to sexual selection is limited by pleiotropic costs mediated through other traits. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models.

PubMed

Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

2016-10-01

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Random mutagenesis by error-prone pol plasmid replication in Escherichia coli.

PubMed

Alexander, David L; Lilly, Joshua; Hernandez, Jaime; Romsdahl, Jillian; Troll, Christopher J; Camps, Manel

2014-01-01

Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail, and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available.

Natural history collections as windows on evolutionary processes.

PubMed

Holmes, Michael W; Hammond, Talisin T; Wogan, Guinevere O U; Walsh, Rachel E; LaBarbera, Katie; Wommack, Elizabeth A; Martins, Felipe M; Crawford, Jeremy C; Mack, Katya L; Bloch, Luke M; Nachman, Michael W

2016-02-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. © 2016 John Wiley & Sons Ltd.

Natural history collections as windows on evolutionary processes

PubMed Central

Holmes, Michael W.; Hammond, Talisin T.; Wogan, Guinevere O.U.; Walsh, Rachel E.; LaBarbera, Katie; Wommack, Elizabeth A.; Martins, Felipe M.; Crawford, Jeremy C.; Mack, Katya L.; Bloch, Luke M.; Nachman, Michael W.

2016-01-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics, and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the lab, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short time scales in response to presumably strong selective pressures. In some instances evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. PMID:26757135

Highly parallel single-molecule amplification approach based on agarose droplet polymerase chain reaction for efficient and cost-effective aptamer selection.

PubMed

Zhang, Wei Yun; Zhang, Wenhua; Liu, Zhiyuan; Li, Cong; Zhu, Zhi; Yang, Chaoyong James

2012-01-03

We have developed a novel method for efficiently screening affinity ligands (aptamers) from a complex single-stranded DNA (ssDNA) library by employing single-molecule emulsion polymerase chain reaction (PCR) based on the agarose droplet microfluidic technology. In a typical systematic evolution of ligands by exponential enrichment (SELEX) process, the enriched library is sequenced first, and tens to hundreds of aptamer candidates are analyzed via a bioinformatic approach. Possible candidates are then chemically synthesized, and their binding affinities are measured individually. Such a process is time-consuming, labor-intensive, inefficient, and expensive. To address these problems, we have developed a highly efficient single-molecule approach for aptamer screening using our agarose droplet microfluidic technology. Statistically diluted ssDNA of the pre-enriched library evolved through conventional SELEX against cancer biomarker Shp2 protein was encapsulated into individual uniform agarose droplets for droplet PCR to generate clonal agarose beads. The binding capacity of amplified ssDNA from each clonal bead was then screened via high-throughput fluorescence cytometry. DNA clones with high binding capacity and low K(d) were chosen as the aptamer and can be directly used for downstream biomedical applications. We have identified an ssDNA aptamer that selectively recognizes Shp2 with a K(d) of 24.9 nM. Compared to a conventional sequencing-chemical synthesis-screening work flow, our approach avoids large-scale DNA sequencing and expensive, time-consuming DNA synthesis of large populations of DNA candidates. The agarose droplet microfluidic approach is thus highly efficient and cost-effective for molecular evolution approaches and will find wide application in molecular evolution technologies, including mRNA display, phage display, and so on. © 2011 American Chemical Society

Evolution in plant populations as a driver of ecological changes in arthropod communities

PubMed Central

Johnson, Marc T.J.; Vellend, Mark; Stinchcombe, John R.

2009-01-01

Heritable variation in traits can have wide-ranging impacts on species interactions, but the effects that ongoing evolution has on the temporal ecological dynamics of communities are not well understood. Here, we identify three conditions that, if experimentally satisfied, support the hypothesis that evolution by natural selection can drive ecological changes in communities. These conditions are: (i) a focal population exhibits genetic variation in a trait(s), (ii) there is measurable directional selection on the trait(s), and (iii) the trait(s) under selection affects variation in a community variable(s). When these conditions are met, we expect evolution by natural selection to cause ecological changes in the community. We tested these conditions in a field experiment examining the interactions between a native plant (Oenothera biennis) and its associated arthropod community (more than 90 spp.). Oenothera biennis exhibited genetic variation in several plant traits and there was directional selection on plant biomass, life-history strategy (annual versus biennial reproduction) and herbivore resistance. Genetically based variation in biomass and life-history strategy consistently affected the abundance of common arthropod species, total arthropod abundance and arthropod species richness. Using two modelling approaches, we show that evolution by natural selection in large O. biennis populations is predicted to cause changes in the abundance of individual arthropod species, increases in the total abundance of arthropods and a decline in the number of arthropod species. In small O. biennis populations, genetic drift is predicted to swamp out the effects of selection, making the evolution of plant populations unpredictable. In short, evolution by natural selection can play an important role in affecting the dynamics of communities, but these effects depend on several ecological factors. The framework presented here is general and can be applied to other systems to examine the community-level effects of ongoing evolution. PMID:19414473

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance.

PubMed

Nyerges, Ákos; Csörgő, Bálint; Draskovits, Gábor; Kintses, Bálint; Szili, Petra; Ferenc, Györgyi; Révész, Tamás; Ari, Eszter; Nagy, István; Bálint, Balázs; Vásárhelyi, Bálint Márk; Bihari, Péter; Számel, Mónika; Balogh, Dávid; Papp, Henrietta; Kalapis, Dorottya; Papp, Balázs; Pál, Csaba

2018-06-19

Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology. Copyright © 2018 the Author(s). Published by PNAS.

Direct Simulation of Evolution and Control of Three-Dimensional Instabilities in Attachment-Line Boundary Layers

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.

1995-01-01

The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier-Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic- source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in at-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

Why the predictions for monsoon rainfall fail?

NASA Astrophysics Data System (ADS)

Lee, J.

2016-12-01

To be in line with the Global Land/Atmosphere System Study (GLASS) of the Global Energy and Water Cycle Experiment (GEWEX) international research scheme, this study discusses classical arguments about the feedback mechanisms between land surface and precipitation to improve the predictions of African monsoon rainfall. In order to clarify the impact of antecedent soil moisture on subsequent rainfall evolution, several data sets will be presented. First, in-situ soil moisture field measurements acquired by the AMMA field campaign will be shown together with rain gauge data. This data set will validate various model and satellite data sets such as NOAH land surface model, TRMM rainfall, CMORPH rainfall and HadGEM climate models, SMOS soil moisture. To relate soil moisture with precipitation, two approaches are employed: one approach makes a direct comparison between the spatial distributions of soil moisture as an absolute value and rainfall, while the other measures a temporal evolution of the consecutive dry days (i.e. a relative change within the same soil moisture data set over time) and rainfall occurrences. Consecutive dry days shows consistent results of a negative feedback between soil moisture and rainfall across various data sets, contrary to the direct comparison of soil moisture state. This negative mechanism needs attention, as most climate models usually focus on a positive feedback only. The approach of consecutive dry days takes into account the systematic errors in satellite observations, reminding us that it may cause the misinterpretation to directly compare model with satellite data, due to their difference in data retrievals. This finding is significant, as the climate indices employed by the Intergovernmental Panel on Climate Change (IPCC) modelling archive are based on the atmospheric variable rathr than land.

Student Teachers' Approaches to Teaching Biological Evolution

NASA Astrophysics Data System (ADS)

Borgerding, Lisa A.; Klein, Vanessa A.; Ghosh, Rajlakshmi; Eibel, Albert

2015-06-01

Evolution is fundamental to biology and scientific literacy, but teaching high school evolution is often difficult. Evolution teachers face several challenges including limited content knowledge, personal conflicts with evolution, expectations of resistance, concerns about students' conflicts with religion, and curricular constraints. Evolution teaching can be particularly challenging for student teachers who are just beginning to gain pedagogical knowledge and pedagogical content knowledge related to evolution teaching and who seek approval from university supervisors and cooperating teachers. Science teacher educators need to know how to best support student teachers as they broach the sometimes daunting task of teaching evolution within student teaching placements. This multiple case study report documents how three student teachers approached evolution instruction and what influenced their approaches. Data sources included student teacher interviews, field note observations for 4-5 days of evolution instruction, and evolution instructional artifacts. Data were analyzed using grounded theory approaches to develop individual cases and a cross-case analysis. Seven influences (state exams and standards, cooperating teacher, ideas about teaching and learning, concerns about evolution controversy, personal commitment to evolution, knowledge and preparation for teaching evolution, and own evolution learning experiences) were identified and compared across cases. Implications for science teacher preparation and future research are provided.

Modeling and optimization of the multiobjective stochastic joint replenishment and delivery problem under supply chain environment.

PubMed

Wang, Lin; Qu, Hui; Liu, Shan; Dun, Cai-xia

2013-01-01

As a practical inventory and transportation problem, it is important to synthesize several objectives for the joint replenishment and delivery (JRD) decision. In this paper, a new multiobjective stochastic JRD (MSJRD) of the one-warehouse and n-retailer systems considering the balance of service level and total cost simultaneously is proposed. The goal of this problem is to decide the reasonable replenishment interval, safety stock factor, and traveling routing. Secondly, two approaches are designed to handle this complex multi-objective optimization problem. Linear programming (LP) approach converts the multi-objective to single objective, while a multi-objective evolution algorithm (MOEA) solves a multi-objective problem directly. Thirdly, three intelligent optimization algorithms, differential evolution algorithm (DE), hybrid DE (HDE), and genetic algorithm (GA), are utilized in LP-based and MOEA-based approaches. Results of the MSJRD with LP-based and MOEA-based approaches are compared by a contrastive numerical example. To analyses the nondominated solution of MOEA, a metric is also used to measure the distribution of the last generation solution. Results show that HDE outperforms DE and GA whenever LP or MOEA is adopted.

Modeling and Optimization of the Multiobjective Stochastic Joint Replenishment and Delivery Problem under Supply Chain Environment

PubMed Central

Dun, Cai-xia

2013-01-01

As a practical inventory and transportation problem, it is important to synthesize several objectives for the joint replenishment and delivery (JRD) decision. In this paper, a new multiobjective stochastic JRD (MSJRD) of the one-warehouse and n-retailer systems considering the balance of service level and total cost simultaneously is proposed. The goal of this problem is to decide the reasonable replenishment interval, safety stock factor, and traveling routing. Secondly, two approaches are designed to handle this complex multi-objective optimization problem. Linear programming (LP) approach converts the multi-objective to single objective, while a multi-objective evolution algorithm (MOEA) solves a multi-objective problem directly. Thirdly, three intelligent optimization algorithms, differential evolution algorithm (DE), hybrid DE (HDE), and genetic algorithm (GA), are utilized in LP-based and MOEA-based approaches. Results of the MSJRD with LP-based and MOEA-based approaches are compared by a contrastive numerical example. To analyses the nondominated solution of MOEA, a metric is also used to measure the distribution of the last generation solution. Results show that HDE outperforms DE and GA whenever LP or MOEA is adopted. PMID:24302880

Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chugh, Rajiv, E-mail: rajivchug@gmail.com; Kumar, Rohit, E-mail: rohitksharma.pu@gmail.com; Vinayak, Karan Singh, E-mail: drksvinayak@gmail.com

2016-05-06

Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetrymore » energy.« less

Macrovascular Decompression of the Brainstem and Cranial Nerves: Evolution of an Anteromedial Vertebrobasilar Artery Transposition Technique.

PubMed

Choudhri, Omar; Connolly, Ian D; Lawton, Michael T

2017-08-01

Tortuous and dolichoectatic vertebrobasilar arteries can impinge on the brainstem and cranial nerves to cause compression syndromes. Transposition techniques are often required to decompress the brainstem with dolichoectatic pathology. We describe our evolution of an anteromedial transposition technique and its efficacy in decompressing the brainstem and relieving symptoms. To present the anteromedial vertebrobasilar artery transposition technique for macrovascular decompression of the brainstem and cranial nerves. All patients who underwent vertebrobasilar artery transposition were identified from the prospectively maintained database of the Vascular Neurosurgery service, and their medical records were reviewed retrospectively. The extent of arterial displacement was measured pre- and postoperatively on imaging. Vertebrobasilar arterial transposition and macrovascular decompression was performed in 12 patients. Evolution in technique was characterized by gradual preference for the far-lateral approach, use of a sling technique with muslin wrap, and an anteromedial direction of pull on the vertebrobasilar artery with clip-assisted tethering to the clival dura. With this technique, mean lateral displacement decreased from 6.6 mm in the first half of the series to 3.8 mm in the last half of the series, and mean anterior displacement increased from 0.8 to 2.5 mm, with corresponding increases in satisfaction and relief of symptoms. Compressive dolichoectatic pathology directed laterally into cranial nerves and posteriorly into the brainstem can be corrected with anteromedial transposition towards the clivus. Our technique accomplishes this anteromedial transposition from an inferolateral surgical approach through the vagoaccessory triangle, with sling fixation to clival dura using aneurysm clips. Copyright © 2017 by the Congress of Neurological Surgeons

Can mathematics explain the evolution of human language?

PubMed

Witzany, Guenther

2011-09-01

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer science-based formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language.

Preparing Biology Teachers to Teach Evolution in a Project-Based Approach

ERIC Educational Resources Information Center

Cook, Kristin; Buck, Gayle; Park Rogers, Meredith

2012-01-01

This study investigates a project-based learning (PBL) approach to teaching evolution to inform efforts in teacher preparation. Data analysis of a secondary biology educator teaching evolution through a PBL approach illuminated: (1) active student voice, which allowed students to reflect on their positioning on evolution and consider multiple…

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

PubMed

Bednar, David; Beerens, Koen; Sebestova, Eva; Bendl, Jaroslav; Khare, Sagar; Chaloupkova, Radka; Prokop, Zbynek; Brezovsky, Jan; Baker, David; Damborsky, Jiri

2015-11-01

There is great interest in increasing proteins' stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt's reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔTm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.

Strain Gradient Modulated Exciton Evolution and Emission in ZnO Fibers

PubMed Central

Wei, Bin; Ji, Yuan; Gauvin, Raynald; Zhang, Ze; Zou, Jin; Han, Xiaodong

2017-01-01

One-dimensional semiconductor can undergo large deformation including stretching and bending. This homogeneous strain and strain gradient are an easy and effective way to tune the light emission properties and the performance of piezo-phototronic devices. Here, we report that with large strain gradients from 2.1–3.5% μm−1, free-exciton emission was intensified, and the free-exciton interaction (FXI) emission became a prominent FXI-band at the tensile side of the ZnO fiber. These led to an asymmetric variation in energy and intensity along the cross-section as well as a redshift of the total near-band-edge (NBE) emission. This evolution of the exciton emission was directly demonstrated using spatially resolved CL spectrometry combined with an in situ tensile-bending approach at liquid nitrogen temperature for individual fibers and nanowires. A distinctive mechanism of the evolution of exciton emission is proposed: the enhancement of the free-exciton-related emission is attributed to the aggregated free excitons and their interaction in the narrow bandgap in the presence of high bandgap gradients and a transverse piezoelectric field. These results might facilitate new approaches for energy conversion and sensing applications via strained nanowires and fibers. PMID:28084427

Strain Gradient Modulated Exciton Evolution and Emission in ZnO Fibers.

PubMed

Wei, Bin; Ji, Yuan; Gauvin, Raynald; Zhang, Ze; Zou, Jin; Han, Xiaodong

2017-01-13

One-dimensional semiconductor can undergo large deformation including stretching and bending. This homogeneous strain and strain gradient are an easy and effective way to tune the light emission properties and the performance of piezo-phototronic devices. Here, we report that with large strain gradients from 2.1-3.5% μm -1 , free-exciton emission was intensified, and the free-exciton interaction (FXI) emission became a prominent FXI-band at the tensile side of the ZnO fiber. These led to an asymmetric variation in energy and intensity along the cross-section as well as a redshift of the total near-band-edge (NBE) emission. This evolution of the exciton emission was directly demonstrated using spatially resolved CL spectrometry combined with an in situ tensile-bending approach at liquid nitrogen temperature for individual fibers and nanowires. A distinctive mechanism of the evolution of exciton emission is proposed: the enhancement of the free-exciton-related emission is attributed to the aggregated free excitons and their interaction in the narrow bandgap in the presence of high bandgap gradients and a transverse piezoelectric field. These results might facilitate new approaches for energy conversion and sensing applications via strained nanowires and fibers.

Time-domain measurement of terahertz frequency magnetoplasmon resonances in a two-dimensional electron system by the direct injection of picosecond pulsed currents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Jingbo; Mayorov, Alexander S.; Wood, Christopher D.

2016-02-29

We have investigated terahertz (THz) frequency magnetoplasmon resonances in a two-dimensional electron system through the direct injection of picosecond duration current pulses. The evolution of the time-domain signals was measured as a function of magnetic field, and the results were found to be in agreement with calculations using a mode-matching approach for four modes observed in the frequency range above 0.1 THz. This introduces a generic technique suitable for sampling ultrafast carrier dynamics in low-dimensional semiconductor nanostructures at THz frequencies.

Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts.

PubMed

Prier, Christopher K; Arnold, Frances H

2015-11-11

Despite the astonishing breadth of enzymes in nature, no enzymes are known for many of the valuable catalytic transformations discovered by chemists. Recent work in enzyme design and evolution, however, gives us good reason to think that this will change. We describe a chemomimetic biocatalysis approach that draws from small-molecule catalysis and synthetic chemistry, enzymology, and molecular evolution to discover or create enzymes with non-natural reactivities. We illustrate how cofactor-dependent enzymes can be exploited to promote reactions first established with related chemical catalysts. The cofactors can be biological, or they can be non-biological to further expand catalytic possibilities. The ability of enzymes to amplify and precisely control the reactivity of their cofactors together with the ability to optimize non-natural reactivity by directed evolution promises to yield exceptional catalysts for challenging transformations that have no biological counterparts.

Evolution of a designed retro-aldolase leads to complete active site remodeling

PubMed Central

Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

2013-01-01

Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that dramatic molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400 fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate, and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. PMID:23748672

Precise tuning in platinum-nickel/nickel sulfide interface nanowires for synergistic hydrogen evolution catalysis

PubMed Central

Wang, Pengtang; Zhang, Xu; Zhang, Jin; Wan, Sheng; Guo, Shaojun; Lu, Gang; Yao, Jianlin; Huang, Xiaoqing

2017-01-01

Comprising abundant interfaces, multicomponent heterostructures can integrate distinct building blocks into single entities and yield exceptional functionalities enabled by the synergistic components. Here we report an efficient approach to construct one-dimensional metal/sulfide heterostructures by directly sulfuring highly composition-segregated platinum-nickel nanowires. The heterostructures possess a high density of interfaces between platinum-nickel and nickel sulfide components, which cooperate synergistically towards alkaline hydrogen evolution reaction. The platinum-nickel/nickel sulfide heterostructures can deliver a current density of 37.2 mA cm−2 at an overpotential of 70 mV, which is 9.7 times higher than that of commercial Pt/C. The heterostructures also offer enhanced stability revealed by long-term chronopotentiometry measurements. The present work highlights a potentially powerful interface-engineering strategy for designing multicomponent heterostructures with advanced performance in hydrogen evolution reaction and beyond. PMID:28239145

Stochastic modeling of mode interactions via linear parabolized stability equations

NASA Astrophysics Data System (ADS)

Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanovic, Mihailo

2017-11-01

Low-complexity approximations of the Navier-Stokes equations have been widely used in the analysis of wall-bounded shear flows. In particular, the parabolized stability equations (PSE) and Floquet theory have been employed to capture the evolution of primary and secondary instabilities in spatially-evolving flows. We augment linear PSE with Floquet analysis to formally treat modal interactions and the evolution of secondary instabilities in the transitional boundary layer via a linear progression. To this end, we leverage Floquet theory by incorporating the primary instability into the base flow and accounting for different harmonics in the flow state. A stochastic forcing is introduced into the resulting linear dynamics to model the effect of nonlinear interactions on the evolution of modes. We examine the H-type transition scenario to demonstrate how our approach can be used to model nonlinear effects and capture the growth of the fundamental and subharmonic modes observed in direct numerical simulations and experiments.

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression, direct costs, mating constraints, and polyandry as a threshold trait.

PubMed

Duthie, A Bradley; Bocedi, Greta; Reid, Jane M

2016-09-01

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual-based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The Evolution of the Mexican Military: From the Mexican Revolution In 1910 to 2014

DTIC Science & Technology

2015-03-01

government, the Mexican army’s track record and SEDENA’s laissez - faire approach demonstrate that the sheltering of the military, which was...Changes to the Modern Military’s Leadership and Structure ......41 D. THE MEXICAN MILITARY AND THE HUMAN RIGHTS VIOLATIONS... leadership and structure of the contemporary Mexican military was directly shaped by the events and actions of the Mexican Revolution. Through the research

Models of Protocellular Structure, Function and Evolution

NASA Technical Reports Server (NTRS)

New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

2001-01-01

In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

Vertical Integration of Biomass Saccharification of Enzymes for Sustainable Cellulosic Biofuel Production in a Biorefinery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Manoj

2011-05-09

These are a set of slides from this conference. Lignocellulosic biomass is the most abundant, least expensive renewable natural biological resource for the production of biobased products and bioenergy is important for the sustainable development of human civilization in 21st century. For making the fermentable sugars from lignocellulosic biomass, a reduction in cellulase production cost, an improvement in cellulase performance, and an increase in sugar yields are all vital to reduce the processing costs of biorefineries. Improvements in specific cellulase activities for non-complexed cellulase mixtures can be implemented through cellulase engineering based on rational design or directed evolution for eachmore » cellulase component enzyme, as well as on the reconstitution of cellulase components. In this paper, we will provide DSM's efforts in cellulase research and developments and focus on limitations. Cellulase improvement strategies based on directed evolution using screening on relevant substrates, screening for higher thermal tolerance based on activity screening approaches such as continuous culture using insoluble cellulosic substrates as a powerful selection tool for enriching beneficial cellulase mutants from the large library. We will illustrate why and how thermostable cellulases are vital for economic delivery of bioproducts from cellulosic biomass using biochemical conversion approach.« less

Systems biology: the case for a systems science approach to diabetes.

PubMed

Petrasek, Danny

2008-01-01

The unprecedented accumulation of biological data in recent decades has underscored the need to organize and integrate the massive collection of information. In addition, there is rising agreement among biologists that a complete understanding of a single cell will not lead directly to a complete understanding of a system of cells. The success of a systems science approach in engineering and physics may be of great value in the evolution of biological science. This article reviews some examples that suggest the importance of a systems biology approach and, in addition, advance one specific systems science principle, the conservation of uncertainty, which may give insight into the emergent behavior of numerous biological and physiological phenomena.

Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

PubMed

Renata, Hans; Wang, Z Jane; Arnold, Frances H

2015-03-09

High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature's known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolving Methanococcoides burtonii archaeal Rubisco for improved photosynthesis and plant growth

PubMed Central

Wilson, Robert H.; Alonso, Hernan; Whitney, Spencer M.

2016-01-01

In photosynthesis Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the often rate limiting CO2-fixation step in the Calvin cycle. This makes Rubisco both the gatekeeper for carbon entry into the biosphere and a target for functional improvement to enhance photosynthesis and plant growth. Encumbering the catalytic performance of Rubisco is its highly conserved, complex catalytic chemistry. Accordingly, traditional efforts to enhance Rubisco catalysis using protracted “trial and error” protein engineering approaches have met with limited success. Here we demonstrate the versatility of high throughput directed (laboratory) protein evolution for improving the carboxylation properties of a non-photosynthetic Rubisco from the archaea Methanococcoides burtonii. Using chloroplast transformation in the model plant Nicotiana tabacum (tobacco) we confirm the improved forms of M. burtonii Rubisco increased photosynthesis and growth relative to tobacco controls producing wild-type M. burtonii Rubisco. Our findings indicate continued directed evolution of archaeal Rubisco offers new potential for enhancing leaf photosynthesis and plant growth. PMID:26926260

Evolving Methanococcoides burtonii archaeal Rubisco for improved photosynthesis and plant growth.

PubMed

Wilson, Robert H; Alonso, Hernan; Whitney, Spencer M

2016-03-01

In photosynthesis Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the often rate limiting CO2-fixation step in the Calvin cycle. This makes Rubisco both the gatekeeper for carbon entry into the biosphere and a target for functional improvement to enhance photosynthesis and plant growth. Encumbering the catalytic performance of Rubisco is its highly conserved, complex catalytic chemistry. Accordingly, traditional efforts to enhance Rubisco catalysis using protracted "trial and error" protein engineering approaches have met with limited success. Here we demonstrate the versatility of high throughput directed (laboratory) protein evolution for improving the carboxylation properties of a non-photosynthetic Rubisco from the archaea Methanococcoides burtonii. Using chloroplast transformation in the model plant Nicotiana tabacum (tobacco) we confirm the improved forms of M. burtonii Rubisco increased photosynthesis and growth relative to tobacco controls producing wild-type M. burtonii Rubisco. Our findings indicate continued directed evolution of archaeal Rubisco offers new potential for enhancing leaf photosynthesis and plant growth.

HIV Surveillance Among Pregnant Women Attending Antenatal Clinics: Evolution and Current Direction

PubMed Central

Garcia Calleja, Jesus M; Marsh, Kimberly; Zaidi, Irum; Murrill, Christopher; Swaminathan, Mahesh

2017-01-01

Since the late 1980s, human immunodeficiency virus (HIV) sentinel serosurveillance among pregnant women attending select antenatal clinics (ANCs) based on unlinked anonymous testing (UAT) has provided invaluable information for tracking HIV prevalence and trends and informing global and national HIV models in most countries with generalized HIV epidemics. However, increased coverage of HIV testing, prevention of mother-to-child transmission (PMTCT), and antiretroviral therapy has heightened ethical concerns about UAT. PMTCT programs now routinely collect demographic and HIV testing information from the same pregnant women as serosurveillance and therefore present an alternative to UAT-based ANC serosurveillance. This paper reports on the evolution and current direction of the global approach to HIV surveillance among pregnant women attending ANCs, including the transition away from traditional UAT-based serosurveillance and toward new guidance from the World Health Organization and the Joint United Nations Programme on HIV/AIDS on the implementation of surveillance among pregnant women attending ANCs based on routine PMTCT program data. PMID:29208587

Direct approach for bioprocess optimization in a continuous flat-bed photobioreactor system.

PubMed

Kwon, Jong-Hee; Rögner, Matthias; Rexroth, Sascha

2012-11-30

Application of photosynthetic micro-organisms, such as cyanobacteria and green algae, for the carbon neutral energy production raises the need for cost-efficient photobiological processes. Optimization of these processes requires permanent control of many independent and mutably dependent parameters, for which a continuous cultivation approach has significant advantages. As central factors like the cell density can be kept constant by turbidostatic control, light intensity and iron content with its strong impact on productivity can be optimized. Both are key parameters due to their strong dependence on photosynthetic activity. Here we introduce an engineered low-cost 5 L flat-plate photobioreactor in combination with a simple and efficient optimization procedure for continuous photo-cultivation of microalgae. Based on direct determination of the growth rate at constant cell densities and the continuous measurement of O₂ evolution, stress conditions and their effect on the photosynthetic productivity can be directly observed. Copyright © 2012 Elsevier B.V. All rights reserved.

Self-organisation and communication in groups of simulated and physical robots.

PubMed

Trianni, Vito; Dorigo, Marco

2006-09-01

In social insects, both self-organisation and communication play a crucial role for the accomplishment of many tasks at a collective level. Communication is performed with different modalities, which can be roughly classified into three classes: indirect (stigmergic) communication, direct interactions and direct communication. The use of stigmergic communication is predominant in social insects (e.g. the pheromone trails in ants), where, however, direct interactions (e.g. antennation in ants) and direct communication (e.g. the waggle dance in honey bees) can also be observed. Taking inspiration from insect societies, we present an experimental study of self-organising behaviours for a group of robots, which exploit communication to coordinate their activities. In particular, the robots are placed in an arena presenting holes and open borders, which they should avoid while moving coordinately. Artificial evolution is responsible for the synthesis in a simulated environment of the robot's neural controllers, which are subsequently tested on physical robots. We study different communication strategies among the robots: no direct communication, handcrafted signalling and a completely evolved approach. We show that the latter is the most efficient, suggesting that artificial evolution can produce behaviours that are more adaptive than those obtained with conventional design methodologies. Moreover, we show that the evolved controllers produce a self-organising system that is robust enough to be tested on physical robots, notwithstanding the huge gap between simulation and reality.

Sex differences, sexual selection, and ageing: an experimental evolution approach.

PubMed

Maklakov, Alexei A; Bonduriansky, Russell; Brooks, Robert C

2009-10-01

Life-history (LH) theory predicts that selection will optimize the trade-off between reproduction and somatic maintenance. Reproductive ageing and finite life span are direct consequences of such optimization. Sexual selection and conflict profoundly affect the reproductive strategies of the sexes and thus can play an important role in the evolution of life span and ageing. In theory, sexual selection can favor the evolution of either faster or slower ageing, but the evidence is equivocal. We used a novel selection experiment to investigate the potential of sexual selection to influence the adaptive evolution of age-specific LH traits. We selected replicate populations of the seed beetle Callosobruchus maculatus for age at reproduction ("Young" and "Old") either with or without sexual selection. We found that LH selection resulted in the evolution of age-specific reproduction and mortality but these changes were largely unaffected by sexual selection. Sexual selection depressed net reproductive performance and failed to promote adaptation. Nonetheless, the evolution of several traits differed between males and females. These data challenge the importance of current sexual selection in promoting rapid adaptation to environmental change but support the hypothesis that sex differences in LH-a historical signature of sexual selection-are key in shaping trait responses to novel selection.

Genetic approaches in comparative and evolutionary physiology

PubMed Central

Bridgham, Jamie T.; Kelly, Scott A.; Garland, Theodore

2015-01-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

Genetic approaches in comparative and evolutionary physiology.

PubMed

Storz, Jay F; Bridgham, Jamie T; Kelly, Scott A; Garland, Theodore

2015-08-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. Copyright © 2015 the American Physiological Society.

Radiative transport produced by oblique illumination of turbid media with collimated beams

NASA Astrophysics Data System (ADS)

Gardner, Adam R.; Kim, Arnold D.; Venugopalan, Vasan

2013-06-01

We examine the general problem of light transport initiated by oblique illumination of a turbid medium with a collimated beam. This situation has direct relevance to the analysis of cloudy atmospheres, terrestrial surfaces, soft condensed matter, and biological tissues. We introduce a solution approach to the equation of radiative transfer that governs this problem, and develop a comprehensive spherical harmonics expansion method utilizing Fourier decomposition (SHEFN). The SHEFN approach enables the solution of problems lacking azimuthal symmetry and provides both the spatial and directional dependence of the radiance. We also introduce the method of sequential-order smoothing that enables the calculation of accurate solutions from the results of two sequential low-order approximations. We apply the SHEFN approach to determine the spatial and angular dependence of both internal and boundary radiances from strongly and weakly scattering turbid media. These solutions are validated using more costly Monte Carlo simulations and reveal important insights regarding the evolution of the radiant field generated by oblique collimated beams spanning ballistic and diffusely scattering regimes.

Active magnetic force microscopy of Sr-ferrite magnet by stimulating magnetization under an AC magnetic field: Direct observation of reversible and irreversible magnetization processes

NASA Astrophysics Data System (ADS)

Cao, Yongze; Kumar, Pawan; Zhao, Yue; Yoshimura, Satoru; Saito, Hitoshi

2018-05-01

Understanding the dynamic magnetization process of magnetic materials is crucial to improving their fundamental properties and technological applications. Here, we propose active magnetic force microscopy for observing reversible and irreversible magnetization processes by stimulating magnetization with an AC magnetic field based on alternating magnetic force microscopy with a sensitive superparamagnetic tip. This approach simultaneously measures sample's DC and AC magnetic fields. We used this microscopy approach to an anisotropic Sr-ferrite (SrF) sintered magnet. This is a single domain type magnet where magnetization mainly changes via magnetic rotation. The proposed method can directly observe the reversible and irreversible magnetization processes of SrF and clearly reveal magnetic domain evolution of SrF (without stimulating magnetization—stimulating reversible magnetization—stimulating irreversible magnetization switching) by slowly increasing the amplitude of the external AC magnetic field. This microscopy approach can evaluate magnetic inhomogeneity and explain the local magnetic process within the permanent magnet.

Temporal slow-growth formulation for direct numerical simulation of compressible wall-bounded flows

NASA Astrophysics Data System (ADS)

Topalian, Victor; Oliver, Todd A.; Ulerich, Rhys; Moser, Robert D.

2017-08-01

A slow-growth formulation for DNS of wall-bounded turbulent flow is developed and demonstrated to enable extension of slow-growth modeling concepts to wall-bounded flows with complex physics. As in previous slow-growth approaches, the formulation assumes scale separation between the fast scales of turbulence and the slow evolution of statistics such as the mean flow. This separation enables the development of approaches where the fast scales of turbulence are directly simulated while the forcing provided by the slow evolution is modeled. The resulting model admits periodic boundary conditions in the streamwise direction, which avoids the need for extremely long domains and complex inflow conditions that typically accompany spatially developing simulations. Further, it enables the use of efficient Fourier numerics. Unlike previous approaches [Guarini, Moser, Shariff, and Wray, J. Fluid Mech. 414, 1 (2000), 10.1017/S0022112000008466; Maeder, Adams, and Kleiser, J. Fluid Mech. 429, 187 (2001), 10.1017/S0022112000002718; Spalart, J. Fluid Mech. 187, 61 (1988), 10.1017/S0022112088000345], the present approach is based on a temporally evolving boundary layer and is specifically tailored to give results for calibration and validation of Reynolds-averaged Navier-Stokes (RANS) turbulence models. The use of a temporal homogenization simplifies the modeling, enabling straightforward extension to flows with complicating features, including cold and blowing walls. To generate data useful for calibration and validation of RANS models, special care is taken to ensure that the mean slow-growth forcing is closed in terms of the mean and other quantities that appear in standard RANS models, ensuring that there is no confounding between typical RANS closures and additional closures required for the slow-growth problem. The performance of the method is demonstrated on two problems: an essentially incompressible, zero-pressure-gradient boundary layer and a transonic boundary layer over a cooled, transpiring wall. The results show that the approach produces flows that are qualitatively similar to other slow-growth methods as well as spatially developing simulations and that the method can be a useful tool in investigating wall-bounded flows with complex physics.

Beam width evolution of astigmatic hollow Gaussian beams in highly nonlocal nonlinear media

NASA Astrophysics Data System (ADS)

Yang, Zhen-Feng; Jiang, Xue-Song; Yang, Zhen-Jun; Li, Jian-Xing; Zhang, Shu-Min

We investigate the beam width evolution of astigmatic hollow Gaussian beams propagating in highly nonlocal nonlinear media. The input-power-induced different evolutions of the beam width are illustrated: (i) the beam widths in two transverse directions are compressed or broadened at the same time; (ii) the beam width in one transverse direction keeps invariant, and the other is compressed or broadened; (iii) furthermore, the beam width in one transverse direction is compressed, whereas it in the other transverse direction is broadened.

Analytical approach to Eigen-emittance evolution in storage rings

NASA Astrophysics Data System (ADS)

Nash, Boaz

This dissertation develops the subject of beam evolution in storage rings with nearly uncoupled symplectic linear dynamics. Linear coupling and dissipative/diffusive processes are treated perturbatively. The beam distribution is assumed Gaussian and a function of the invariants. The development requires two pieces: the global invariants and the local stochastic processes which change the emittances, or averages of the invariants. A map based perturbation theory is described, providing explicit expressions for the invariants near each linear resonance, where small perturbations can have a large effect. Emittance evolution is determined by the damping and diffusion coefficients. The discussion is divided into the cases of uniform and non-uniform stochasticity, synchrotron radiation an example of the former and intrabeam scattering the latter. For the uniform case, the beam dynamics is captured by a global diffusion coefficent and damping decrement for each eigen-invariant. Explicit expressions for these quantities near coupling resonances are given. In many cases, they are simply related to the uncoupled values. Near a sum resonance, it is found that one of the damping decrements becomes negative, indicating an anti-damping instability. The formalism is applied to a number of examples, including synchrobetatron coupling caused by a crab cavity, a case of current interest where there is concern about operation near half integer betatron tune. In the non-uniform case, the moment evolution is computed directly, which is illustrated through the example of intrabeam scattering. Our approach to intrabeam scattering damping and diffusion has the advantage of not requiring a loosely-defined Coulomb Logarithm. It is found that in some situations there is a small difference between our results and the standard approaches such as Bjorken-Mtingwa, which is illustrated by comparison of the two approaches and with a measurement of Au evolution in RHIC. Finally, in combining IBS with the global invariants some general statements about IBS equilibrium can be made. Specifically, it is emphasized that no such equilibrium is possible in a non-smooth lattice, even below transition. Near enough to a synchrobetatron coupling resonance, it is found that even for a smooth ring, no IBS equilibrium occurs.

Improving care and wellness in bipolar disorder: origins, evolution and future directions of a collaborative knowledge exchange network

PubMed Central

2012-01-01

The Collaborative RESearch team to study psychosocial factors in bipolar disorder (CREST.BD) is a multidisciplinary, cross-sectoral network dedicated to both fundamental research and knowledge exchange on bipolar disorder (BD). The core mission of the network is to advance the science and understanding of psychological and social issues associated with BD, improve the care and wellness of people living with BD, and strengthen services and supports for these individuals. CREST.BD bridges traditional and newer research approaches, particularly embracing community-based participatory research (CBPR) methods. Membership of CREST is broad, including academic researchers, people with BD, their family members and supports, and a variety of health care providers. Here, we describe the origins, evolution, approach to planning and evaluation and future vision for our network within the landscape of CBPR and integrated knowledge translation (KT), and explore the keys and challenges to success we have encountered working within this framework. PMID:22963889

The Evolution of Kidney Transplantation Surgery into the Robotic Era and it prospects for obese recipients.

PubMed

Hameed, Ahmer M; Yao, Jinna; Allen, Richard D M; Hawthorne, Wayne J; Pleass, Henry C; Lau, Howard

2018-06-18

Robotic-assisted kidney transplantation (RAKT) represents the most recent innovation in the evolution of kidney transplantation surgery. Vascular techniques enabling kidney transplantation have existed since the early 20 century and contributed to the first successful open kidney transplant procedure in 1954. Technical advances have since facilitated minimally invasive laparoscopic and robotic techniques in live-donor surgery, and subsequently for the recipient procedure. This review follows the development of surgical techniques for kidney transplantation, with a special focus on the advent of robotic-assisted transplantation because of its potential to facilitate transplantation of those deemed previously too obese to transplant by standard means. The different techniques, indications, advantages, disadvantages, and future directions of this approach will be explored in detail. Robot-assisted kidney transplantation may become the preferred means of transplanting morbidly obese recipients, although its availability to such recipients remains extremely limited and strategies targeting weight loss pretransplantation should never be abandoned in favor of a 'RAKT-first' approach.

From Astrochemistry to prebiotic chemistry? An hypothetical approach toward Astrobiology

NASA Astrophysics Data System (ADS)

Le Sergeant d'Hendecourt, L.; Danger, G.

2012-12-01

We present in this paper a general perspective about the evolution of molecular complexity, as observed from an astrophysicist point of view and its possible relation to the problem of the origin of life on Earth. Based on the cosmic abundances of the elements and the molecular composition of our life, we propose that life cannot really be based on other elements. We discuss where the necessary molecular complexity is built-up in astrophysical environments, actually within inter/circumstellar solid state materials known as ``grains''. Considerations based on non-directed laboratory experiments, that must be further extended in the prebiotic domain, lead to the hypothesis that if the chemistry at the origin of life may indeed be a rather universal and deterministic phenomenon, once molecular complexity is installed, the chemical evolution that generated the first prebiotic reactions that involve autoreplication must be treated in a systemic approach because of the strong contingency imposed by the complex local environment(s) and associated processes in which these chemical systems have evolved.

Towards understanding turbulent scalar mixing

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.

1992-01-01

In an effort towards understanding turbulent scalar mixing, we study the effect of molecular mixing, first in isolation and then by accounting for the effects of the velocity field. The chief motivation for this approach stems from the strong resemblance of the scalar probability density function (PDF) obtained from the scalar field evolving from the heat conduction equation that arises in a turbulent velocity field. However, the evolution of the scalar dissipation is different for the two cases. We attempt to account for these differences, which are due to the velocity field, using a Lagrangian frame analysis. After establishing the usefulness of this approach, we use the heat-conduction simulations (HCS), in lieu of the more expensive direct numerical simulations (DNS), to study many of the less understood aspects of turbulent mixing. Comparison between the HCS data and available models are made whenever possible. It is established that the beta PDF characterizes the evolution of the scalar PDF during mixing from all types of non-premixed initial conditions.

EVOLUTION OF DIVERGENT FEMALE MATING PREFERENCE IN RESPONSE TO EXPERIMENTAL SEXUAL SELECTION

PubMed Central

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-01-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. PMID:24931497

Simple versus complex models of trait evolution and stasis as a response to environmental change

NASA Astrophysics Data System (ADS)

Hunt, Gene; Hopkins, Melanie J.; Lidgard, Scott

2015-04-01

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

The sources of adaptive variation

PubMed Central

2017-01-01

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. PMID:28566483

The sources of adaptive variation.

PubMed

Charlesworth, Deborah; Barton, Nicholas H; Charlesworth, Brian

2017-05-31

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. © 2017 The Author(s).

Evolving a Behavioral Repertoire for a Walking Robot.

PubMed

Cully, A; Mouret, J-B

2016-01-01

Numerous algorithms have been proposed to allow legged robots to learn to walk. However, most of these algorithms are devised to learn walking in a straight line, which is not sufficient to accomplish any real-world mission. Here we introduce the Transferability-based Behavioral Repertoire Evolution algorithm (TBR-Evolution), a novel evolutionary algorithm that simultaneously discovers several hundreds of simple walking controllers, one for each possible direction. By taking advantage of solutions that are usually discarded by evolutionary processes, TBR-Evolution is substantially faster than independently evolving each controller. Our technique relies on two methods: (1) novelty search with local competition, which searches for both high-performing and diverse solutions, and (2) the transferability approach, which combines simulations and real tests to evolve controllers for a physical robot. We evaluate this new technique on a hexapod robot. Results show that with only a few dozen short experiments performed on the robot, the algorithm learns a repertoire of controllers that allows the robot to reach every point in its reachable space. Overall, TBR-Evolution introduced a new kind of learning algorithm that simultaneously optimizes all the achievable behaviors of a robot.

In-vitro engineering of novel bioactivity in the natural enzymes

NASA Astrophysics Data System (ADS)

Tiwari, Vishvanath

2016-10-01

Enzymes catalyze various biochemical functions with high efficiency and specificity. In-vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing and structure-based designing using chemical modifications. Similarly, combined computational and in-vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme. DNA shuffling, error prone PCR and staggered extension process are used to artificially redesign active site of enzyme, which can alter its efficiency and specificity. Modifications of the enzyme can lead to the discovery of new path of molecular evolution, designing of efficient enzymes, locating active sites and crucial residues, shift in substrate and cofactor specificity. The methods and thermodynamics of in-vitro designing of the enzyme are also discussed. Similarly, engineered thermophilic and psychrophilic enzymes attain substrate specificity and activity of mesophilic enzymes that may also be beneficial for industry and therapeutics.

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor

PubMed Central

2015-01-01

Background Multiscale approaches for integrating submodels of various levels of biological organization into a single model became the major tool of systems biology. In this paper, we have constructed and simulated a set of multiscale models of spatially distributed microbial communities and study an influence of unevenly distributed environmental factors on the genetic diversity and evolution of the community members. Results Haploid Evolutionary Constructor software http://evol-constructor.bionet.nsc.ru/ was expanded by adding the tool for the spatial modeling of a microbial community (1D, 2D and 3D versions). A set of the models of spatially distributed communities was built to demonstrate that the spatial distribution of cells affects both intensity of selection and evolution rate. Conclusion In spatially heterogeneous communities, the change in the direction of the environmental flow might be reflected in local irregular population dynamics, while the genetic structure of populations (frequencies of the alleles) remains stable. Furthermore, in spatially heterogeneous communities, the chemotaxis might dramatically affect the evolution of community members. PMID:25708911

Optimizing the deposition of hydrogen evolution sites on suspended semiconductor particles using on-line photocatalytic reforming of aqueous methanol solutions.

PubMed

Busser, G Wilma; Mei, Bastian; Muhler, Martin

2012-11-01

The deposition of hydrogen evolution sites on photocatalysts is a crucial step in the multistep process of synthesizing a catalyst that is active for overall photocatalytic water splitting. An alternative approach to conventional photodeposition was developed, applying the photocatalytic reforming of aqueous methanol solutions to deposit metal particles on semiconductor materials such as Ga₂O₃ and (Ga₀.₆ Zn₀.₄)(N₀.₆O₀.₄). The method allows optimizing the loading of the co-catalysts based on the stepwise addition of their precursors and the continuous online monitoring of the evolved hydrogen. Moreover, a synergetic effect between different co-catalysts can be directly established. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion.

PubMed

Wang, Peng; Chang, Angela Y; Novosad, Valentyn; Chupin, Vladimir V; Schaller, Richard D; Rozhkova, Elena A

2017-07-25

We report on an entirely man-made nano-bio architecture fabricated through noncovalent assembly of a cell-free expressed transmembrane proton pump and TiO 2 semiconductor nanoparticles as an efficient nanophotocatalyst for H 2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H 2 (μmol protein) -1 h -1 and 17.74 mmol of H 2 (μmol protein) -1 h -1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allow for systemic manipulation at the nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.

The Astrophysics of Merging Black Holes

NASA Technical Reports Server (NTRS)

Schnittman, Jeremy D.

2011-01-01

When two supermassive black holes (SMBHs) approach within 1-10 mpc, gravitational wave (GW) losses begin to dominate the evolution of the binary, pushing the system to merge in a relatively small time. During this final inspiral regime, the system will emit copious energy in GWs, which should be directly detectable by pulsar timing arrays and space-based interferometers. At the same time, any gas or stars in the immediate vicinity of the merging 5MBHs can get heated and produce bright electromagnetic (EM) counterparts to the GW signals. We present here a number of possible mechanisms by which simultaneous EM and GW signals will yield valuable new information about galaxy evolution, accretion disk dynamics, and fundamental physics in the most extreme gravitational fields.

Why Do Sex Chromosomes Stop Recombining?

PubMed

Ponnikas, Suvi; Sigeman, Hanna; Abbott, Jessica K; Hansson, Bengt

2018-04-28

It is commonly assumed that sex chromosomes evolve recombination suppression because selection favours linkage between sex-determining and sexually antagonistic genes. However, although the role of sexual antagonism during sex chromosome evolution has attained strong support from theory, experimental and observational evidence is rare or equivocal. Here, we highlight alternative, often neglected, hypotheses for recombination suppression on sex chromosomes, which invoke meiotic drive, heterozygote advantage, and genetic drift, respectively. We contrast the hypotheses, the situations when they are likely to be of importance, and outline why it is surprisingly difficult to test them. Lastly, we discuss future research directions (including modelling, population genomics, comparative approaches, and experiments) to disentangle the different hypotheses of sex chromosome evolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electromagnetic Signatures of SMBH Coalescence

NASA Technical Reports Server (NTRS)

Schnittman, Jeremy

2012-01-01

When two supermassive black holes (SMBHs) approach within 1-10 mpc, gravitational wave (GW) losses begin to dominate the evolution of the binary, pushing the system to merge in a relatively small time. During this final inspiral regime, the system will emit copious energy in GWs, which should be directly detectable by pulsar timing arrays and space-based interferometers. At the same time, any gas or stars in the immediate vicinity of the merging 5MBHs can get heated and produce bright electromagnetic (EM) counterparts to the GW signals. We present here a number of possible mechanisms by which simultaneous EM and GW signals will yield valuable new information about galaxy evolution, accretion disk dynamics, and fundamental physics in the most extreme gravitational fields.

Black Hole Coalescence: The Gravitational Wave Driven Phase

NASA Technical Reports Server (NTRS)

Schnittman, Jeremy D.

2011-01-01

When two supermassive black holes (SMBHS) approach within 1-10 mpc, gravitational wave (GW) losses begin to dominate the evolution of the binary, pushing the system to merge in a relatively small time. During this final inspiral regime, the system will emit copious energy in GWs, which should be directly detectable by pulsar timing arrays and space-based interferometers. At the same time, any gas or stars in the immediate vicinity of the merging 5MBHs can get heated and produce bright electromagnetic (EM) counterparts to the GW signals. We present here a number of possible mechanisms by which simultaneous EM and GW signals will yield valuable new information about galaxy evolution, accretion disk dynamics, and fundamental physics in the most extreme gravitational fields.

Enzyme catalysis: Evolution made easy

NASA Astrophysics Data System (ADS)

Wee, Eugene J. H.; Trau, Matt

2014-09-01

Directed evolution is a powerful tool for the development of improved enzyme catalysts. Now, a method that enables an enzyme, its encoding DNA and a fluorescent reaction product to be encapsulated in a gel bead enables the application of directed evolution in an ultra-high-throughput format.

Networks of lexical borrowing and lateral gene transfer in language and genome evolution

PubMed Central

List, Johann-Mattis; Nelson-Sathi, Shijulal; Geisler, Hans; Martin, William

2014-01-01

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. PMID:24375688

Directed evolution of enzymes using microfluidic chips

NASA Astrophysics Data System (ADS)

Pilát, Zdeněk.; Ježek, Jan; Šmatlo, Filip; Kaůka, Jan; Zemánek, Pavel

2016-12-01

Enzymes are highly versatile and ubiquitous biological catalysts. They can greatly accelerate large variety of reactions, while ensuring appropriate catalytic activity and high selectivity. These properties make enzymes attractive biocatalysts for a wide range of industrial and biomedical applications. Over the last two decades, directed evolution of enzymes has transformed the field of protein engineering. We have devised microfluidic systems for directed evolution of haloalkane dehalogenases in emulsion droplets. In such a device, individual bacterial cells producing mutated variants of the same enzyme are encapsulated in microdroplets and supplied with a substrate. The conversion of a substrate by the enzyme produced by a single bacterium changes the pH in the droplet which is signalized by pH dependent fluorescence probe. The droplets with the highest enzymatic activity can be separated directly on the chip by dielectrophoresis and the resultant cell lineage can be used for enzyme production or for further rounds of directed evolution. This platform is applicable for fast screening of large libraries in directed evolution experiments requiring mutagenesis at multiple sites of a protein structure.

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression, direct costs, mating constraints, and polyandry as a threshold trait

PubMed Central

Duthie, A. Bradley; Bocedi, Greta; Reid, Jane M.

2016-01-01

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual‐based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment. PMID:27464756

Molecular Phylogeny of Heme Peroxidases

NASA Astrophysics Data System (ADS)

Zámocký, Marcel; Obinger, Christian

All currently available gene sequences of heme peroxidases can be phylogenetically divided in two superfamilies and three families. In this chapter, the phylogenetics and genomic distribution of each group are presented. Within the peroxidase-cyclooxygenase superfamily, the main evolutionary direction developed peroxidatic heme proteins involved in the innate immune defense system and in biosynthesis of (iodinated) hormones. The peroxidase-catalase superfamily is widely spread mainly among bacteria, fungi, and plants, and particularly in Class I led to the evolution of bifunctional catalase-peroxidases. Its numerous fungal representatives of Class II are involved in carbon recycling via lignin degradation, whereas Class III secretory peroxidases from algae and plants are included in various forms of secondary metabolism. The family of di-heme peroxidases are predominantly bacteria-inducible enzymes; however, a few corresponding genes were also detected in archaeal genomes. Four subfamilies of dyp-type peroxidases capable of degradation of various xenobiotics are abundant mainly among bacteria and fungi. Heme-haloperoxidase genes are widely spread among sac and club fungi, but corresponding genes were recently found also among oomycetes. All described families herein represent heme peroxidases of broad diversity in structure and function. Our accumulating knowledge about the evolution of various enzymatic functions and physiological roles can be exploited in future directed evolution approaches for engineering peroxidase genes de novo for various demands.

Modeling the evolution of lithium-ion particle contact distributions using a fabric tensor approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stershic, A. J.; Simunovic, S.; Nanda, J.

2015-08-25

Electrode microstructure and processing can strongly influence lithium-ion battery performance such as capacity retention, power, and rate. Battery electrodes are multi-phase composite structures wherein conductive diluents and binder bond active material to a current collector. The structure and response of this composite network during repeated electrochemical cycling directly affects battery performance characteristics. We propose the fabric tensor formalism for describing the structure and evolution of the electrode microstructure. Fabric tensors are directional measures of particulate assemblies based on inter-particle connectivity, relating to the structural and transport properties of the electrode. Fabric tensor analysis is applied to experimental data-sets for positivemore » electrode made of lithium nickel manganese cobalt oxide, captured by X-ray tomography for several compositions and consolidation pressures. We show that fabric tensors capture the evolution of inter-particle contact distribution and are therefore good measures for the internal state of and electronic transport within the electrode. The fabric tensor analysis is also applied to Discrete Element Method (DEM) simulations of electrode microstructures using spherical particles with size distributions from the tomography. Furthermore, these results do not follow the experimental trends, which indicates that the particle size distribution alone is not a sufficient measure for the electrode microstructures in DEM simulations.« less

Evolution of the microstructure during the process of consolidation and bonding in soft granular solids.

PubMed

Yohannes, B; Gonzalez, M; Abebe, A; Sprockel, O; Nikfar, F; Kiang, S; Cuitiño, A M

2016-04-30

The evolution of microstructure during powder compaction process was investigated using a discrete particle modeling, which accounts for particle size distribution and material properties, such as plasticity, elasticity, and inter-particle bonding. The material properties were calibrated based on powder compaction experiments and validated based on tensile strength test experiments for lactose monohydrate and microcrystalline cellulose, which are commonly used excipient in pharmaceutical industry. The probability distribution function and the orientation of contact forces were used to study the evolution of the microstructure during the application of compaction pressure, unloading, and ejection of the compact from the die. The probability distribution function reveals that the compression contact forces increase as the compaction force increases (or the relative density increases), while the maximum value of the tensile contact forces remains the same. During unloading of the compaction pressure, the distribution approaches a normal distribution with a mean value of zero. As the contact forces evolve, the anisotropy of the powder bed also changes. Particularly, during loading, the compression contact forces are aligned along the direction of the compaction pressure, whereas the tensile contact forces are oriented perpendicular to direction of the compaction pressure. After ejection, the contact forces become isotropic. Copyright © 2016 Elsevier B.V. All rights reserved.

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

PubMed Central

Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C.; Bell, Thomas

2015-01-01

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. PMID:25833854

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities.

PubMed

Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C; Bell, Thomas

2015-05-07

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Secondary phloem diversity and evolution in Bignonieae (Bignoniaceae)

PubMed Central

Pace, Marcelo R.; Alcantara, Suzana; Lohmann, Lúcia G.; Angyalossy, Veronica

2015-01-01

Background and Aims Phloem evolution has been explored in the literature across very broad scales, either for vascular plants as a whole or for major plant groups, such as the monocotyledons or the former dicotyledons. However, it has never been examined in a way that would elucidate evolutionary shifts leading to the diversification of phloem in single lineages. Therefore, the present study explores in detail the patterns of phloem evolution in the tribe Bignonieae (Bignoniaceae). This group represents a particularly good model for phloem studies since it is known to have a very conspicuous and diverse phloem. Methods A total of 19 phloem characters were coded in 56 species from all 21 genera currently recognized in the tribe Bignonieae, accounting for phloem wedge growth and for all the anatomical cell diversity encountered in the phloem. Phloem evolution was explored by reconstructing ancestral character states using maximum-likelihood assumptions with a time-calibrated molecular phylogeny for the group. Directionality and the effect of phylogenetic transformations in the current variation of quantitative traits and evolutionary correlations of selected discrete phloem traits were also tested under a maximum-likelihood approach. Key Results Individual phloem features are quite diverse in the tribe, but generally conserved within smaller clades. Contrasting phloem patterns were found when comparing major groups, with certain lineages having the phloem marked by a background of phloem fibres where all other cells are embedded, tangentially arranged sieve tubes and sieve-tubecentric parenchyma. In contrast, other lineages exhibited a scarcely fibrous phloem, regularly stratified phloem, sieve tube elements in radial or diffuse arrangement, and diffuse parenchyma. We found signals of directional evolution in fibre abundance and number of sieve areas, which increased in the ‘Fridericia and allies extended clade’ and decreased in the ‘Multiples of four extended clade’, resulting in no signal of directionality when the whole Bignonieae was considered. In contrast, no indication of directional evolution was found for the axial parenchyma, either in single clades within Bignonieae or in the entire tribe. Positive correlation was found between sieve element length and both sieve plate type and the presence of a storied structure. Correlated evolution was also found between fibre abundance and several traits, such as sieve tube arrangement, sieve plate type, parenchyma arrangement, ray lignification and number of companion cells. Conclusions The secondary phloem of Bignonieae is extremely diverse, with sister lineages exhibiting distinct phloem anatomies derived from contrasting patterns of evolution in fibre abundance. Fibre abundance in the tribe has diversified in correlation with sieve tube arrangement, sieve tube morphology, number of companion cells and parenchyma type. The results challenge long-standing hypotheses regarding general trends in cell abundance and morphological cell evolution within the phloem, and demonstrate the need to expand studies in phloem anatomy both at a narrow taxonomic scale and at a broad one, such as to families and orders. PMID:26311709

Remote monitoring of environmental particulate pollution - A problem in inversion of first-kind integral equations

NASA Technical Reports Server (NTRS)

Fymat, A. L.

1975-01-01

The determination of the microstructure, chemical nature, and dynamical evolution of scattering particulates in the atmosphere is considered. A description is given of indirect sampling techniques which can circumvent most of the difficulties associated with direct sampling techniques, taking into account methods based on scattering, extinction, and diffraction of an incident light beam. Approaches for reconstructing the particulate size distribution from the direct and the scattered radiation are discussed. A new method is proposed for determining the chemical composition of the particulates and attention is given to the relevance of methods of solution involving first kind Fredholm integral equations.

Sex in a test tube: testing the benefits of in vitro recombination.

PubMed

Pesce, Diego; Lehman, Niles; de Visser, J Arjan G M

2016-10-19

The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Linearized Flux Evolution (LiFE): A technique for rapidly adapting fluxes from full-physics radiative transfer models

NASA Astrophysics Data System (ADS)

Robinson, Tyler D.; Crisp, David

2018-05-01

Solar and thermal radiation are critical aspects of planetary climate, with gradients in radiative energy fluxes driving heating and cooling. Climate models require that radiative transfer tools be versatile, computationally efficient, and accurate. Here, we describe a technique that uses an accurate full-physics radiative transfer model to generate a set of atmospheric radiative quantities which can be used to linearly adapt radiative flux profiles to changes in the atmospheric and surface state-the Linearized Flux Evolution (LiFE) approach. These radiative quantities describe how each model layer in a plane-parallel atmosphere reflects and transmits light, as well as how the layer generates diffuse radiation by thermal emission and by scattering light from the direct solar beam. By computing derivatives of these layer radiative properties with respect to dynamic elements of the atmospheric state, we can then efficiently adapt the flux profiles computed by the full-physics model to new atmospheric states. We validate the LiFE approach, and then apply this approach to Mars, Earth, and Venus, demonstrating the information contained in the layer radiative properties and their derivatives, as well as how the LiFE approach can be used to determine the thermal structure of radiative and radiative-convective equilibrium states in one-dimensional atmospheric models.

Generative inference for cultural evolution.

PubMed

Kandler, Anne; Powell, Adam

2018-04-05

One of the major challenges in cultural evolution is to understand why and how various forms of social learning are used in human populations, both now and in the past. To date, much of the theoretical work on social learning has been done in isolation of data, and consequently many insights focus on revealing the learning processes or the distributions of cultural variants that are expected to have evolved in human populations. In population genetics, recent methodological advances have allowed a greater understanding of the explicit demographic and/or selection mechanisms that underlie observed allele frequency distributions across the globe, and their change through time. In particular, generative frameworks-often using coalescent-based simulation coupled with approximate Bayesian computation (ABC)-have provided robust inferences on the human past, with no reliance on a priori assumptions of equilibrium. Here, we demonstrate the applicability and utility of generative inference approaches to the field of cultural evolution. The framework advocated here uses observed population-level frequency data directly to establish the likely presence or absence of particular hypothesized learning strategies. In this context, we discuss the problem of equifinality and argue that, in the light of sparse cultural data and the multiplicity of possible social learning processes, the exclusion of those processes inconsistent with the observed data might be the most instructive outcome. Finally, we summarize the findings of generative inference approaches applied to a number of case studies.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Computer Aided Enzyme Design and Catalytic Concepts

PubMed Central

Frushicheva, Maria P.; Mills, Matthew J. L.; Schopf, Patrick; Singh, Manoj K.; Warshel, Arieh

2014-01-01

Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration of effective rational enzyme design. Here we make the point that the main current advances in enzyme design are basically advances in directed evolution and that computer aided enzyme design must involve approaches that can reproduce catalysis in well-defined test cases. Such an approach is provided by the empirical valence bond method. PMID:24814389

A Peridynamic Approach for Nanoscratch Simulation of the Cement Mortar

NASA Astrophysics Data System (ADS)

Zhao, Jingjing; Zhang, Qing; Lu, Guangda; Chen, Depeng

2018-03-01

The present study develops a peridynamic approach for simulating the nanoscratch procedure on the cement mortar interface. In this approach, the cement and sand are considered as discrete particles with certain mechanical properties on the nanoscale. Besides, the interaction force functions for different components in the interface are represented by combining the van der Waals force and the peridynamic force. The nanoscratch procedures with the indenter moving along certain direction either parallel or perpendicular to the interface are simulated in this paper. The simulation results show the damage evolution processes and the final damage distributions of the cement mortar under different scratching speed and depth of the indenter, indicating that the interface between cement and sand is a weak area.

Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: Evolution across a continuum of indicator mechanisms.

PubMed

Dhole, Sumit; Stern, Caitlin A; Servedio, Maria R

2018-04-01

The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality influences the evolution of female choosiness and male displays. We use a continuum framework that incorporates indicator mechanisms that are traditionally modeled separately. Counter to intuition, we find that intermediate levels of direct detection of male quality can facilitate, rather than impede, the evolution of female choosiness and male displays in broad regions of this continuum. We examine how this evolution is driven by selective forces on genetic quality and on the display, and find that direct detection of male quality results in stronger indirect selection favoring female choosiness. Our results imply that displays maybe more likely to evolve when female choosiness has already evolved to discriminate perceptible forms of male quality. They also highlight the importance of considering general female choosiness, as well as preference, in studies of "good genes." © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

A new kernel-based fuzzy level set method for automated segmentation of medical images in the presence of intensity inhomogeneity.

PubMed

Rastgarpour, Maryam; Shanbehzadeh, Jamshid

2014-01-01

Researchers recently apply an integrative approach to automate medical image segmentation for benefiting available methods and eliminating their disadvantages. Intensity inhomogeneity is a challenging and open problem in this area, which has received less attention by this approach. It has considerable effects on segmentation accuracy. This paper proposes a new kernel-based fuzzy level set algorithm by an integrative approach to deal with this problem. It can directly evolve from the initial level set obtained by Gaussian Kernel-Based Fuzzy C-Means (GKFCM). The controlling parameters of level set evolution are also estimated from the results of GKFCM. Moreover the proposed algorithm is enhanced with locally regularized evolution based on an image model that describes the composition of real-world images, in which intensity inhomogeneity is assumed as a component of an image. Such improvements make level set manipulation easier and lead to more robust segmentation in intensity inhomogeneity. The proposed algorithm has valuable benefits including automation, invariant of intensity inhomogeneity, and high accuracy. Performance evaluation of the proposed algorithm was carried on medical images from different modalities. The results confirm its effectiveness for medical image segmentation.

Interpreting Evidence: An Approach to Teaching Human Evolution in the Classroom

ERIC Educational Resources Information Center

DeSilva, Jeremy

2004-01-01

Paleoanthropology, which is the study of human evolution through fossil records, can be used as a tool for teaching human evolution in the classrooms. An updated approach to teaching human evolution and a model for explaining what is science and how it is done, is presented.

A Successful Component Architecture for Interoperable and Evolvable Ground Data Systems

NASA Technical Reports Server (NTRS)

Smith, Danford S.; Bristow, John O.; Wilmot, Jonathan

2006-01-01

The National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) has adopted an open architecture approach for satellite control centers and is now realizing benefits beyond those originally envisioned. The Goddard Mission Services Evolution Center (GMSEC) architecture utilizes standardized interfaces and a middleware software bus to allow functional components to be easily integrated. This paper presents the GMSEC architectural goals and concepts, the capabilities enabled and the benefits realized by adopting this framework approach. NASA experiences with applying the GMSEC architecture on multiple missions are discussed. The paper concludes with a summary of lessons learned, future directions for GMSEC and the possible applications beyond NASA GSFC.

The plant perceptron connects environment to development.

PubMed

Scheres, Ben; van der Putten, Wim H

2017-03-15

Plants cope with the environment in a variety of ways, and ecological analyses attempt to capture this through life-history strategies or trait-based categorization. These approaches are limited because they treat the trade-off mechanisms that underlie plant responses as a black box. Approaches that involve the molecular or physiological analysis of plant responses to the environment have elucidated intricate connections between developmental and environmental signals, but in only a few well-studied model species. By considering diversity in the plant response to the environment as the adaptation of an information-processing network, new directions can be found for the study of life-history strategies, trade-offs and evolution in plants.

Directional Communication in Evolved Multiagent Teams

DTIC Science & Technology

2013-06-10

decentralized localization proposed by Franchi et al. [9]. Overall, the significant advantage of directional communication over non- directional...reception benefits the evolution of communicating autonomous agents because it simplifies the language required to express positional information, which...systems. This paper hypothesizes that such directional reception benefits the evolution of communicating autonomous agents because it simplifies the

Current status and future clinical directions in the prevention and treatment of relapse following hematopoietic transplantation for acute myeloid and lymphoblastic leukemia.

PubMed

Craddock, Charles; Hoelzer, Dieter; Komanduri, Krishna V

2018-05-31

In recent years we have seen a dramatic evolution of therapeutic approaches in the management of acute leukemia with hematopoietic stem cell transplantation (HCT). For both acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), alloHCT provides the best chance of long-term disease-free survival for significant subsets of patients. During this interval, we have witnessed an evolution of HCT from a therapy based on high-dose conditioning to our current understanding that its success depends both on cytoreduction and graft-versus-leukemia (GVL) effects mediated by adoptively transferred donor immune cells. Improvements in conditioning, infectious disease monitoring and management, histocompatibility testing and graft selection have successively improved outcomes, primarily due to a reduction in non-relapse mortality. Unfortunately, disease relapse remains a significant cause of treatment failure in both AML and ALL. Here, two distinguished experts, Prof. Charles Craddock and Prof. Dieter Hoelzer, reflect on the significant challenge of disease relapse following allogeneic HCT for AML and ALL, respectively. This is a review of the biology, current approaches, and future directions in the field and reflects concepts that were presented at the Third International Workshop on Biology, Prevention, and Treatment of Relapse after Stem Cell Transplantation held in Hamburg, Germany in November 2016 under the auspices of the EBMT and the ASBMT.

Self-organized behavior of modeled shoreline shapes

NASA Astrophysics Data System (ADS)

Ashton, A.; Murray, A. B.

2003-04-01

Whenever waves approach a coast and break at oblique angles, they drive a current along the shore. This current, along with wave-induced sediment suspension, transports relatively large amounts of sediment, affecting the shape and evolution of a coastline. Traditionally, researchers have assumed that alongshore sediment transport will diffuse, or smooth, bumps along a shoreline. Recent research, however, shows that when the angle between wave crests in deep water and the shoreline is sufficiently high (greater than approximately 45 degrees), a shoreline is unstable. Linear stability analysis does not predict that this instability will cause a preferred wavelength of shoreline perturbation growth or that organized patterns will emerge. However, a simple numerical model of shoreline change shows those when there is a predominance of high angle waves approaching a shoreline, finite-amplitude features will develop that interact with each other and increase in wavelength over time, translating in the direction of net alongshore sediment transport. Some of these simulated features resemble naturally occurring shoreline features, such as 'alongshore sandwaves', 'ords', 'cuspate spits', and 'cuspate forelands'. By varying two wave climate parameters, one describing the relative dominance of waves approaching at high angles and the other controlling the signs of the approach angle of incoming waves (i.e., the asymmetry of waves approaching from the right vs. the left), we investigate how the attributes of the input wave climate determine the aspect ratio and characteristic form of the simulated features. Varying these two parameters also affects the wavelength of the initially fastest growing perturbation. By tracking the average wavelength of simulated features, which increases over time for all simulations, we show that more complicated phenomena, such as rapid period doubling, can dominate simulated shoreline evolution. These rich behaviors result from large-scale emergent interactions. Although the wave distribution determines the character of shoreline features, their specific configuration and evolution is sensitively dependant on both initial conditions and the stochastic sequencing of wave approach angles.

Mandible reconstruction: History, state of the art and persistent problems.

PubMed

Ferreira, José J; Zagalo, Carlos M; Oliveira, Marta L; Correia, André M; Reis, Ana R

2015-06-01

Mandibular reconstruction has been experiencing an amazing evolution. Several different approaches are used to reconstruct this bone and therefore have a fundamental role in the recovery of oral functions. This review aims to highlight the persistent problems associated with the approaches identified, whether bone grafts or prosthetic devices are used. A brief summary of the historical evolution of the surgical procedures is presented, as well as an insight into possible future pathways. A literature review was conducted from September to December 2012 using the PubMed database. The keyword used was "mandible reconstruction." Articles published in the last three years were included as well as the relevant references from those articles and the "historical articles" were referred. This research resulted in a monograph that this article aims to summarize. Titanium plates, bone grafts, pediculate flaps, free osteomyocutaneous flaps, rapid prototyping, and tissue engineering strategies are some of the identified possibilities. The classical approaches present considerable associated morbidity donor-site-related problems. Research that results in the development of new prosthetics devices is needed. A new prosthetic approach could minimize the identified problems and offer the patients more predictable, affordable, and comfortable solutions. This review, while affirming the evolution and the good results found with the actual approaches, emphasizes the negative aspects that still subsist. Thus, it shows that mandible reconstruction is not a closed issue. On the contrary, it remains as a research field where new findings could have a direct positive impact on patients' life quality. The identification of the persistent problems reveals the characteristics to be considered in a new prosthetic device. This could overcome the current difficulties and result in more comfortable solutions. Medical teams have the responsibility to keep patients informed about the predictable problems related with each elected approach, even understanding that a perfect reconstruction is a secondary goal when compared with maintenance of life. © The International Society for Prosthetics and Orthotics 2014.

Quantum information and the problem of mechanisms of biological evolution.

PubMed

Melkikh, Alexey V

2014-01-01

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

On the Legal Issues of Teaching Evolution in Public Schools

ERIC Educational Resources Information Center

Hermann, Ronald S.

2013-01-01

In order to effectively teach evolution to all students, even those resistant to learning evolution, science teachers may question the extent to which religion can legally be discussed in the public high school science classroom. Evolution is taught from a variety of approaches, each of which has legal implications. Four approaches to teaching…

Programmed Evolution for Optimization of Orthogonal Metabolic Output in Bacteria

PubMed Central

Eckdahl, Todd T.; Campbell, A. Malcolm; Heyer, Laurie J.; Poet, Jeffrey L.; Blauch, David N.; Snyder, Nicole L.; Atchley, Dustin T.; Baker, Erich J.; Brown, Micah; Brunner, Elizabeth C.; Callen, Sean A.; Campbell, Jesse S.; Carr, Caleb J.; Carr, David R.; Chadinha, Spencer A.; Chester, Grace I.; Chester, Josh; Clarkson, Ben R.; Cochran, Kelly E.; Doherty, Shannon E.; Doyle, Catherine; Dwyer, Sarah; Edlin, Linnea M.; Evans, Rebecca A.; Fluharty, Taylor; Frederick, Janna; Galeota-Sprung, Jonah; Gammon, Betsy L.; Grieshaber, Brandon; Gronniger, Jessica; Gutteridge, Katelyn; Henningsen, Joel; Isom, Bradley; Itell, Hannah L.; Keffeler, Erica C.; Lantz, Andrew J.; Lim, Jonathan N.; McGuire, Erin P.; Moore, Alexander K.; Morton, Jerrad; Nakano, Meredith; Pearson, Sara A.; Perkins, Virginia; Parrish, Phoebe; Pierson, Claire E.; Polpityaarachchige, Sachith; Quaney, Michael J.; Slattery, Abagael; Smith, Kathryn E.; Spell, Jackson; Spencer, Morgan; Taye, Telavive; Trueblood, Kamay; Vrana, Caroline J.; Whitesides, E. Tucker

2015-01-01

Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields – evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation. PMID:25714374

Programmed evolution for optimization of orthogonal metabolic output in bacteria.

PubMed

Eckdahl, Todd T; Campbell, A Malcolm; Heyer, Laurie J; Poet, Jeffrey L; Blauch, David N; Snyder, Nicole L; Atchley, Dustin T; Baker, Erich J; Brown, Micah; Brunner, Elizabeth C; Callen, Sean A; Campbell, Jesse S; Carr, Caleb J; Carr, David R; Chadinha, Spencer A; Chester, Grace I; Chester, Josh; Clarkson, Ben R; Cochran, Kelly E; Doherty, Shannon E; Doyle, Catherine; Dwyer, Sarah; Edlin, Linnea M; Evans, Rebecca A; Fluharty, Taylor; Frederick, Janna; Galeota-Sprung, Jonah; Gammon, Betsy L; Grieshaber, Brandon; Gronniger, Jessica; Gutteridge, Katelyn; Henningsen, Joel; Isom, Bradley; Itell, Hannah L; Keffeler, Erica C; Lantz, Andrew J; Lim, Jonathan N; McGuire, Erin P; Moore, Alexander K; Morton, Jerrad; Nakano, Meredith; Pearson, Sara A; Perkins, Virginia; Parrish, Phoebe; Pierson, Claire E; Polpityaarachchige, Sachith; Quaney, Michael J; Slattery, Abagael; Smith, Kathryn E; Spell, Jackson; Spencer, Morgan; Taye, Telavive; Trueblood, Kamay; Vrana, Caroline J; Whitesides, E Tucker

2015-01-01

Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation.

On the stability of the solutions of the general problem of three bodies

NASA Technical Reports Server (NTRS)

Standish, E. M., Jr.

1976-01-01

The extent through which the initial conditions of a given three-body system may be varied without completely changing the qualitative nature of the subsequent system evolution is investigated. It is assumed that the three masses are equal, all initial velocities are zero, the first two bodies initially lie on the x-axis, and the position of the third body is confined to a specific region of space. Analysis of the system evolution for different initial positions of the third body shows that there is a whole area or 'island' in the x-y plane throughout which the initial position of the third body may be moved in a continuous fashion to produce an evolution which also changes in a continuous manner. A Monte Carlo approach is adopted to determine the full extent of this island in the general problem. It is concluded that the stability of a full solution may be directly related to the size of its island in phase space.

Evolution of synthetic signaling scaffolds by recombination of modular protein domains.

PubMed

Lai, Andicus; Sato, Paloma M; Peisajovich, Sergio G

2015-06-19

Signaling scaffolds are proteins that interact via modular domains with multiple partners, regulating signaling networks in space and time and providing an ideal platform from which to alter signaling functions. However, to better exploit scaffolds for signaling engineering, it is necessary to understand the full extent of their modularity. We used a directed evolution approach to identify, from a large library of randomly shuffled protein interaction domains, variants capable of rescuing the signaling defect of a yeast strain in which Ste5, the scaffold in the mating pathway, had been deleted. After a single round of selection, we identified multiple synthetic scaffold variants with diverse domain architectures, able to mediate mating pathway activation in a pheromone-dependent manner. The facility with which this signaling network accommodates changes in scaffold architecture suggests that the mating signaling complex does not possess a single, precisely defined geometry into which the scaffold has to fit. These relaxed geometric constraints may facilitate the evolution of signaling networks, as well as their engineering for applications in synthetic biology.

Creep-induced anisotropy in covalent adaptable network polymers.

PubMed

Hanzon, Drew W; He, Xu; Yang, Hua; Shi, Qian; Yu, Kai

2017-10-11

Anisotropic polymers with aligned macromolecule chains exhibit directional strengthening of mechanical and physical properties. However, manipulating the orientation of polymer chains in a fully cured thermoset is almost impossible due to its permanently crosslinked nature. In this paper, we demonstrate that rearrangeable networks with bond exchange reactions (BERs) can be utilized to tailor the anisotropic mechanical properties of thermosetting polymers. When a constant force is maintained at BER activated temperatures, the malleable thermoset creeps in the direction of stress, and macromolecule chains align themselves in the same direction. The aligned polymer chains result in an anisotropic network with a stiffer mechanical behavior in the direction of creep, while with a more compliant behavior in the transverse direction. The degree of network anisotropy is proportional to the amount of creep strain. A multi-length scale constitutive model is developed to study the creep-induced anisotropy of thermosetting polymers. The model connects the micro-scale BER kinetics, orientation of polymer chains, and directional mechanical properties of network polymers. Without any fitting parameters, it is able to predict the evolution of creep strain at different temperatures and anisotropic stress-strain behaviors of CANs after creep. Predictions on the chain orientation are verified by molecular dynamics (MD) simulation. Based on parametric studies, it is shown that the influences of creep time and temperature on the network anisotropy can be generalized into a single parameter, and the evolution of directional modulus follows an Arrhenius type time-temperature superposition principle (TTSP). The presented work provides a facile approach to transform isotropic thermosets into anisotropic ones using simple heating, and their directional properties can be readily tailored by the processing conditions.

The evolution of trade-offs under directional and correlational selection.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2012-08-01

Using quantitative genetic theory, we develop predictions for the evolution of trade-offs in response to directional and correlational selection. We predict that directional selection favoring an increase in one trait in a trade-off will result in change in the intercept but not the slope of the trade-off function, with the mean value of the selected trait increasing and that of the correlated trait decreasing. Natural selection will generally favor an increase in some combination of trait values, which can be represented as directional selection on an index value. Such selection induces both directional and correlational selection on the component traits. Theory predicts that selection on an index value will also change the intercept but not the slope of the trade-off function but because of correlational selection, the direction of change in component traits may be in the same or opposite directions. We test these predictions using artificial selection on the well-established trade-off between fecundity and flight capability in the cricket, Gryllus firmus and compare the empirical results with a priori predictions made using genetic parameters from a separate half-sibling experiment. Our results support the predictions and illustrate the complexity of trade-off evolution when component traits are subject to both directional and correlational selection. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)

PubMed Central

Gielen, Fabrice; Hours, Raphaelle; Emond, Stephane; Fischlechner, Martin; Schell, Ursula

2016-01-01

Ultrahigh-throughput screening, in which members of enzyme libraries compartmentalized in water-in-oil emulsion droplets are assayed, has emerged as a powerful format for directed evolution and functional metagenomics but is currently limited to fluorescence readouts. Here we describe a highly efficient microfluidic absorbance-activated droplet sorter (AADS) that extends the range of assays amenable to this approach. Using this module, microdroplets can be sorted based on absorbance readout at rates of up to 300 droplets per second (i.e., >1 million droplets per hour). To validate this device, we implemented a miniaturized coupled assay for NAD+-dependent amino acid dehydrogenases. The detection limit (10 μM in a coupled assay producing a formazan dye) enables accurate kinetic readouts sensitive enough to detect a minimum of 1,300 turnovers per enzyme molecule, expressed in a single cell, and released by lysis within a droplet. Sorting experiments showed that the AADS successfully enriched active variants up to 2,800-fold from an overwhelming majority of inactive ones at ∼100 Hz. To demonstrate the utility of this module for protein engineering, two rounds of directed evolution were performed to improve the activity of phenylalanine dehydrogenase toward its native substrate. Fourteen hits showed increased activity (improved >4.5-fold in lysate; kcat increased >2.7-fold), soluble protein expression levels (up 60%), and thermostability (Tm, 12 °C higher). The AADS module makes the most widely used optical detection format amenable to screens of unprecedented size, paving the way for the implementation of chromogenic assays in droplet microfluidics workflows. PMID:27821774

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.

PubMed

Dias, Raquel; Manny, Austin; Kolaczkowski, Oralia; Kolaczkowski, Bryan

2017-06-01

Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Coastal Foredune Evolution, Part 2: Modeling Approaches for Meso-Scale Morphologic Evolution

DTIC Science & Technology

2017-03-01

ERDC/CHL CHETN-II-57 March 2017 Approved for public release; distribution is unlimited. Coastal Foredune Evolution, Part 2: Modeling Approaches...for Meso-Scale Morphologic Evolution by Margaret L. Palmsten1, Katherine L. Brodie2, and Nicholas J. Spore2 PURPOSE: This Coastal and Hydraulics...Engineering Technical Note (CHETN) is the second of two CHETNs focused on improving technologies to forecast coastal foredune evolution. Part 1

Porphyrin-Sensitized Evolution of Hydrogen using Dawson and Keplerate Polyoxometalate Photocatalysts.

PubMed

Panagiotopoulos, Athanassios; Douvas, Antonios M; Argitis, Panagiotis; Coutsolelos, Athanassios G

2016-11-23

Hydrogen evolution using photocatalytic systems based on artificial photosynthesis is a major approach toward solar energy conversion and storage. In the polyoxometalate-based photocatalytic systems proposed in the past, middle/near UV light irradiation and noble-metal catalysts were mainly used. Although recently polyoxometalates were sensitized in visible light, photosensitizers or catalysts based on noble metals, and/or poor activity of polyoxometalates were generally obtained. Here we show the highly efficient [turnover number (TON)=215] hydrogen evolution induced by the zinc(II) mesotetrakis(N-methyl-pyridinium-4-yl)porphyrin (ZnTMPyP 4+ ) sensitization of a series of polyoxometalate catalysts (two Dawson type, P 2 Mo 18 O 62 6- and P 2 W 18 O 62 6- anions, and one Keplerate {Mo 132 } cluster) in a visible-light-driven, noble-metal-free, and fully water-soluble system. We attributed the high efficiency for hydrogen evolution to the multi-electron reduction of polyoxometalates and found that: (a) both Dawson polyoxometalates exhibit higher hydrogen evolution efficiency upon ZnTMPyP 4+ sensitization in relation to the direct photoreduction of those compounds; (b) the P 2 Mo 18 O 62 6- anion is more efficient (TON=65 vs. 38, respectively) for hydrogen evolution than the P 2 W 18 O 62 6- anion; and (c) the high nuclearity Keplerate {Mo 132 } cluster exhibits the highest efficiency (TON=215) for hydrogen evolution compared with the polyoxometalates studied. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pervasive genetic integration directs the evolution of human skull shape.

PubMed

Martínez-Abadías, Neus; Esparza, Mireia; Sjøvold, Torstein; González-José, Rolando; Santos, Mauro; Hernández, Miquel; Klingenberg, Christian Peter

2012-04-01

It has long been unclear whether the different derived cranial traits of modern humans evolved independently in response to separate selection pressures or whether they resulted from the inherent morphological integration throughout the skull. In a novel approach to this issue, we combine evolutionary quantitative genetics and geometric morphometrics to analyze genetic and phenotypic integration in human skull shape. We measured human skulls in the ossuary of Hallstatt (Austria), which offer a unique opportunity because they are associated with genealogical data. Our results indicate pronounced covariation of traits throughout the skull. Separate simulations of selection for localized shape changes corresponding to some of the principal derived characters of modern human skulls produced outcomes that were similar to each other and involved a joint response in all of these traits. The data for both genetic and phenotypic shape variation were not consistent with the hypothesis that the face, cranial base, and cranial vault are completely independent modules but relatively strongly integrated structures. These results indicate pervasive integration in the human skull and suggest a reinterpretation of the selective scenario for human evolution where the origin of any one of the derived characters may have facilitated the evolution of the others. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Evolution of music score watermarking algorithm

NASA Astrophysics Data System (ADS)

Busch, Christoph; Nesi, Paolo; Schmucker, Martin; Spinu, Marius B.

2002-04-01

Content protection for multimedia data is widely recognized especially for data types that are frequently distributed, sold or shared using the Internet. Particularly music industry dealing with audio files realized the necessity for content protection. Distribution of music sheets will face the same problems. Digital watermarking techniques provide a certain level of protection for these music sheets. But classical raster-oriented watermarking algorithms for images suffer several drawbacks when directly applied to image representations of music sheets. Therefore new solutions have been developed which are designed regarding the content of the music sheets. In Comparison to other media types the development for watermarking of music scores is a rather young art. The paper reviews the evolution of the early approaches and describes the current state of the art in the field.

Models of Protocellular Structure, Function and Evolution

NASA Technical Reports Server (NTRS)

New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

Maternal Lipid Provisioning Mirrors Evolution of Reproductive Strategies in Direct-Developing Whelks.

PubMed

Carrasco, Sergio A; Phillips, Nicole E; Sewell, Mary A

2016-06-01

The energetic input that offspring receive from their mothers is a well-studied maternal effect that can influence the evolution of life histories. Using the offspring of three sympatric whelks: Cominella virgata (one embryo per capsule); Cominella maculosa (multiple embryos per capsule); and Haustrum scobina (multiple embryos per capsule and nurse-embryo consumption), we examined how contrasting reproductive strategies mediate inter- and intraspecific differences in hatchling provisioning. Total lipid content (as measured in μg hatchling(-1) ± SE) was unrelated to size among the 3 species; the hatchlings of H. scobina were the smallest but had the highest lipid content (33.8 ± 8.1 μg hatchling(-1)). In offspring of C. maculosa, lipid content was 6.6 ± 0.4 μg hatchling(-1), and in offspring of C. virgata, it was 21.7 ± 3.2 μg hatchling(-1) The multi-encapsulated hatchlings of C. maculosa and H. scobina were the only species that contained the energetic lipids, wax ester (WE) and methyl ester (ME). However, the overall composition of energetic lipid between hatchlings of the two Cominella species reflected strong affinities of taxonomy, suggesting a phylogenetic evolution of the non-adelphophagic development strategy. Inter- and intracapsular variability in sibling provisioning was highest in H. scobina, a finding that implies less control of allocation to individual hatchlings in this adelphophagic developer. We suggest that interspecific variability of lipids offers a useful approach to understanding the evolution of maternal provisioning in direct-developing species. © 2016 Marine Biological Laboratory.

Interacting tilt and kink instabilities in repelling current channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keppens, R.; Porth, O.; Xia, C., E-mail: rony.keppens@wis.kuleuven.be

2014-11-01

We present a numerical study in resistive magnetohydrodynamics (MHD) where the initial equilibrium configuration contains adjacent, oppositely directed, parallel current channels. Since oppositely directed current channels repel, the equilibrium is liable to an ideal magnetohydrodynamic tilt instability. This tilt evolution, previously studied in planar settings, involves two magnetic islands or flux ropes, which on Alfvénic timescales undergo a combined rotation and separation. This in turn leads to the creation of (near) singular current layers, posing severe challenges to numerical approaches. Using our open-source grid-adaptive MPI-AMRVAC software, we revisit the planar evolution case in compressible MHD, as well as its extensionmore » to two-and-a-half-dimensional (2.5D) and full three-dimensional (3D) scenarios. As long as the third dimension can be ignored, pure tilt evolutions result that are hardly affected by out of plane magnetic field components. In all 2.5D runs, our simulations do show secondary tearing type disruptions throughout the near singular current sheets in the far nonlinear saturation regime. In full 3D runs, both current channels can be liable to additional ideal kink deformations. We discuss the effects of having both tilt and kink instabilities acting simultaneously in the violent, reconnection-dominated evolution. In 3D, both the tilt and the kink instabilities can be stabilized by tension forces. As a concrete space plasma application, we argue that interacting tilt-kink instabilities in repelling current channels provide a novel route to initiate solar coronal mass ejections, distinctly different from the currently favored pure kink or torus instability routes.« less

Evolution of US military space doctrine: precedents, prospects, and challenges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, D.J.

This dissertation examines the evolution of US military space doctrine by: (1) defining military doctrine, its importance, and how it should be evaluated; (2) identifying principles of geopolitics, strategy, and war applicable to military space operations; (3) establishing how well does Air Force aerospace doctrine treat space issues and requirements for itself and the other Services: (4) identifying future directions for military space doctrine; and (5) postulating what might constitute a US military space doctrine in the future. The approach utilized incorporates analyses of the space environment, geopolitics, strategy, the principles of war, and the development of air power andmore » sea power to provide a framework of constants or invariants within which military space operations must be conducted. It also utilizes a framework of inconstants or variants, consisting of technology impacts and organizational requirements, to which military space doctrine must respond. Other doctrinal requirements are derived from the 1987 DOD space policy, the Strategic Defense Initiative, and international space law. Finally, an assessment is made of future concepts and directions of US military space doctrine.« less

Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes

PubMed Central

Fischbach, Michael A.; Lai, Jonathan R.; Roche, Eric D.; Walsh, Christopher T.; Liu, David R.

2007-01-01

Nonribosomal peptides (NRPs) are produced by NRP synthetase (NRPS) enzymes that function as molecular assembly lines. The modular architecture of NRPSs suggests that a domain responsible for activating a building block could be replaced with a domain from a foreign NRPS to create a chimeric assembly line that produces a new variant of a natural NRP. However, such chimeric NRPS modules are often heavily impaired, impeding efforts to create novel NRP variants by swapping domains from different modules or organisms. Here we show that impaired chimeric NRPSs can be functionally restored by directed evolution. Using rounds of mutagenesis coupled with in vivo screens for NRP production, we rapidly isolated variants of two different chimeric NRPSs with ≈10-fold improvements in enzyme activity and product yield, including one that produces new derivatives of the potent NRP/polyketide antibiotic andrimid. Because functional restoration in these examples required only modest library sizes (103 to 104 clones) and three or fewer rounds of screening, our approach may be widely applicable even for NRPSs from genetically challenging hosts. PMID:17620609

Features in chemical kinetics. I. Signatures of self-emerging dimensional reduction from a general format of the evolution law

NASA Astrophysics Data System (ADS)

Nicolini, Paolo; Frezzato, Diego

2013-06-01

Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an "attractiveness" region in the phase-space where a well-defined state-dependent rate function ω has the simple evolution dot{ω }= - ω ^2 along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234102 (2013)], 10.1063/1.4809593 this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.

One-step combined focused epPCR and saturation mutagenesis for thermostability evolution of a new cold-active xylanase.

PubMed

Acevedo, Juan Pablo; Reetz, Manfred T; Asenjo, Juan A; Parra, Loreto P

2017-05-01

Enzymes active at low temperature are of great interest for industrial bioprocesses due to their high efficiency at a low energy cost. One of the particularities of naturally evolved cold-active enzymes is their increased enzymatic activity at low temperature, however the low thermostability presented in this type of enzymes is still a major drawback for their application in biocatalysis. Directed evolution of cold-adapted enzymes to a more thermostable version, appears as an attractive strategy to fulfill the stability and activity requirements for the industry. This paper describes the recombinant expression and characterization of a new and highly active cold-adapted xylanase from the GH-family 10 (Xyl-L), and the use of a novel one step combined directed evolution technique that comprises saturation mutagenesis and focused epPCR as a feasible semi-rational strategy to improve the thermostability. The Xyl-L enzyme was cloned from a marine-Antarctic bacterium, Psychrobacter sp. strain 2-17, recombinantly expressed in E. coli strain BL21(DE3) and characterized enzymatically. Molecular dynamic simulations using a homology model of the catalytic domain of Xyl-L were performed to detect flexible regions and residues, which are considered to be the possible structural elements that define the thermolability of this enzyme. Mutagenic libraries were designed in order to stabilize the protein introducing mutations in some of the flexible regions and residues identified. Twelve positive mutant clones were found to improve the T 50 15 value of the enzyme, in some cases without affecting the activity at 25°C. The best mutant showed a 4.3°C increase in its T 50 15 . The efficiency of the directed evolution approach can also be expected to work in the protein engineering of stereoselectivity. Copyright © 2017 Elsevier Inc. All rights reserved.

Scattering transform for nonstationary Schroedinger equation with bidimensionally perturbed N-soliton potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiti, M.; Pempinelli, F.; Pogrebkov, A. K.

2006-12-15

In the framework of the extended resolvent approach the direct and inverse scattering problems for the nonstationary Schroedinger equation with a potential being a perturbation of the N-soliton potential by means of a generic bidimensional smooth function decaying at large spaces are introduced and investigated. The initial value problem of the Kadomtsev-Petviashvili I equation for a solution describing N wave solitons on a generic smooth decaying background is then linearized, giving the time evolution of the spectral data.

The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development.

PubMed

Vojvodic, Svjetlana; Johnson, Brian R; Harpur, Brock A; Kent, Clement F; Zayed, Amro; Anderson, Kirk E; Linksvayer, Timothy A

2015-11-01

The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the production of new queens by removing the current colony queen, and we used RNA sequencing to study the gene expression profiles of both developing larvae and their caregiving nurses before and after queen removal. By comparing the gene expression profiles of queen-destined versus worker-destined larvae as well as nurses observed feeding these two types of larvae, we identified larval and nurse genes associated with caste development. Of 950 differentially expressed genes associated with caste, 82% were expressed in larvae with putative direct effects on larval caste, and 18% were expressed in nurses with putative indirect effects on caste. Estimated selection coefficients suggest that both nurse and larval genes putatively associated with caste are rapidly evolving, especially those genes associated with worker development. Altogether, our results suggest that indirect effect genes play important roles in both the expression and evolution of socially influenced traits such as caste.

Dispersal Timing: Emigration of Insects Living in Patchy Environments.

PubMed

Lakovic, Milica; Poethke, Hans-Joachim; Hovestadt, Thomas

2015-01-01

Dispersal is a life-history trait affecting dynamics and persistence of populations; it evolves under various known selective pressures. Theoretical studies on dispersal typically assume 'natal dispersal', where individuals emigrate right after birth. But emigration may also occur during a later moment within a reproductive season ('breeding dispersal'). For example, some female butterflies first deposit eggs in their natal patch before migrating to other site(s) to continue egg-laying there. How breeding compared to natal dispersal influences the evolution of dispersal has not been explored. To close this gap we used an individual-based simulation approach to analyze (i) the evolution of timing of breeding dispersal in annual organisms, (ii) its influence on dispersal (compared to natal dispersal). Furthermore, we tested (iii) its performance in direct evolutionary contest with individuals following a natal dispersal strategy. Our results show that evolution should typically result in lower dispersal under breeding dispersal, especially when costs of dispersal are low and population size is small. By distributing offspring evenly across two patches, breeding dispersal allows reducing direct sibling competition in the next generation whereas natal dispersal can only reduce trans-generational kin competition by producing highly dispersive offspring in each generation. The added benefit of breeding dispersal is most prominent in patches with small population sizes. Finally, the evolutionary contests show that a breeding dispersal strategy would universally out-compete natal dispersal.

Brain enlargement and dental reduction were not linked in hominin evolution

PubMed Central

Smaers, Jeroen B.; Holloway, Ralph L.

2017-01-01

The large brain and small postcanine teeth of modern humans are among our most distinctive features, and trends in their evolution are well studied within the hominin clade. Classic accounts hypothesize that larger brains and smaller teeth coevolved because behavioral changes associated with increased brain size allowed a subsequent dental reduction. However, recent studies have found mismatches between trends in brain enlargement and posterior tooth size reduction in some hominin species. We use a multiple-variance Brownian motion approach in association with evolutionary simulations to measure the tempo and mode of the evolution of endocranial and dental size and shape within the hominin clade. We show that hominin postcanine teeth have evolved at a relatively consistent neutral rate, whereas brain size evolved at comparatively more heterogeneous rates that cannot be explained by a neutral model, with rapid pulses in the branches leading to later Homo species. Brain reorganization shows evidence of elevated rates only much later in hominin evolution, suggesting that fast-evolving traits such as the acquisition of a globular shape may be the result of direct or indirect selection for functional or structural traits typical of modern humans. PMID:28049819

A non-affine micro-macro approach to strain-crystallizing rubber-like materials

NASA Astrophysics Data System (ADS)

Rastak, Reza; Linder, Christian

2018-02-01

Crystallization can occur in rubber materials at large strains due to a phenomenon called strain-induced crystallization. We propose a multi-scale polymer network model to capture this process in rubber-like materials. At the microscopic scale, we present a chain formulation by studying the thermodynamic behavior of a polymer chain and its crystallization mechanism inside a stretching polymer network. The chain model accounts for the thermodynamics of crystallization and presents a rate-dependent evolution law for crystallization based on the gradient of the free energy with respect to the crystallinity variables to ensures the dissipation is always non-negative. The multiscale framework allows the anisotropic crystallization of rubber which has been observed experimentally. Two different approaches for formulating the orientational distribution of crystallinity are studied. In the first approach, the algorithm tracks the crystallization at a finite number of orientations. In contrast, the continuous distribution describes the crystallization for all polymer chain orientations and describes its evolution with only a few distribution parameters. To connect the deformation of the micro with that of the macro scale, our model combines the recently developed maximal advance path constraint with the principal of minimum average free energy, resulting in a non-affine deformation model for polymer chains. Various aspects of the proposed model are validated by existing experimental results, including the stress response, crystallinity evolution during loading and unloading, crystallinity distribution, and the rotation of the principal crystallization direction. As a case study, we simulate the formation of crystalline regions around a pre-existing notch in a 3D rubber block and we compare the results with experimental data.

Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach

PubMed Central

Abi-Ghanem, Josephine; Chusainow, Janet; Karimova, Madina; Spiegel, Christopher; Hofmann-Sieber, Helga; Hauber, Joachim; Buchholz, Frank; Pisabarro, M. Teresa

2013-01-01

Site-specific recombinases (SSRs) can perform DNA rearrangements, including deletions, inversions and translocations when their naive target sequences are placed strategically into the genome of an organism. Hence, in order to employ SSRs in heterologous hosts, their target sites have to be introduced into the genome of an organism before the enzyme can be practically employed. Engineered SSRs hold great promise for biotechnology and advanced biomedical applications, as they promise to extend the usefulness of SSRs to allow efficient and specific recombination of pre-existing, natural genomic sequences. However, the generation of enzymes with desired properties remains challenging. Here, we use substrate-linked directed evolution in combination with molecular modeling to rationally engineer an efficient and specific recombinase (sTre) that readily and specifically recombines a sequence present in the HIV-1 genome. We elucidate the role of key residues implicated in the molecular recognition mechanism and we present a rationale for sTre’s enhanced specificity. Combining evolutionary and rational approaches should help in accelerating the generation of enzymes with desired properties for use in biotechnology and biomedicine. PMID:23275541

On Quantitative Comparative Research in Communication and Language Evolution

PubMed Central

Oller, D. Kimbrough; Griebel, Ulrike

2014-01-01

Quantitative comparison of human language and natural animal communication requires improved conceptualizations. We argue that an infrastructural approach to development and evolution incorporating an extended interpretation of the distinctions among illocution, perlocution, and meaning (Austin 1962; Oller and Griebel 2008) can help place the issues relevant to quantitative comparison in perspective. The approach can illuminate the controversy revolving around the notion of functional referentiality as applied to alarm calls, for example in the vervet monkey. We argue that referentiality offers a poor point of quantitative comparison across language and animal communication in the wild. Evidence shows that even newborn human cry could be deemed to show functional referentiality according to the criteria typically invoked by advocates of referentiality in animal communication. Exploring the essence of the idea of illocution, we illustrate an important realm of commonality among animal communication systems and human language, a commonality that opens the door to more productive, quantifiable comparisons. Finally, we delineate two examples of infrastructural communicative capabilities that should be particularly amenable to direct quantitative comparison across humans and our closest relatives. PMID:25285057

On Quantitative Comparative Research in Communication and Language Evolution.

PubMed

Oller, D Kimbrough; Griebel, Ulrike

2014-09-01

Quantitative comparison of human language and natural animal communication requires improved conceptualizations. We argue that an infrastructural approach to development and evolution incorporating an extended interpretation of the distinctions among illocution, perlocution, and meaning (Austin 1962; Oller and Griebel 2008) can help place the issues relevant to quantitative comparison in perspective. The approach can illuminate the controversy revolving around the notion of functional referentiality as applied to alarm calls, for example in the vervet monkey. We argue that referentiality offers a poor point of quantitative comparison across language and animal communication in the wild. Evidence shows that even newborn human cry could be deemed to show functional referentiality according to the criteria typically invoked by advocates of referentiality in animal communication. Exploring the essence of the idea of illocution, we illustrate an important realm of commonality among animal communication systems and human language, a commonality that opens the door to more productive, quantifiable comparisons. Finally, we delineate two examples of infrastructural communicative capabilities that should be particularly amenable to direct quantitative comparison across humans and our closest relatives.

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

NASA Astrophysics Data System (ADS)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

PubMed

Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

2015-09-17

Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively little attention; however, our results suggest that it may be an important mechanism that predicts evolutionary responses to new environments.

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, L.; Kim, B. K.; Was, G. S.

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

DOE PAGES

Tan, L.; Kim, B. K.; Was, G. S.

2017-09-06

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Numerically Simulating Collisions of Plastic and Foam Laser-Driven Foils

NASA Astrophysics Data System (ADS)

Zalesak, S. T.; Velikovich, A. L.; Schmitt, A. J.; Aglitskiy, Y.; Metzler, N.

2007-11-01

Interest in experiments on colliding planar foils has recently been stimulated by (a) the Impact Fast Ignition approach to laser fusion [1], and (b) the approach to a high-repetition rate ignition facility based on direct drive with the KrF laser [2]. Simulating the evolution of perturbations to such foils can be a numerical challenge, especially if the initial perturbation amplitudes are small. We discuss the numerical issues involved in such simulations, describe their benchmarking against recently-developed analytic results, and present simulations of such experiments on NRL's Nike laser. [1] M. Murakami et al., Nucl. Fusion 46, 99 (2006) [2] S. P. Obenschain et al., Phys. Plasmas 13, 056320 (2006).

Extraterrestrial civilizations: Problems of their evolution

NASA Technical Reports Server (NTRS)

Leskov, L. V.

1987-01-01

The problem of finding extraterrestrial civilizations and establishing contact with them is directly related to the problem of their evolution. Possible patterns in this evolution and the stages in the evolution of extraterrestrial civilizations are examined.

Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture.

PubMed

Gouda, Sushanto; Kerry, Rout George; Das, Gitishree; Paramithiotis, Spiros; Shin, Han-Seung; Patra, Jayanta Kumar

2018-01-01

The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential. Copyright © 2017 Elsevier GmbH. All rights reserved.

Rheo-SAXS investigation of shear-thinning behaviour of very anisometric repulsive disc-like clay suspensions.

PubMed

Philippe, A M; Baravian, C; Imperor-Clerc, M; De Silva, J; Paineau, E; Bihannic, I; Davidson, P; Meneau, F; Levitz, P; Michot, L J

2011-05-18

Aqueous suspensions of swelling clay minerals exhibit a rich and complex rheological behaviour. In particular, these repulsive systems display strong shear-thinning at very low volume fractions in both the isotropic and gel states. In this paper, we investigate the evolution with shear of the orientational distribution of aqueous clay suspensions by synchrotron-based rheo-SAXS experiments using a Couette device. Measurements in radial and tangential configurations were carried out for two swelling clay minerals of similar morphology and size, Wyoming montmorillonite and Idaho beidellite. The shear evolution of the small angle x-ray scattering (SAXS) patterns displays significantly different features for these two minerals. The detailed analysis of the angular dependence of the SAXS patterns in both directions provides the average Euler angles of the statistical effective particle in the shear plane. We show that for both samples, the average orientation is fully controlled by the local shear stress around the particle. We then apply an effective approach to take into account multiple hydrodynamic interactions in the system. Using such an approach, it is possible to calculate the evolution of viscosity as a function of shear rate from the knowledge of the average orientation of the particles. The viscosity thus recalculated almost perfectly matches the measured values as long as collective effects are not too important in the system.

In Situ Electrochemical Oxidation Tuning of Transition Metal Disulfides to Oxides for Enhanced Water Oxidation

DOE PAGES

Chen, Wei; Wang, Haotian; Li, Yuzhang; ...

2015-07-15

The development of catalysts with earth-abundant elements for efficient oxygen evolution reactions is of paramount significance for clean and sustainable energy storage and conversion devices. Our group demonstrated recently that the electrochemical tuning of catalysts via lithium insertion and extraction has emerged as a powerful approach to improve catalytic activity. Here we report a novel in situ electrochemical oxidation tuning approach to develop a series of binary, ternary, and quaternary transition metal (e.g., Co, Ni, Fe) oxides from their corresponding sulfides as highly active catalysts for much enhanced water oxidation. The electrochemically tuned cobalt–nickel–iron oxides grown directly on the three-dimensionalmore » carbon fiber electrodes exhibit a low overpotential of 232 mV at current density of 10 mA cm –2, small Tafel slope of 37.6 mV dec –1, and exceptional long-term stability of electrolysis for over 100 h in 1 M KOH alkaline medium, superior to most non-noble oxygen evolution catalysts reported so far. The materials evolution associated with the electrochemical oxidation tuning is systematically investigated by various characterizations, manifesting that the improved activities are attributed to the significant grain size reduction and increase of surface area and electroactive sites. This work provides a promising strategy to develop electrocatalysts for large-scale water-splitting systems and many other applications.« less

A mass-conserving mixed Fourier-Galerkin B-Spline-collocation method for Direct Numerical Simulation of the variable-density Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Reuter, Bryan; Oliver, Todd; Lee, M. K.; Moser, Robert

2017-11-01

We present an algorithm for a Direct Numerical Simulation of the variable-density Navier-Stokes equations based on the velocity-vorticity approach introduced by Kim, Moin, and Moser (1987). In the current work, a Helmholtz decomposition of the momentum is performed. Evolution equations for the curl and the Laplacian of the divergence-free portion are formulated by manipulation of the momentum equations and the curl-free portion is reconstructed by enforcing continuity. The solution is expanded in Fourier bases in the homogeneous directions and B-Spline bases in the inhomogeneous directions. Discrete equations are obtained through a mixed Fourier-Galerkin and collocation weighted residual method. The scheme is designed such that the numerical solution conserves mass locally and globally by ensuring the discrete divergence projection is exact through the use of higher order splines in the inhomogeneous directions. The formulation is tested on multiple variable-density flow problems.

Major Hurdles for the Evolution of Sociality.

PubMed

Korb, Judith; Heinze, Jürgen

2016-01-01

Why do most animals live solitarily, while complex social life is restricted to a few cooperatively breeding vertebrates and social insects? Here, we synthesize concepts and theories in social evolution and discuss its underlying ecological causes. Social evolution can be partitioned into (a) formation of stable social groups, (b) evolution of helping, and (c) transition to a new evolutionary level. Stable social groups rarely evolve due to competition over food and/or reproduction. Food competition is overcome in social insects with central-place foraging or bonanza-type food resources, whereas competition over reproduction commonly occurs because staying individuals are rarely sterile. Hence, the evolution of helping is shaped by direct and indirect fitness options and helping is only altruism if it reduces the helper's direct fitness. The helper's capability to gain direct fitness also creates within-colony conflict. This prevents transition to a new evolutionary level.

Eye evolution and its functional basis.

PubMed

Nilsson, Dan-E

2013-03-01

Eye evolution is driven by the evolution of visually guided behavior. Accumulation of gradually more demanding behaviors have continuously increased the performance requirements on the photoreceptor organs. Starting with nondirectional photoreception, I argue for an evolutionary sequence continuing with directional photoreception, low-resolution vision, and finally, high-resolution vision. Calculations of the physical requirements for these four sensory tasks show that they correlate with major innovations in eye evolution and thus work as a relevant classification for a functional analysis of eye evolution. Together with existing molecular and morphological data, the functional analysis suggests that urbilateria had a simple set of rhabdomeric and ciliary receptors used for directional photoreception, and that organ duplications, positional shifts and functional shifts account for the diverse patterns of eyes and photoreceptors seen in extant animals. The analysis also suggests that directional photoreception evolved independently at least twice before the last common ancestor of bilateria and proceeded several times independently to true vision in different bilaterian and cnidarian groups. This scenario is compatible with Pax-gene expression in eye development in the different animal groups. The whole process from the first opsin to high-resolution vision took about 170 million years and was largely completed by the onset of the Cambrian, about 530 million years ago. Evolution from shadow detectors to multiple directional photoreceptors has further led to secondary cases of eye evolution in bivalves, fan worms, and chitons.

Evolution Of USDOE Performance Assessments Over 20 Years

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seitz, Roger R.; Suttora, Linda C.

2013-02-26

Performance assessments (PAs) have been used for many years for the analysis of post-closure hazards associated with a radioactive waste disposal facility and to provide a reasonable expectation of the ability of the site and facility design to meet objectives for the protection of members of the public and the environment. The use of PA to support decision-making for LLW disposal facilities has been mandated in United States Department of Energy (USDOE) directives governing radioactive waste management since 1988 (currently DOE Order 435.1, Radioactive Waste Management). Prior to that time, PAs were also used in a less formal role. Overmore » the past 20+ years, the USDOE approach to conduct, review and apply PAs has evolved into an efficient, rigorous and mature process that includes specific requirements for continuous improvement and independent reviews. The PA process has evolved through refinement of a graded and iterative approach designed to help focus efforts on those aspects of the problem expected to have the greatest influence on the decision being made. Many of the evolutionary changes to the PA process are linked to the refinement of the PA maintenance concept that has proven to be an important element of USDOE PA requirements in the context of supporting decision-making for safe disposal of LLW. The PA maintenance concept represents the evolution of the graded and iterative philosophy and has helped to drive the evolution of PAs from a deterministic compliance calculation into a systematic approach that helps to focus on critical aspects of the disposal system in a manner designed to provide a more informed basis for decision-making throughout the life of a disposal facility (e.g., monitoring, research and testing, waste acceptance criteria, design improvements, data collection, model refinements). A significant evolution in PA modeling has been associated with improved use of uncertainty and sensitivity analysis techniques to support efficient implementation of the graded and iterative approach. Rather than attempt to exactly predict the migration of radionuclides in a disposal unit, the best PAs have evolved into tools that provide a range of results to guide decision-makers in planning the most efficient, cost effective, and safe disposal of radionuclides.« less

Organogenesis in deep time: A problem in genomics, development, and paleontology.

PubMed

Pieretti, Joyce; Gehrke, Andrew R; Schneider, Igor; Adachi, Noritaka; Nakamura, Tetsuya; Shubin, Neil H

2015-04-21

The fossil record is a unique repository of information on major morphological transitions. Increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. Here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. We discuss classical theories on the origins of paired fins, recent data on regulatory modulations of fish fins and tetrapod limbs, and case studies exploring the mechanisms of digit loss in tetrapods. We envision an era of research in which the deep history of morphological evolution can be revealed by integrating fossils of transitional forms with direct experimentation in the laboratory via genome manipulation, thereby shedding light on the relationship between genes, developmental processes, and the evolving phenotype.

From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution.

PubMed

Ye, Lidan; Yang, Chengcheng; Yu, Hongwei

2018-01-01

With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.

Efficient rolling texture predictions and texture-sensitive properties of α-uranium foils

DOE PAGES

Steiner, Matthew A.; Klein, Robert W.; Calhoun, Christopher A.; ...

2017-01-01

Here, finite element (FE) analysis was used to simulate the strain history of an α-uranium foil during cold-rolling, with the sheet modeled as an isotropic elastoplastic continuum. The resulting strain history was then used as input for a viscoplastic self-consistent (VPSC) polycrystal plasticity model to simulate crystallographic texture evolution. Mid-plane textures predicted via the combined FE→VPSC approach show alignment of the (010) poles along the rolling direction (RD), and the (001) poles along the normal direction (ND) with a symmetric splitting along RD. The surface texture is similar to that of the mid-plane, but with a shear-induced asymmetry that favorsmore » one of the RD split features of the (001) pole figure. Both the mid-plane and surface textures predicted by the FE→VPSC approach agree with published experimental results for cold-rolled α-uranium plates, as well as predictions made by a more computationally intensive full-field crystal plasticity based finite element model. α-uranium foils produced by cold-rolling must typically undergo a final recrystallization anneal to restore ductility prior to their final application, resulting in significant texture evolution from the cold-rolled plate deformation texture. Using the texture measured from a foil in the final recrystallized state, coefficients of the thermal expansion and elastic stiffness tensors were calculated using a thermo-elastic self-consistent model, and the anisotropic yield loci and flow curves along the RD, TD, and ND were predicted using the VPSC code.« less

Efficient rolling texture predictions and texture-sensitive properties of α-uranium foils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steiner, Matthew A.; Klein, Robert W.; Calhoun, Christopher A.

Here, finite element (FE) analysis was used to simulate the strain history of an α-uranium foil during cold-rolling, with the sheet modeled as an isotropic elastoplastic continuum. The resulting strain history was then used as input for a viscoplastic self-consistent (VPSC) polycrystal plasticity model to simulate crystallographic texture evolution. Mid-plane textures predicted via the combined FE→VPSC approach show alignment of the (010) poles along the rolling direction (RD), and the (001) poles along the normal direction (ND) with a symmetric splitting along RD. The surface texture is similar to that of the mid-plane, but with a shear-induced asymmetry that favorsmore » one of the RD split features of the (001) pole figure. Both the mid-plane and surface textures predicted by the FE→VPSC approach agree with published experimental results for cold-rolled α-uranium plates, as well as predictions made by a more computationally intensive full-field crystal plasticity based finite element model. α-uranium foils produced by cold-rolling must typically undergo a final recrystallization anneal to restore ductility prior to their final application, resulting in significant texture evolution from the cold-rolled plate deformation texture. Using the texture measured from a foil in the final recrystallized state, coefficients of the thermal expansion and elastic stiffness tensors were calculated using a thermo-elastic self-consistent model, and the anisotropic yield loci and flow curves along the RD, TD, and ND were predicted using the VPSC code.« less

Efficient rolling texture predictions and texture-sensitive thermomechanical properties of α-uranium foils

NASA Astrophysics Data System (ADS)

Steiner, Matthew A.; Klein, Robert W.; Calhoun, Christopher A.; Knezevic, Marko; Garlea, Elena; Agnew, Sean R.

2017-11-01

Finite element (FE) analysis was used to simulate the strain history of an α-uranium foil during cold straight-rolling, with the sheet modeled as an isotropic elastoplastic continuum. The resulting strain history was then used as input for a viscoplastic self-consistent (VPSC) polycrystal plasticity model to simulate crystallographic texture evolution. Mid-plane textures predicted via the combined FE→VPSC approach show alignment of the (010) poles along the rolling direction (RD), and the (001) poles along the normal direction (ND) with a symmetric splitting along RD. The surface texture is similar to that of the mid-plane, but with a shear-induced asymmetry that favors one of the RD split features of the (001) pole figure. Both the mid-plane and surface textures predicted by the FE→VPSC approach agree with published experimental results for cold straight-rolled α-uranium plates, as well as predictions made by a more computationally intensive full-field crystal plasticity based finite element model. α-uranium foils produced by cold-rolling must typically undergo a recrystallization anneal to restore ductility prior to their final application, resulting in significant texture evolution from the cold-rolled plate deformation texture. Using the texture measured from a foil in the final recrystallized state, coefficients of thermal expansion and the elastic stiffness tensors were calculated using a thermo-elastic self-consistent model, and the anisotropic yield loci and flow curves along the RD, TD, and ND were predicted using the VPSC code.

Review of complex networks application in hydroclimatic extremes with an implementation to characterize spatio-temporal drought propagation in continental USA

NASA Astrophysics Data System (ADS)

Konapala, Goutam; Mishra, Ashok

2017-12-01

The quantification of spatio-temporal hydroclimatic extreme events is a key variable in water resources planning, disaster mitigation, and preparing climate resilient society. However, quantification of these extreme events has always been a great challenge, which is further compounded by climate variability and change. Recently complex network theory was applied in earth science community to investigate spatial connections among hydrologic fluxes (e.g., rainfall and streamflow) in water cycle. However, there are limited applications of complex network theory for investigating hydroclimatic extreme events. This article attempts to provide an overview of complex networks and extreme events, event synchronization method, construction of networks, their statistical significance and the associated network evaluation metrics. For illustration purpose, we apply the complex network approach to study the spatio-temporal evolution of droughts in Continental USA (CONUS). A different drought threshold leads to a new drought event as well as different socio-economic implications. Therefore, it would be interesting to explore the role of thresholds on spatio-temporal evolution of drought through network analysis. In this study, long term (1900-2016) Palmer drought severity index (PDSI) was selected for spatio-temporal drought analysis using three network-based metrics (i.e., strength, direction and distance). The results indicate that the drought events propagate differently at different thresholds associated with initiation of drought events. The direction metrics indicated that onset of mild drought events usually propagate in a more spatially clustered and uniform approach compared to onsets of moderate droughts. The distance metric shows that the drought events propagate for longer distance in western part compared to eastern part of CONUS. We believe that the network-aided metrics utilized in this study can be an important tool in advancing our knowledge on drought propagation as well as other hydroclimatic extreme events. Although the propagation of droughts is investigated using the network approach, however process (physics) based approaches is essential to further understand the dynamics of hydroclimatic extreme events.

The Arrow of Time in the Collapse of Collisionless Self-gravitating Systems: Non-validity of the Vlasov-Poisson Equation during Violent Relaxation

NASA Astrophysics Data System (ADS)

Beraldo e Silva, Leandro; de Siqueira Pedra, Walter; Sodré, Laerte; Perico, Eder L. D.; Lima, Marcos

2017-09-01

The collapse of a collisionless self-gravitating system, with the fast achievement of a quasi-stationary state, is driven by violent relaxation, with a typical particle interacting with the time-changing collective potential. It is traditionally assumed that this evolution is governed by the Vlasov-Poisson equation, in which case entropy must be conserved. We run N-body simulations of isolated self-gravitating systems, using three simulation codes, NBODY-6 (direct summation without softening), NBODY-2 (direct summation with softening), and GADGET-2 (tree code with softening), for different numbers of particles and initial conditions. At each snapshot, we estimate the Shannon entropy of the distribution function with three different techniques: Kernel, Nearest Neighbor, and EnBiD. For all simulation codes and estimators, the entropy evolution converges to the same limit as N increases. During violent relaxation, the entropy has a fast increase followed by damping oscillations, indicating that violent relaxation must be described by a kinetic equation other than the Vlasov-Poisson equation, even for N as large as that of astronomical structures. This indicates that violent relaxation cannot be described by a time-reversible equation, shedding some light on the so-called “fundamental paradox of stellar dynamics.” The long-term evolution is well-described by the orbit-averaged Fokker-Planck model, with Coulomb logarithm values in the expected range 10{--}12. By means of NBODY-2, we also study the dependence of the two-body relaxation timescale on the softening length. The approach presented in the current work can potentially provide a general method for testing any kinetic equation intended to describe the macroscopic evolution of N-body systems.

Direct Revascularization with Autotransplant Technique for a True Aneurysm of the Renal Artery 20 Years after Kidney Transplantation.

PubMed

Mezzetto, Luca; Boschiero, Luigino; Fior, Francesca; Nguefouet Momo, Rostand Emmanuel; Nacchia, Francesco; Eccher, Albino; Macrì, Marco; Veraldi, Gian Franco

2016-04-01

True degenerative aneurysm of renal artery represents a very rare evolution in kidney transplantation. The cases presented in the literature are usually perianastomotic or mycotic pseudoaneurysm related to surgical technical defects or local infections. Herewith, we present the case of a voluminous true aneurysm developed in a young patient transplanted at our hospital 20 years before. All follow-up ultrasounds were always normal until the last disclosing a voluminous aneurysm of the transplanted renal artery. The subsequent angio-CT-scan confirmed the presence of a 52-mm saccular dilatation of the renal artery. For the complex anatomy, the endovascular approach was excluded, and a surgical revascularization was staged. We treated this lesion with the autotransplant technique, preserving the transplanted kidney, resecting the aneurysm, and performing a direct anastomosis after cold perfusion of the kidney. The autotransplant technique demonstrated to be a safe and effective approach in this challenging and very unusual situation. Copyright © 2016 Elsevier Inc. All rights reserved.

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Chaos, oscillation and the evolution of indirect reciprocity in n-person games.

PubMed

Suzuki, Shinsuke; Akiyama, Eizo

2008-06-21

Evolution of cooperation among genetically unrelated individuals has been of considerable concern in various fields such as biology, economics, and psychology. The evolution of cooperation is often explained by reciprocity. Under reciprocity, cooperation can prevail in a society because a donor of cooperation receives reciprocation from the recipient of the cooperation, called direct reciprocity, or from someone else in the community, called indirect reciprocity. Nowak and Sigmund [1993. Chaos and the evolution of cooperation. Proc. Natl. Acad. Sci. USA 90, 5091-5094] have demonstrated that directly reciprocal cooperation in two-person prisoner's dilemma games with mutation of strategies can be maintained dynamically as periodic or chaotic oscillation. Furthermore, Eriksson and Lindgren [2005. Cooperation driven by mutations in multi-person Prisoner's Dilemma. J. Theor. Biol. 232, 399-409] have reported that directly reciprocal cooperation in n-person prisoner's dilemma games (n>2) can be maintained as periodic oscillation. Is dynamic cooperation observed only in direct reciprocity? Results of this study show that indirectly reciprocal cooperation in n-person prisoner's dilemma games can be maintained dynamically as periodic or chaotic oscillation. This is, to our knowledge, the first demonstration of chaos in indirect reciprocity. Furthermore, the results show that oscillatory dynamics are observed in common in the evolution of reciprocal cooperation whether for direct or indirect.

The Evolution of Morphospace in Phytophagous Scarab Chafers: No Competition - No Divergence?

PubMed Central

Eberle, Jonas; Myburgh, Renier; Ahrens, Dirk

2014-01-01

Body shape reflects species' evolution and mediates its role in the environment as it integrates gene expression, life style, and structural morphology. Its comparative analysis may reveal insight on what shapes shape, being a useful approach when other evidence is lacking. Here we investigated evolutionary patterns of body shape in the highly diverse phytophagous chafers (Scarabaeidae: Pleurosticti), a polyphagous group utilizing different parts of angiosperms. Because the reasons of their successful diversification are largely unknown, we used a phylogenetic tree and multivariate analysis on twenty linear measurements of body morphology including all major Pleurosticti lineages to infer patterns of morphospace covariation and divergence. The chafer's different feeding types resulted to be not distinguishable in the described morphospace which was largely attributed to large occupancy of the morphospace of some feeding types and to multiple convergences of feeding behavior (particularly of anthophagy). Low correlation between molecular and morphological rates of evolution, including significant rate shifts for some lineages, indicated directed selection within feeding types. This is supported by morphospace divergence within feeding types and convergent evolution in Australian Melolonthinae. Traits driving morphospace divergence were extremities and traits linked with locomotion behavior, but also body size. Being highly adaptive for burrowing and locomotion these traits showed major changes in the evolution of pleurostict scarabs. These activities also affected another trait, the metacoxal length, which is highly influenced by key innovations of the metacoxa (extended mesal process, secondary closure) particularly in one lineage, the Sericini. Significant shape divergence between major lineages and a lack of strong differentiation among closely related lineages indicated that the question about the presence or absence of competition-derived directed selection needs to be addressed for different time scales. Striking divergence between some sister lineages at their origin revealed strong driven selection towards morphospace divergence, possibly linked with resource partitioning. PMID:24875856

Service oriented architecture for clinical decision support: a systematic review and future directions.

PubMed

Loya, Salvador Rodriguez; Kawamoto, Kensaku; Chatwin, Chris; Huser, Vojtech

2014-12-01

The use of a service-oriented architecture (SOA) has been identified as a promising approach for improving health care by facilitating reliable clinical decision support (CDS). A review of the literature through October 2013 identified 44 articles on this topic. The review suggests that SOA related technologies such as Business Process Model and Notation (BPMN) and Service Component Architecture (SCA) have not been generally adopted to impact health IT systems' performance for better care solutions. Additionally, technologies such as Enterprise Service Bus (ESB) and architectural approaches like Service Choreography have not been generally exploited among researchers and developers. Based on the experience of other industries and our observation of the evolution of SOA, we found that the greater use of these approaches have the potential to significantly impact SOA implementations for CDS.

Service Oriented Architecture for Clinical Decision Support: A Systematic Review and Future Directions

PubMed Central

Loya, Salvador Rodriguez; Kawamoto, Kensaku; Chatwin, Chris; Huser, Vojtech

2017-01-01

The use of a service-oriented architecture (SOA) has been identified as a promising approach for improving health care by facilitating reliable clinical decision support (CDS). A review of the literature through October 2013 identified 44 articles on this topic. The review suggests that SOA related technologies such as Business Process Model and Notation (BPMN) and Service Component Architecture (SCA) have not been generally adopted to impact health IT systems’ performance for better care solutions. Additionally, technologies such as Enterprise Service Bus (ESB) and architectural approaches like Service Choreography have not been generally exploited among researchers and developers. Based on the experience of other industries and our observation of the evolution of SOA, we found that the greater use of these approaches have the potential to significantly impact SOA implementations for CDS PMID:25325996

Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding.

PubMed

Podevin, Nancy; Davies, Howard V; Hartung, Frank; Nogué, Fabien; Casacuberta, Josep M

2013-06-01

Conventional plant breeding exploits existing genetic variability and introduces new variability by mutagenesis. This has proven highly successful in securing food supplies for an ever-growing human population. The use of genetically modified plants is a complementary approach but all plant breeding techniques have limitations. Here, we discuss how the recent evolution of targeted mutagenesis and DNA insertion techniques based on tailor-made site-directed nucleases (SDNs) provides opportunities to overcome such limitations. Plant breeding companies are exploiting SDNs to develop a new generation of crops with new and improved traits. Nevertheless, some technical limitations as well as significant uncertainties on the regulatory status of SDNs may challenge their use for commercial plant breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Directed evolution of bacteriorhodopsin for applications in bioelectronics

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Ranaghan, Matthew J.; Birge, Robert R.

2013-01-01

In nature, biological systems gradually evolve through complex, algorithmic processes involving mutation and differential selection. Evolution has optimized biological macromolecules for a variety of functions to provide a comparative advantage. However, nature does not optimize molecules for use in human-made devices, as it would gain no survival advantage in such cooperation. Recent advancements in genetic engineering, most notably directed evolution, have allowed for the stepwise manipulation of the properties of living organisms, promoting the expansion of protein-based devices in nanotechnology. In this review, we highlight the use of directed evolution to optimize photoactive proteins, with an emphasis on bacteriorhodopsin (BR), for device applications. BR, a highly stable light-activated proton pump, has shown great promise in three-dimensional optical memories, real-time holographic processors and artificial retinas. PMID:23676894

Variation of River Islands around a Large City along the Yangtze River from Satellite Remote Sensing Images

PubMed Central

Shi, Haiyun; Gao, Chao; Dong, Changming; Xia, Changshui; Xu, Guanglai

2017-01-01

River islands are sandbars formed by scouring and silting. Their evolution is affected by several factors, among which are runoff and sediment discharge. The spatial-temporal evolution of seven river islands in the Nanjing Section of the Yangtze River of China was examined using TM (Thematic Mapper) and ETM (Enhanced Thematic Mapper)+ images from 1985 to 2015 at five year intervals. The following approaches were applied in this study: the threshold value method, binarization model, image registration, image cropping, convolution and cluster analysis. Annual runoff and sediment discharge data as measured at the Datong hydrological station upstream of Nanjing section were also used to determine the roles and impacts of various factors. The results indicated that: (1) TM/ETM+ images met the criteria of information extraction of river islands; (2) generally, the total area of these islands in this section and their changing rate decreased over time; (3) sediment and river discharge were the most significant factors in island evolution. They directly affect river islands through silting or erosion. Additionally, anthropocentric influences could play increasingly important roles. PMID:28953218

Solar Photoelectrochemical Energy Conversion using Earth-Abundant Nanomaterials

NASA Astrophysics Data System (ADS)

Lukowski, Mark A.

Although the vast majority of energy consumed worldwide is derived from fossil fuels, the growing interest in making cleaner alternative energies more economically viable has motivated recent research efforts aimed to improve photovoltaic, wind, and biomass power generation. Clean power generation also requires clean burning fuels, such as H2 and O2, so that energy can still be provided on demand at all times, despite the intermittent nature inherent to solar or wind power. My research has focused on the rational approach to synthesizing earth-abundant nanomaterials with applications in the generation of clean alternative fuels and understanding the structure-property relationships which directly influence their performance. Herein, we describe the development of low-cost, earth-abundant layered metal chalcogenides as high-performance electrocatalysts for hydrogen evolution, and hematite photoanodes for photoelectrochemical oxygen evolution. This work has revealed a particularly interesting concept where catalytic performance can be enhanced by controlling the phase behavior of the material and taking advantage of previously unexploited properties to overcome the challenges traditionally limiting the performance of these layered materials for hydrogen evolution catalysis.

Plant domestication slows pest evolution.

PubMed

Turcotte, Martin M; Lochab, Amaneet K; Turley, Nash E; Johnson, Marc T J

2015-09-01

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest - the green peach aphid (Myzus persicae) - growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual-based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Post-Paleogene (post-Middle Eocene-pre-Miocene) Geodynamic evolution of the Upper Cretaceous-Paleogene Basins in Central Anatolia, Turkey

NASA Astrophysics Data System (ADS)

Rojay, Bora

2017-04-01

Central Anatolia is one of the key areas on the evolution of Cretaceous-Paleogene Tethys where stratigraphy of the region is well studied. However not well linked with tectonics. The so-called "Ankara Mélange" belt (AOM) and the basins on top are important elements in the understanding of the İzmir-Ankara-Erzincan suture belt (İAES) evolution in Anatolia (Turkey) and in the evolution of Tethys in minor Asia (Turkey). Some of the basins are directly situated on top of the tectonic slices of the accretionary prism (IAES). However, some are not tectonically well explained as in the case of Haymana basin. The southern continental fragments (eg. Kütahya-Bolkardaǧ and Kırşehir blocks from Gondwana) are approaching to northern continents (Pontides of Lauriasia) where basins like Haymana, Alçı, Kırıkkale and Orhaniye extensional basins are evolved in between the closing margins of two continents. Haymana basin is an extensional basin developed under contractional regime on top of both northward subducting oceanic fragments and an approaching fragments of southern continents. Paleogene (end of Eocene) is the time where the Seas were retreated to S-SE Anatolia leaving a continental setting in Anatolia during Oligocene-Miocene. The slip data gathered from the faults cross-cutting the Paleogene Units and the fabric from Cretaceous mélanges depicts a NNW-SSE to NNE-SSW compressional stress regime operated during post-Eocene-pre-Miocene period. Lately the slip surfaces were overprinted by post-Pliocene normal faulting. Key words: fault slip data, Paleogene, NNW-SSE compression, Anatolia.

A Surrogate Approach to Study the Evolution of Noncoding DNA Elements That Organize Eukaryotic Genomes

PubMed Central

Vermaak, Danielle; Bayes, Joshua J.

2009-01-01

Comparative genomics provides a facile way to address issues of evolutionary constraint acting on different elements of the genome. However, several important DNA elements have not reaped the benefits of this new approach. Some have proved intractable to current day sequencing technology. These include centromeric and heterochromatic DNA, which are essential for chromosome segregation as well as gene regulation, but the highly repetitive nature of the DNA sequences in these regions make them difficult to assemble into longer contigs. Other sequences, like dosage compensation X chromosomal sites, origins of DNA replication, or heterochromatic sequences that encode piwi-associated RNAs, have proved difficult to study because they do not have recognizable DNA features that allow them to be described functionally or computationally. We have employed an alternate approach to the direct study of these DNA elements. By using proteins that specifically bind these noncoding DNAs as surrogates, we can indirectly assay the evolutionary constraints acting on these important DNA elements. We review the impact that such “surrogate strategies” have had on our understanding of the evolutionary constraints shaping centromeres, origins of DNA replication, and dosage compensation X chromosomal sites. These have begun to reveal that in contrast to the view that such structural DNA elements are either highly constrained (under purifying selection) or free to drift (under neutral evolution), some of them may instead be shaped by adaptive evolution and genetic conflicts (these are not mutually exclusive). These insights also help to explain why the same elements (e.g., centromeres and replication origins), which are so complex in some eukaryotic genomes, can be simple and well defined in other where similar conflicts do not exist. PMID:19635763

[The liaison psychiatry approach of the psychiatric crisis, urgencies and emergencies].

PubMed

Tenconi, Juan Cristóbal

2003-01-01

The purpose of this paper is to differentiate crisis, emergencies and urgencies within the frame of Liaison psychiatry. It begins with the definition of each one of the terms, later the emphasis is put in the clinical characteristics of each one of these situations. These characteristics are determined by the patient and the therapeutic team. At last therapeutic guidelines are stated, which allow more precision in the intervention, in function of the direct involvement of these situations in the development and evolution of the patients.

Investigation of the influence of the chemical composition of HSLA steel grades on the microstructure homogeneity during hot rolling in continuous rolling mills using a fast layer model

NASA Astrophysics Data System (ADS)

Schmidtchen, M.; Rimnac, A.; Warczok, P.; Kozeschnik, E.; Bernhard, C.; Bragin, S.; Kawalla, R.; Linzer, B.

2016-03-01

The newly developed LaySiMS simulation tool provides new insight for inhomogeneous material flow and microstructure evolution in an endless strip production (ESP) plant. A deepened understanding of the influence of inhomogeneities in initial material state, temperature profile and material flow and their impact on the finished product can be reached e.g. by allowing for variable layer thickness distributions in the roll gap. Coupling temperature, deformation work and work hardening/recrystallization phenomena accounts for covering important effects in the roll gap. The underlying concept of the LaySiMS approach will be outlined and new insight gained regarding microstructural evolution, shear and inhomogeneous stress and strain states in the roll gap as well as local residual stresses will be presented. For the case of thin slab casting and direct rolling (TSDR) the interrelation of inhomogeneous initial state, micro structure evolution and dissolution state of micro alloying elements within the roughing section of an ESP line will be discussed. Special emphasis is put on the influence of the local chemical composition arising from direct charging on throughthickness homogeneity of the final product. It is concluded that, due to the specific combination of large reductions in the high reduction mills (HRM) and the highly inhomogeneous inverse temperature profile, the ESP-concept provides great opportunities for homogenizing the microstructure across the strip thickness.

The Expanding Role of Applications in the Development and Validation of CFD at NASA

NASA Technical Reports Server (NTRS)

Schuster, David M.

2010-01-01

This paper focuses on the recent escalation in application of CFD to manned and unmanned flight projects at NASA and the need to often apply these methods to problems for which little or no previous validation data directly applies. The paper discusses the evolution of NASA.s CFD development from a strict Develop, Validate, Apply strategy to sometimes allowing for a Develop, Apply, Validate approach. The risks of this approach and some of its unforeseen benefits are discussed and tied to specific operational examples. There are distinct advantages for the CFD developer that is able to operate in this paradigm, and recommendations are provided for those inclined and willing to work in this environment.

Estimating the Effect of Competition on Trait Evolution Using Maximum Likelihood Inference.

PubMed

Drury, Jonathan; Clavel, Julien; Manceau, Marc; Morlon, Hélène

2016-07-01

Many classical ecological and evolutionary theoretical frameworks posit that competition between species is an important selective force. For example, in adaptive radiations, resource competition between evolving lineages plays a role in driving phenotypic diversification and exploration of novel ecological space. Nevertheless, current models of trait evolution fit to phylogenies and comparative data sets are not designed to incorporate the effect of competition. The most advanced models in this direction are diversity-dependent models where evolutionary rates depend on lineage diversity. However, these models still treat changes in traits in one branch as independent of the value of traits on other branches, thus ignoring the effect of species similarity on trait evolution. Here, we consider a model where the evolutionary dynamics of traits involved in interspecific interactions are influenced by species similarity in trait values and where we can specify which lineages are in sympatry. We develop a maximum likelihood based approach to fit this model to combined phylogenetic and phenotypic data. Using simulations, we demonstrate that the approach accurately estimates the simulated parameter values across a broad range of parameter space. Additionally, we develop tools for specifying the biogeographic context in which trait evolution occurs. In order to compare models, we also apply these biogeographic methods to specify which lineages interact sympatrically for two diversity-dependent models. Finally, we fit these various models to morphological data from a classical adaptive radiation (Greater Antillean Anolis lizards). We show that models that account for competition and geography perform better than other models. The matching competition model is an important new tool for studying the influence of interspecific interactions, in particular competition, on phenotypic evolution. More generally, it constitutes a step toward a better integration of interspecific interactions in many ecological and evolutionary processes. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Laccase engineering: from rational design to directed evolution.

PubMed

Mate, Diana M; Alcalde, Miguel

2015-01-01

Laccases are multicopper oxidoreductases considered by many in the biotechonology field as the ultimate "green catalysts". This is mainly due to their broad substrate specificity and relative autonomy (they use molecular oxygen from air as an electron acceptor and they only produce water as by-product), making them suitable for a wide array of applications: biofuel production, bioremediation, organic synthesis, pulp biobleaching, textiles, the beverage and food industries, biosensor and biofuel cell development. Since the beginning of the 21st century, specific features of bacterial and fungal laccases have been exhaustively adapted in order to reach the industrial demands for high catalytic activity and stability in conjunction with reduced production cost. Among the goals established for laccase engineering, heterologous functional expression, improved activity and thermostability, tolerance to non-natural media (organic solvents, ionic liquids, physiological fluids) and resistance to different types of inhibitors are all challenges that have been met, while obtaining a more comprehensive understanding of laccase structure-function relationships. In this review we examine the most significant advances in this exciting research area in which rational, semi-rational and directed evolution approaches have been employed to ultimately convert laccases into high value-added biocatalysts. Copyright © 2014 Elsevier Inc. All rights reserved.

HIV Surveillance Among Pregnant Women Attending Antenatal Clinics: Evolution and Current Direction.

PubMed

Dee, Jacob; Garcia Calleja, Jesus M; Marsh, Kimberly; Zaidi, Irum; Murrill, Christopher; Swaminathan, Mahesh

2017-12-05

Since the late 1980s, human immunodeficiency virus (HIV) sentinel serosurveillance among pregnant women attending select antenatal clinics (ANCs) based on unlinked anonymous testing (UAT) has provided invaluable information for tracking HIV prevalence and trends and informing global and national HIV models in most countries with generalized HIV epidemics. However, increased coverage of HIV testing, prevention of mother-to-child transmission (PMTCT), and antiretroviral therapy has heightened ethical concerns about UAT. PMTCT programs now routinely collect demographic and HIV testing information from the same pregnant women as serosurveillance and therefore present an alternative to UAT-based ANC serosurveillance. This paper reports on the evolution and current direction of the global approach to HIV surveillance among pregnant women attending ANCs, including the transition away from traditional UAT-based serosurveillance and toward new guidance from the World Health Organization and the Joint United Nations Programme on HIV/AIDS on the implementation of surveillance among pregnant women attending ANCs based on routine PMTCT program data. ©Jacob Dee, Jesus M Garcia Calleja, Kimberly Marsh, Irum Zaidi, Christopher Murrill, Mahesh Swaminathan. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 05.12.2017.

Extracting remanent magnetization from magnetic data inversion

NASA Astrophysics Data System (ADS)

Liu, S.; Fedi, M.; Baniamerian, J.; Hu, X.

2017-12-01

Remanent magnetization is an important vector parameter of rocks' and ores' magnetism, which is related to the intensity and direction of primary geomagnetic fields at all geological periods and hence shows critical evidences of geological tectonic movement and sedimentary evolution. We extract the remanence information from the distributions of the inverted magnetization vector. Firstly, directions of total magnetization vector are estimated from reduced-to-pole anomaly (max-min algorithm) and by its correlations with other magnitude magnetic transforms such as magnitude magnetic anomaly and normalized source strength. Then we invert data for the magnetization intensity and finally the intensity and direction of the remanent magnetization are separated from the total magnetization vector with a generalized formula of the apparent susceptibility based on a priori information on the Koenigsberger ratio. Our approach is used to investigate the targeted resources and geologic processes of the mining areas in China.

Effects of Space Environment on Flow and Concentration During Directional Solidification

NASA Technical Reports Server (NTRS)

Benjapiyaporn, C.; Timchenko, V.; Leonardi, E.; deVahlDavis, G.; deGroh, H. C., III

2000-01-01

A study of directional solidification of a weak binary alloy (specifically, Bi - 1 at% Sn) based on the fixed grid single domain approach is being undertaken. The enthalpy method is used to solve for the temperature field over the computational domain including both the solid and liquid phases; latent heat evolution is treated with the aid of an effective specific heat coefficient. A source term accounting for the release of solute into the liquid during solidification has been incorporated into the solute transport equation. The vorticity-stream function formulation is used to describe thermosolutal convection in the liquid region. In this paper we numerically investigate the effects of g-jitter on directional solidification. A background gravity of 1 micro-g has been assumed, and new results for the effects of periodic disturbances over a range of amplitudes and frequencies on solute field and segregation have been presented.

The evolution of recombinant thrombolytics: Current status and future directions

PubMed Central

Adivitiya; Khasa, Yogender Pal

2017-01-01

ABSTRACT Cardiovascular disorders are on the rise worldwide due to alcohol abuse, obesity, hypertension, raised blood lipids, diabetes and age-related risks. The use of classical antiplatelet and anticoagulant therapies combined with surgical intervention helped to clear blood clots during the inceptive years. However, the discovery of streptokinase and urokinase ushered the way of using these enzymes as thrombolytic agents to degrade the fibrin network with an issue of systemic hemorrhage. The development of second generation plasminogen activators like anistreplase and tissue plasminogen activator partially controlled this problem. The third generation molecules, majorly t-PA variants, showed desirable properties of improved stability, safety and efficacy with enhanced fibrin specificity. Plasmin variants are produced as direct fibrinolytic agents as a futuristic approach with targeted delivery of these drugs using liposome technlogy. The novel molecules from microbial, plant and animal origin present the future of direct thrombolytics due to their safety and ease of administration. PMID:27696935

Directed evolution of Oenococcus oeni strains for more efficient malolactic fermentation in a multi-stressor wine environment.

PubMed

Jiang, Jiao; Sumby, Krista M; Sundstrom, Joanna F; Grbin, Paul R; Jiranek, Vladimir

2018-08-01

High concentrations of ethanol, low pH, the presence of sulfur dioxide and some polyphenols have been reported to inhibit Oenococcus oeni growth, thereby negatively affecting malolactic fermentation (MLF) of wine. In order to generate superior O. oeni strains that can conduct more efficient MLF, despite these multiple stressors, a continuous culture approach was designed to directly evolve an existing ethanol tolerant O. oeni strain, A90. The strain was grown for ∼350 generations in a red wine-like environment with increasing levels of stressors. Three strains were selected from screening experiments based on their completion of fermentation in a synthetic wine/wine blend with 15.1% (v/v) ethanol, 26 mg/L SO 2 at pH 3.35 within 160 h, while the parent strain fermented no more than two thirds of l-malic acid in this medium. These superior strains also fermented faster and/or had a larger population in four different wines. A reduced or equivalent amount of the undesirable volatile, acetic acid, was produced by the optimised strains compared to a commercial strain in Mouvedre and Merlot wines. These findings demonstrate the feasibility of using directed evolution as a tool to generate more efficient MLF starters tailored for wines with multiple stressors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

PubMed Central

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M.; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel

2017-01-01

Abstract Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. PMID:28204787

Neutral biogeography and the evolution of climatic niches.

PubMed

Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

2014-05-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.

Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae.

PubMed

Ushida, Kazunari; Tsuchida, Sayaka; Ogura, Yoshitoshi; Toyoda, Atsushi; Maruyama, Fumito

2016-06-01

Intestinal microbiota are characterized by host-specific microorganisms, which have been selected through host-microbe interactions under phylogenetic evolution and transition of feeding behavior by the host. Although many studies have focused on disease-related intestinal microbiota, the origin and evolution of host-specific intestinal microbiota have not been well elucidated. Pig is the ideal mammal model to reveal the origin and evolution of host-specific intestinal microbiota because their direct wild ancestor and close phylogenetic neighbors are available for comparison. The pig has been recognized as a Lactobacillus-type animal. We analyzed the intestinal microbiota of various animals in Suidae: domestic pigs, wild boars and Red river hogs to survey the origin and evolution of Lactobacillus-dominated intestinal microbiota by metagenomic approach and following quantitative PCR confirmation. The metagenomic datasets were separated in two clusters; the wild animal cluster being characterized by a high abundance of Bifidobacterium, whereas the domesticated (or captured) animal cluster by Lactobacillus. In addition, Enterobacteriaceae were harbored as the major family only in domestic Sus scrofa. We conclude that domestication may have induced a larger Enterobacteriaceae population in pigs, and the introduction of modern feeding system further caused the development of Lactobacillus-dominated intestinal microbiota, with genetic and geographical factors possibly having a minor impact. © 2015 Japanese Society of Animal Science.

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Neutral biogeography and the evolution of climatic niches

PubMed Central

Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien

2014-01-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

Phylogenetic trends in phenolic metabolism of milkweeds (Asclepias): evidence for escalation.

PubMed

Agrawal, Anurag A; Salminen, Juha-Pekka; Fishbein, Mark

2009-03-01

Although plant-defense theory has long predicted patterns of chemical defense across taxa, we know remarkably little about the evolution of defense, especially in the context of directional phylogenetic trends. Here we contrast the production of phenolics and cardenolides in 35 species of milkweeds (Asclepias and Gomphocarpus). Maximum-likelihood analyses of character evolution revealed three major patterns. First, consistent with the defense-escalation hypothesis, the diversification of the milkweeds was associated with a trend for increasing phenolic production; this pattern was reversed (a declining evolutionary trend) for cardenolides, toxins sequestered by specialist herbivores. Second, phylogenetically independent correlations existed among phenolic classes across species. For example, coumaric acid derivatives showed negatively correlated evolution with caffeic acid derivatives, and this was likely driven by the fact that the former are used as precursors for the latter. In contrast, coumaric acid derivatives were positively correlated with flavonoids, consistent with competition for the precursor p-coumaric acid. Finally, of the phenolic classes, only flavonoids showed correlated evolution (positive) with cardenolides, consistent with a physiological and evolutionary link between the two via malonate. Thus, this study presents a rigorous test of the defense-escalation hypothesis and a novel phylogenetic approach to understanding the long-term persistence of physiological constraints on secondary metabolism.

Multiobjective Optimization Using a Pareto Differential Evolution Approach

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Differential Evolution is a simple, fast, and robust evolutionary algorithm that has proven effective in determining the global optimum for several difficult single-objective optimization problems. In this paper, the Differential Evolution algorithm is extended to multiobjective optimization problems by using a Pareto-based approach. The algorithm performs well when applied to several test optimization problems from the literature.

Student Teachers' Approaches to Teaching Biological Evolution

ERIC Educational Resources Information Center

Borgerding, Lisa A.; Klein, Vanessa A.; Ghosh, Rajlakshmi; Eibel, Albert

2015-01-01

Evolution is fundamental to biology and scientific literacy, but teaching high school evolution is often difficult. Evolution teachers face several challenges including limited content knowledge, personal conflicts with evolution, expectations of resistance, concerns about students' conflicts with religion, and curricular constraints. Evolution…

Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

PubMed

Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

2014-03-01

Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

PubMed Central

Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

2014-01-01

Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries. PMID:26430388

Continuous "in vitro" Evolution of a Ribozyme Ligase: A Model Experiment for the Evolution of a Biomolecule

ERIC Educational Resources Information Center

Ledbetter, Michael P.; Hwang, Tony W.; Stovall, Gwendolyn M.; Ellington, Andrew D.

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. "In vitro" directed evolution (IVDE) frequently serves as a model system for the study of Darwinian…

Nonmathematical concepts of selection, evolutionary energy, and levels of evolution.

PubMed

Darlington, P J

1972-05-01

The place of mathematics in hypotheticodeductive processes and in biological research is discussed. (Natural) Selection is defined and described as differential elimination of performed sets at any level. Sets and acting sets are groups of units (themselves sets of smaller units) at any level that may or do interact. A pseudomathematical equation describes directional change (evolution) in sets at any level. Selection is the ram of evolution; it cannot generate, but can only direct, evolutionary energy. The energy of evolution is derived from molecular or chemical levels, is transmitted upwards through the increasingly complex sets of sets that form living systems, and is turned in directions determined by the sum of selective processes, at different levels, which may either supplement or oppose each other. All evolutionary processes conform to the pseudomathematical equation referred to above, use energy as described above, and have a P/OE (ratio of programming to open-endedness) that cannot be measured, but can be related to other P/OE values. Phylogeny and ontogeny are compared as processes af directional change with set selection. Stages in the evolution of multi-cellular individuals are suggested, and are essentially the same as stages in the evolution of some multi-individual insect societies. Thinking is considered as a part of ontogeny involving an irreversible, nonrepetitive process of set selection in the brain.

Multiple exciton generation for photoelectrochemical hydrogen evolution reactions with quantum yields exceeding 100%

DOE PAGES

Yan, Yong; Crisp, Ryan W.; Gu, Jing; ...

2017-04-03

Multiple exciton generation (MEG) in quantum dots (QDs) has the potential to greatly increase the power conversion efficiency in solar cells and in solar-fuel production. During the MEG process, two electron-hole pairs (excitons) are created from the absorption of one high-energy photon, bypassing hot-carrier cooling via phonon emission. Here we demonstrate that extra carriers produced via MEG can be used to drive a chemical reaction with quantum efficiency above 100%. We developed a lead sulfide (PbS) QD photoelectrochemical cell that is able to drive hydrogen evolution from aqueous Na 2S solution with a peak external quantum efficiency exceeding 100%. QDmore » photoelectrodes that were measured all demonstrated MEG when the incident photon energy was larger than 2.7 times the bandgap energy. Finally, our results demonstrate a new direction in exploring high-efficiency approaches to solar fuels.« less

Inequity aversion and the evolution of cooperation

NASA Astrophysics Data System (ADS)

Ahmed, Asrar; Karlapalem, Kamalakar

2014-02-01

Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit memory of previous game plays. Our model is based on the notion of inequity aversion, a concept introduced within behavioral economics, whereby individuals care about payoff equality in outcomes. Here we explore the effect of using income inequality to guide partner selection and interaction. We study our model by considering both the well-mixed and the spatially structured population and present the conditions under which cooperation becomes dominant. Our results support the hypothesis that inequity aversion promotes cooperative relationship among nonkin.

Inequity aversion and the evolution of cooperation.

PubMed

Ahmed, Asrar; Karlapalem, Kamalakar

2014-02-01

Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit memory of previous game plays. Our model is based on the notion of inequity aversion, a concept introduced within behavioral economics, whereby individuals care about payoff equality in outcomes. Here we explore the effect of using income inequality to guide partner selection and interaction. We study our model by considering both the well-mixed and the spatially structured population and present the conditions under which cooperation becomes dominant. Our results support the hypothesis that inequity aversion promotes cooperative relationship among nonkin.

High-Performance Rh 2 P Electrocatalyst for Efficient Water Splitting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Haohong; Li, Dongguo; Tang, Yan

2017-04-05

The search for active, stable, and cost-efficient electrocatalysts for hydrogen production via water splitting could make a substantial impact on energy technologies that do not rely on fossil fuels. Here we report the synthesis of rhodium phosphide electrocatalyst with low metal loading in the form of nanocubes (NCs) dispersed in high-surface-area carbon (Rh2P/C) by a facile solvo-thermal approach. The Rh2P/C NCs exhibit remarkable performance for hydrogen evolution reaction and oxygen evolution reaction compared to Rh/C and Pt/C catalysts. The atomic structure of the Rh2P NCs was directly observed by annular dark-field scanning transmission electron microscopy, which revealed a phosphorus-rich outermostmore » atomic layer. Combined experimental and computational studies suggest that surface phosphorus plays a crucial role in determining the robust catalyst properties.« less

High-Performance Rh 2 P Electrocatalyst for Efficient Water Splitting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Haohong; Li, Dongguo; Tang, Yan

2017-04-05

Search for active, stable and cost-efficient electrocatalysts for hydrogen production via water splitting could make substantial impact to the energy technologies that do not rely on fossil fuels. Here we report the synthesis of rhodium phosphide electrocatalyst with low metal loading in the form of nanocubes (NCs) dispersed in high surface area carbon (Rh2P/C) by a facile solvo-thermal approach. The Rh2P/C NCs exhibit remarkable performance for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) compared to Rh/C and Pt/C catalysts. The atomic structure of the rhodium phosphide nanocubes was directly observed by annular dark-field scanning transmission electron microscopy (ADF-STEM),more » which revealed phosphorous-rich outermost atomic layer. Combined experimental and computational studies suggest that surface phosphorous plays crucial role in determining the robust catalyst properties.« less

Sex Chromosome Evolution in Amniotes: Applications for Bacterial Artificial Chromosome Libraries

PubMed Central

Janes, Daniel E.; Valenzuela, Nicole; Ezaz, Tariq; Amemiya, Chris; Edwards, Scott V.

2011-01-01

Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently. These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100–200 kb of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced. With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries. PMID:20981143

Two-layer interfacial flows beyond the Boussinesq approximation: a Hamiltonian approach

NASA Astrophysics Data System (ADS)

Camassa, R.; Falqui, G.; Ortenzi, G.

2017-02-01

The theory of integrable systems of Hamiltonian PDEs and their near-integrable deformations is used to study evolution equations resulting from vertical-averages of the Euler system for two-layer stratified flows in an infinite two-dimensional channel. The Hamiltonian structure of the averaged equations is obtained directly from that of the Euler equations through the process of Hamiltonian reduction. Long-wave asymptotics together with the Boussinesq approximation of neglecting the fluids’ inertia is then applied to reduce the leading order vertically averaged equations to the shallow-water Airy system, albeit in a non-trivial way. The full non-Boussinesq system for the dispersionless limit can then be viewed as a deformation of this well known equation. In a perturbative study of this deformation, a family of approximate constants of the motion are explicitly constructed and used to find local solutions of the evolution equations by means of hodograph-like formulae.

Floquet analysis of Kuznetsov-Ma breathers: A path towards spectral stability of rogue waves.

PubMed

Cuevas-Maraver, J; Kevrekidis, P G; Frantzeskakis, D J; Karachalios, N I; Haragus, M; James, G

2017-07-01

In the present work, we aim at taking a step towards the spectral stability analysis of Peregrine solitons, i.e., wave structures that are used to emulate extreme wave events. Given the space-time localized nature of Peregrine solitons, this is a priori a nontrivial task. Our main tool in this effort will be the study of the spectral stability of the periodic generalization of the Peregrine soliton in the evolution variable, namely the Kuznetsov-Ma breather. Given the periodic structure of the latter, we compute the corresponding Floquet multipliers, and examine them in the limit where the period of the orbit tends to infinity. This way, we extrapolate towards the stability of the limiting structure, namely the Peregrine soliton. We find that multiple unstable modes of the background are enhanced, yet no additional unstable eigenmodes arise as the Peregrine limit is approached. We explore the instability evolution also in direct numerical simulations.

BIOINSPIRED DESIGN AND DIRECTED EVOLUTION OF IRON CONTAINING ENZYMES FOR GREENSYNTHETIC PROCESSES AND BIOREMEDIATION

EPA Science Inventory

SU833912
Title: Bioinspired Design and Directed Evolution of Iron Containing Enzymes for Green Synthetic Processes and BioremediationEdward I. Solomon, Shaun D. Wong, Lei Liu, Caleb B. Bell, IIICynthia Nolt-Helms
Project Period: August 15, 2008 - August 14,...

Molecular evolution and the latitudinal biodiversity gradient.

PubMed

Dowle, E J; Morgan-Richards, M; Trewick, S A

2013-06-01

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Evolution of Automotive Chopper Circuits Towards Ultra High Efficiency and Power Density

NASA Astrophysics Data System (ADS)

Pavlovsky, Martin; Tsuruta, Yukinori; Kawamura, Atsuo

Automotive industry is considered to be one of the main contributors to environmental pollution and global warming. Therefore, many car manufacturers are in near future planning to introduce hybrid electric vehicles (HEV), fuel cell electric vehicles (FCEV) and pure electric vehicles (EV) to make our cars more environmentally friendly. These new vehicles require highly efficient and small power converters. In recent years, considerable improvements were made in designing such converters. In this paper, an approach based on so called Snubber Assisted Zero Voltage and Zero Current Switching topology otherwise also known as SAZZ is presented. This topology has evolved to be one of the leaders in the field of highly efficient converters with high power densities. Evolution and main features of this topology are briefly discussed. Capabilities of the topology are demonstrated on two case study prototypes based on different design approaches. The prototypes are designed to be fully bi-directional for peak power output of 30kW. Both designs reached efficiencies close to 99% in wide load range. Power densities over 40kW/litre are attainable in the same time. Combination of MOSFET technology and SAZZ topology is shown to be very beneficial to converters designed for EV applications.

Recursion equations in predicting band width under gradient elution.

PubMed

Liang, Heng; Liu, Ying

2004-06-18

The evolution of solute zone under gradient elution is a typical problem of non-linear continuity equation since the local diffusion coefficient and local migration velocity of the mass cells of solute zones are the functions of position and time due to space- and time-variable mobile phase composition. In this paper, based on the mesoscopic approaches (Lagrangian description, the continuity theory and the local equilibrium assumption), the evolution of solute zones in space- and time-dependent fields is described by the iterative addition of local probability density of the mass cells of solute zones. Furthermore, on macroscopic levels, the recursion equations have been proposed to simulate zone migration and spreading in reversed-phase high-performance liquid chromatography (RP-HPLC) through directly relating local retention factor and local diffusion coefficient to local mobile phase concentration. This new approach differs entirely from the traditional theories on plate concept with Eulerian description, since band width recursion equation is actually the accumulation of local diffusion coefficients of solute zones to discrete-time slices. Recursion equations and literature equations were used in dealing with same experimental data in RP-HPLC, and the comparison results show that the recursion equations can accurately predict band width under gradient elution.

Regional approaches in high-rise construction

NASA Astrophysics Data System (ADS)

Iconopisceva, O. G.; Proskurin, G. A.

2018-03-01

The evolutionary process of high-rise construction is in the article focus. The aim of the study was to create a retrospective matrix reflecting the tasks of the study such as: structuring the most iconic high-rise objects within historic boundaries. The study is based on contemporary experience of high-rise construction in different countries. The main directions and regional specifics in the field of high-rise construction as well as factors influencing the further evolution process are analyzed. The main changes in architectural stylistics, form-building, constructive solutions that focus on the principles of energy efficiency and bio positivity of "sustainable buildings", as well as the search for a new typology are noted. The most universal constructive methods and solutions that turned out to be particularly popular are generalized. The new typology of high-rises and individual approach to urban context are noted. The results of the study as a graphical scheme made it possible to represent the whole high-rise evolution. The new spatial forms of high-rises lead them to new role within the urban environments. Futuristic hyperscalable concepts take the autonomous urban space functions itself and demonstrate us how high-rises can replace multifunctional urban fabric, developing it inside their shells.

Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism

PubMed Central

Berntson, Gary G.; Norman, Greg J.; Hawkley, Louise C.; Cacioppo, John T.

2012-01-01

Evolution has sculpted the incredibly complex human nervous system, among the most complex functions of which extend beyond the individual to an intricate social structure. Although these functions are deterministic, those determinants are legion, heavily interacting and dependent on a specific evolutionary trajectory. That trajectory was directed by the adaptive significance of quasi-random genetic variations, but was also influenced by chance and caprice. With a different evolutionary pathway, the same neural elements could subserve functions distinctly different from what they do in extant human brains. Consequently, the properties of higher level neural networks cannot be derived readily from the properties of the lower level constituent elements, without studying these elements in the aggregate. Thus, a multi-level approach to integrative neuroscience may offer an optimal strategy. Moreover, the process of calibrative reductionism, by which concepts and understandings from one level of organization or analysis can mutually inform and ‘calibrate’ those from other levels (both higher and lower), may represent a viable approach to the application of reductionism in science. This is especially relevant in social neuroscience, where the basic subject matter of interest is defined by interacting organisms across diverse environments. PMID:23386961

Evolution of double white dwarf binaries undergoing direct-impact accretion: Implications for gravitational wave astronomy

NASA Astrophysics Data System (ADS)

Kremer, Kyle; Breivik, Katelyn; Larson, Shane L.; Kalogera, Vassiliki

2017-01-01

For close double white dwarf binaries, the mass-transfer phenomenon known as direct-impact accretion (when the mass transfer stream impacts the accretor directly rather than forming a disc) may play a pivotal role in the long-term evolution of the systems. In this analysis, we explore the long-term evolution of white dwarf binaries accreting through direct-impact and explore implications of such systems to gravitational wave astronomy. We cover a broad range of parameter space which includes initial component masses and the strength of tidal coupling, and show that these systems, which lie firmly within the LISA frequency range, show strong negative chirps which can last as long as several million years. Detections of double white dwarf systems in the direct-impact phase by detectors such as LISA would provide astronomers with unique ways of probing the physics governing close compact object binaries.

Sensory exploitation and cultural transmission: the late emergence of iconic representations in human evolution.

PubMed

Verpooten, Jan; Nelissen, Mark

2010-09-01

Iconic representations (i.e., figurative imagery and realistic art) only started to appear consistently some 45,000 years ago, although humans have been anatomically modern since 200,000-160,000 years ago. What explains this? Some authors have suggested a neurocognitive change took place, leading to a creative explosion, although this has been contested. Here, we examine the hypothesis that demographic changes caused cultural "cumulative adaptive evolution" and as such the emergence of modern symbolic behavior. This approach usefully explains the evolution of utilitarian skills and tools, and the creation of symbols to identify groups. However, it does not equally effectively explain the evolution of behaviors that may not be directly adaptive, such as the production of iconic representations like figurines and rock art. In order to shed light on their emergence, we propose to combine the above-mentioned cultural hypothesis with the concept of sensory exploitation. The concept essentially states that behavioral traits (in this case iconic art production) which exploit pre-existing sensory sensitivities will evolve if not hindered by costs (i.e., natural selection). In this view, iconic art traditions are evolved by piggy-backing on cumulative adaptive evolution. Since it is to date uncertain whether art has served any adaptive function in human evolution, parsimony demands paying more attention to the primary and a functional mechanism of sensory exploitation as opposed to mechanisms of models based exclusively on secondary benefits (such as Miller's, for instance, in which art is proposed to evolve as a sexual display of fitness).

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics.

PubMed

Ellner, Stephen P; Geber, Monica A; Hairston, Nelson G

2011-06-01

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident. © 2011 Blackwell Publishing Ltd/CNRS.

High School Students' Perceptions of Evolution Instruction: Acceptance and Evolution Learning Experiences

ERIC Educational Resources Information Center

Donnelly, Lisa A.; Kazempour, Mahsa; Amirshokoohi, Aidin

2009-01-01

Evolution is an important and sometimes controversial component of high school biology. In this study, we used a mixed methods approach to explore students' evolution acceptance and views of evolution teaching and learning. Students explained their acceptance and rejection of evolution in terms of evidence and conflicts with religion and…

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p + p collisions at s = 510 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adare, A.; Aidala, C.; Ajitanand, N. N.

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at √s=510 GeV. Correlations of charged hadrons of 0.7T<10 GeV/c with π 0 mesons of 4T<15 GeV/c or isolated direct photons of 7T direct photon or π 0. Nonperturbative evolution effects are extracted from Gaussian fits to the away-side inclusive-charged-hadron yields for different trigger-particle transverse momenta (pmore » $$trig\\atop{T}$$). The Gaussian widths and root mean square of p out are reported as a function of the interaction hard scale p$$trig\\atop{T}$$ to investigate possible transverse-momentum-dependent evolution differences between the π 0-h ± and direct photon-h ± correlations and factorization breaking effects. The widths are found to decrease with p$$trig\\atop{T}$$, which indicates that the Collins-Soper-Sterman soft factor is not driving the evolution with the hard scale in nearly back-to-back dihadron and direct photon-hadron production in p+p collisions. This behavior is in contrast to Drell-Yan and semi-inclusive deep-inelastic scattering measurements.« less

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p + p collisions at s = 510 GeV

DOE PAGES

Adare, A.; Aidala, C.; Ajitanand, N. N.; ...

2017-04-04

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at √s=510 GeV. Correlations of charged hadrons of 0.7T<10 GeV/c with π 0 mesons of 4T<15 GeV/c or isolated direct photons of 7T direct photon or π 0. Nonperturbative evolution effects are extracted from Gaussian fits to the away-side inclusive-charged-hadron yields for different trigger-particle transverse momenta (pmore » $$trig\\atop{T}$$). The Gaussian widths and root mean square of p out are reported as a function of the interaction hard scale p$$trig\\atop{T}$$ to investigate possible transverse-momentum-dependent evolution differences between the π 0-h ± and direct photon-h ± correlations and factorization breaking effects. The widths are found to decrease with p$$trig\\atop{T}$$, which indicates that the Collins-Soper-Sterman soft factor is not driving the evolution with the hard scale in nearly back-to-back dihadron and direct photon-hadron production in p+p collisions. This behavior is in contrast to Drell-Yan and semi-inclusive deep-inelastic scattering measurements.« less

Hybrid discrete/continuum algorithms for stochastic reaction networks

DOE PAGES

Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; ...

2014-10-22

Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components to avoid negative probability values. The numerical construction at the interface between the discretemore » and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. As a result, the performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.« less

Application of proteomics to ecology and population biology.

PubMed

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

The evolution of health care advance planning law and policy.

PubMed

Sabatino, Charles P

2010-06-01

The legal tools of health care advance planning have substantially changed since their emergence in the mid-1970s. Thirty years of policy development, primarily at the state legislative level addressing surrogate decision making and advance directives, have resulted in a disjointed policy landscape, yet with important points of convergence evolving over time. An understanding of the evolution of advance care planning policy has important implications for policy at both the state and federal levels. This article is a longitudinal statutory and literature review of health care advance planning from its origins to the present. While considerable variability across the states still remains, changes in law and policy over time suggest a gradual paradigm shift from what is described as a "legal transactional approach" to a "communications approach," the most recent extension of which is the emergence of Physician Orders for Life-Sustaining Treatment, or POLST. The communications approach helps translate patients' goals into visible and portable medical orders. States are likely to continue gradually moving away from a legal transactional mode of advance planning toward a communications model, albeit with challenges to authentic and reliable communication that accurately translates patients' wishes into the care they receive. In the meantime, the states and their health care institutions will continue to serve as the primary laboratory for advance care planning policy and practice.

Evolution of Minimally Invasive Approaches to the Sella and Parasellar Region

PubMed Central

Louis, Robert G.; Eisenberg, Amy; Barkhoudarian, Garni; Griffiths, Chester; Kelly, Daniel F.

2014-01-01

Introduction Given advancements in endoscopic image quality, instrumentation, surgical navigation, skull base closure techniques, and anatomical understanding, the endonasal endoscopic approach has rapidly evolved into a widely utilized technique for removal of sellar and parasellar tumors. Although pituitary adenomas and Rathke cleft cysts constitute the majority of lesions removed via this route, craniopharyngiomas, clival chordomas, parasellar meningiomas, and other lesions are increasingly removed using this approach. Paralleling the evolution of the endonasal route to the parasellar region, the supraorbital eyebrow craniotomy has also been increasingly used as an alternative minimally invasive approach to reach this skull base region. Similar to the endonasal route, the supraorbital route has been greatly facilitated by advances in endoscopy, along with development of more refined, low-profile instrumentation and surgical navigation technology. Objectives This review, encompassing both transcranial and transsphenoidal routes, will recount the high points and advances that have made minimally invasive approaches to the sellar region possible, the evolution of these approaches, and their relative indications and technical nuances. Data Synthesis The literature is reviewed regarding the evolution of surgical approaches to the sellar region beginning with the earliest attempts and emphasizing technological advances, which have allowed the evolution of the modern technique. The surgical techniques for both endoscopic transsphenoidal and supraorbital approaches are described in detail. The relative indications for each approach are highlighted using case illustrations. Conclusions Although tremendous advances have been made in transitioning toward minimally invasive transcranial and transsphenoidal approaches to the sella, further work remains to be done. Together, the endonasal endoscopic and the supraorbital endoscope-assisted approaches are complementary minimally invasive routes to the parasellar region. PMID:25992138

Application of a Phase-resolving, Directional Nonlinear Spectral Wave Model

NASA Astrophysics Data System (ADS)

Davis, J. R.; Sheremet, A.; Tian, M.; Hanson, J. L.

2014-12-01

We describe several applications of a phase-resolving, directional nonlinear spectral wave model. The model describes a 2D surface gravity wave field approaching a mildly sloping beach with parallel depth contours at an arbitrary angle accounting for nonlinear, quadratic triad interactions. The model is hyperbolic, with the initial wave spectrum specified in deep water. Complex amplitudes are generated based on the random phase approximation. The numerical implementation includes unidirectional propagation as a special case. In directional mode, it solves the system of equations in the frequency-alongshore wave number space. Recent enhancements of the model include the incorporation of dissipation caused by breaking and propagation over a viscous mud layer and the calculation of wave induced setup. Applications presented include: a JONSWAP spectrum with a cos2s directional distribution, for shore-perpendicular and oblique propagation, a study of the evolution of a single directional triad, and several preliminary comparisons to wave spectra collected at the USACE-FRF in Duck, NC which show encouraging results although further validation with a wider range of beach slopes and wave conditions is needed.

Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parent, Lucas R.; Bakalis, Evangelos; Ramírez-Hernández, Abelardo

Amphiphilic small molecules and polymers form commonplace nanoscale macromolecular compartments and bilayers, and as such are truly essential components in all cells and in many cellular processes. The nature of these architectures, including their formation, phase changes, and stimuli-response behaviors, is necessary for the most basic functions of life, and over the past half-century, these natural micellar structures have inspired a vast diversity of industrial products, from biomedicines to detergents, lubricants, and coatings. The importance of these materials and their ubiquity have made them the subject of intense investigation regarding their nanoscale dynamics with increasing interest in obtaining sufficient temporalmore » and spatial resolution to directly observe nanoscale processes. However, the vast majority of experimental methods involve either bulk-averaging techniques including light, neutron, and X-ray scattering, or are static in nature including even the most advanced cryogenic transmission electron microscopy techniques. Here, we employ in situ liquid-cell transmission electron microscopy (LCTEM) to directly observe the evolution of individual amphiphilic block copolymer micellar nanoparticles in solution, in real time with nanometer spatial resolution. These observations, made on a proof-of-concept bioconjugate polymer amphiphile, revealed growth and evolution occurring by unimer addition processes and by particle-particle collision-and-fusion events. The experimental approach, combining direct LCTEM observation, quantitative analysis of LCTEM data, and correlated in silico simulations, provides a unique view of solvated soft matter nanoassemblies as they morph and evolve in time and space, enabling us to capture these phenomena in solution.« less

Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic’s Era

PubMed Central

Moroz, Leonid L.

2015-01-01

The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570–600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the “omic” era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless “experiments” Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity. PMID:26163680

A novel approach to automatic threat detection in MMW imagery of people scanned in portals

NASA Astrophysics Data System (ADS)

Vaidya, Nitin M.; Williams, Thomas

2008-04-01

We have developed a novel approach to performing automatic detection of concealed threat objects in passive MMW imagery of people scanned in a portal setting. It is applicable to the significant class of imaging scanners that use the protocol of having the subject rotate in front of the camera in order to image them from several closely spaced directions. Customary methods of dealing with MMW sequences rely on the analysis of the spatial images in a frame-by-frame manner, with information extracted from separate frames combined by some subsequent technique of data association and tracking over time. We contend that the pooling of information over time in traditional methods is not as direct as can be and potentially less efficient in distinguishing threats from clutter. We have formulated a more direct approach to extracting information about the scene as it evolves over time. We propose an atypical spatio-temporal arrangement of the MMW image data - to which we give the descriptive name Row Evolution Image (REI) sequence. This representation exploits the singular aspect of having the subject rotate in front of the camera. We point out which features in REIs are most relevant to detecting threats, and describe the algorithms we have developed to extract them. We demonstrate results of successful automatic detection of threats, including ones whose faint image contrast renders their disambiguation from clutter very challenging. We highlight the ease afforded by the REI approach in permitting specialization of the detection algorithms to different parts of the subject body. Finally, we describe the execution efficiency advantages of our approach, given its natural fit to parallel processing. mage

Textural Evolution During Micro Direct Metal Deposition of NiTi Alloy

NASA Astrophysics Data System (ADS)

Khademzadeh, Saeed; Bariani, Paolo F.; Bruschi, Stefania

2018-03-01

In this research, a micro direct metal deposition process, newly developed as a potential method for micro additive manufacturing was used to fabricate NiTi builds. The effect of scanning strategy on grain growth and textural evolution was investigated using scanning electron microscope equipped with electron backscattered diffraction detector. Investigations showed that, the angle between the successive single tracks has an important role in grain size distribution and textural evolution of NiTi phase. Unidirectional laser beam scanning pattern developed a fiber texture; conversely, a backward and forward scanning pattern developed a strong < {100} > ‖‖ RD texture on the surface of NiTi cubic samples produced by micro direct metal deposition.

Textural Evolution During Micro Direct Metal Deposition of NiTi Alloy

NASA Astrophysics Data System (ADS)

Khademzadeh, Saeed; Bariani, Paolo F.; Bruschi, Stefania

2018-07-01

In this research, a micro direct metal deposition process, newly developed as a potential method for micro additive manufacturing was used to fabricate NiTi builds. The effect of scanning strategy on grain growth and textural evolution was investigated using scanning electron microscope equipped with electron backscattered diffraction detector. Investigations showed that, the angle between the successive single tracks has an important role in grain size distribution and textural evolution of NiTi phase. Unidirectional laser beam scanning pattern developed a fiber texture; conversely, a backward and forward scanning pattern developed a strong < {100} > ‖‖ RD texture on the surface of NiTi cubic samples produced by micro direct metal deposition.

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis.

PubMed

Koufopanou, Vassiliki; Burt, Austin

2005-07-01

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.

Social evolution and genetic interactions in the short and long term.

PubMed

Van Cleve, Jeremy

2015-08-01

The evolution of social traits remains one of the most fascinating and feisty topics in evolutionary biology even after half a century of theoretical research. W.D. Hamilton shaped much of the field initially with his 1964 papers that laid out the foundation for understanding the effect of genetic relatedness on the evolution of social behavior. Early theoretical investigations revealed two critical assumptions required for Hamilton's rule to hold in dynamical models: weak selection and additive genetic interactions. However, only recently have analytical approaches from population genetics and evolutionary game theory developed sufficiently so that social evolution can be studied under the joint action of selection, mutation, and genetic drift. We review how these approaches suggest two timescales for evolution under weak mutation: (i) a short-term timescale where evolution occurs between a finite set of alleles, and (ii) a long-term timescale where a continuum of alleles are possible and populations evolve continuously from one monomorphic trait to another. We show how Hamilton's rule emerges from the short-term analysis under additivity and how non-additive genetic interactions can be accounted for more generally. This short-term approach reproduces, synthesizes, and generalizes many previous results including the one-third law from evolutionary game theory and risk dominance from economic game theory. Using the long-term approach, we illustrate how trait evolution can be described with a diffusion equation that is a stochastic analogue of the canonical equation of adaptive dynamics. Peaks in the stationary distribution of the diffusion capture classic notions of convergence stability from evolutionary game theory and generally depend on the additive genetic interactions inherent in Hamilton's rule. Surprisingly, the peaks of the long-term stationary distribution can predict the effects of simple kinds of non-additive interactions. Additionally, the peaks capture both weak and strong effects of social payoffs in a manner difficult to replicate with the short-term approach. Together, the results from the short and long-term approaches suggest both how Hamilton's insight may be robust in unexpected ways and how current analytical approaches can expand our understanding of social evolution far beyond Hamilton's original work. Copyright © 2015 Elsevier Inc. All rights reserved.

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Quantitative genetic models of sexual conflict based on interacting phenotypes.

PubMed

Moore, Allen J; Pizzari, Tommaso

2005-05-01

Evolutionary conflict arises between reproductive partners when alternative reproductive opportunities are available. Sexual conflict can generate sexually antagonistic selection, which mediates sexual selection and intersexual coevolution. However, despite intense interest, the evolutionary implications of sexual conflict remain unresolved. We propose a novel theoretical approach to study the evolution of sexually antagonistic phenotypes based on quantitative genetics and the measure of social selection arising from male-female interactions. We consider the phenotype of one sex as both a genetically influenced evolving trait as well as the (evolving) social environment in which the phenotype of the opposite sex evolves. Several important points emerge from our analysis, including the relationship between direct selection on one sex and indirect effects through selection on the opposite sex. We suggest that the proposed approach may be a valuable tool to complement other theoretical approaches currently used to study sexual conflict. Most importantly, our approach highlights areas where additional empirical data can help clarify the role of sexual conflict in the evolutionary process.

The Goal of Evolution Instruction: Belief or Literacy?

ERIC Educational Resources Information Center

Cooper, Robert A.

2001-01-01

Discusses issues regarding evolution instruction in public schools and focuses on misconceptions such as the use of the word "belief", lack of evidence for theories of evolution, and the belief that teaching evolution as fact is proselytizing students. Presents teaching approaches to the topic of evolution. (Contains 33 references.) (YDS)

Understanding Student Approaches to Learning Evolution in the Context of their Perceptions of the Relationship between Science and Religion

NASA Astrophysics Data System (ADS)

Yasri, Pratchayapong; Mancy, Rebecca

2014-01-01

This study investigates a range of positions that learners take on the relationship between science and religion and the potential for these positions to explain student approaches when learning about evolution. A phenomenographic study based on interviews with nine students studying in Christian high schools in Thailand led to the identification of five distinct positions on the relationship between science and religion. Each position was associated with a characteristic pattern of learning about evolution that could be explained as an attempt by the students to align their particular learning approach with their position. Three of the positions have the potential to support scientifically valid understandings of evolution while avoiding emotional conflict. We suggest that knowledge of the range of positions and associated learning approaches can help educators to focus on the form and timing of support of benefit to those holding different viewpoints.

Artificial evolution: a new path for artificial intelligence?

PubMed

Husbands, P; Harvey, I; Cliff, D; Miller, G

1997-06-01

Recently there have been a number of proposals for the use of artificial evolution as a radically new approach to the development of control systems for autonomous robots. This paper explains the artificial evolution approach, using work at Sussex to illustrate it. The paper revolves around a case study on the concurrent evolution of control networks and visual sensor morphologies for a mobile robot. Wider intellectual issues surrounding the work are discussed, as is the use of more abstract evolutionary simulations as a new potentially useful tool in theoretical biology.

From Classical to Quantum: New Canonical Tools for the Dynamics of Gravity

NASA Astrophysics Data System (ADS)

Höhn, P. A.

2012-05-01

In a gravitational context, canonical methods offer an intuitive picture of the dynamics and simplify an identification of the degrees of freedom. Nevertheless, extracting dynamical information from background independent approaches to quantum gravity is a highly non-trivial challenge. In this thesis, the conundrum of (quantum) gravitational dynamics is approached from two different directions by means of new canonical tools. This thesis is accordingly divided into two parts: In the first part, a general canonical formalism for discrete systems featuring a variational action principle is developed which is equivalent to the covariant formulation following directly from the action. This formalism can handle evolving phase spaces and is thus appropriate for describing evolving lattices. Attention will be devoted to a characterization of the constraints, symmetries and degrees of freedom appearing in such discrete systems which, in the case of evolving phase spaces, is time step dependent. The advantage of this formalism is that it does not depend on the particular discretization and, hence, is suitable for coarse graining procedures. This formalism is applicable to discrete mechanics, lattice field theories and discrete gravity models---underlying some approaches to quantum gravity---and, furthermore, may prove useful for numerical imple mentations. For concreteness, these new tools are employed to formulate Regge Calculus canonically as a theory of the dynamics of discrete hypersurfaces in discrete spacetimes, thereby removing a longstanding obstacle to connecting covariant simplicial gravity models with canonical frameworks. This result is interesting in view of several background independent approaches to quantum gravity. In addition, perturbative expansions around symmetric background solutions of Regge Calculus are studied up to second order. Background gauge modes generically become propagating at second order as a consequence of a symmetry breaking. In the second part of this thesis, the paradigm of relational dynamics is considered. Dynamical observables in gravity are relational. Unfortunately, their construction and evaluation is notoriously difficult, especially in the quantum theory. An effective canonical framework is devised which permits to evaluate the semiclassical relational dynamics of constrained quantum systems by sidestepping technical problems associated with explicit constructions of physical Hilbert spaces. This effective approach is well-geared for addressing the concept of relational evolution in general quantum cosmological models since it (i) allows to depart from idealized relational `clock references’ and, instead, to employ generic degrees of freedom as imperfect relational `clocks’, (ii) enables one to systematically switch between different such `clocks’ and (iii) yields a consistent (temporally) local time evolution with transient observables so long as semiclassicality holds. These techniques are illustrated by toy models and, finally, are applied to a non-integrable cosmological model. It is argued that relational evolution is generically only a transient and semiclassical phenomenon

Collection Directions: The Evolution of Library Collections and Collecting

ERIC Educational Resources Information Center

Dempsey, Lorcan; Malpas, Constance; Lavoie, Brian

2014-01-01

This article takes a broad view of the evolution of collecting behaviors in a network environment and suggests some future directions based on various simple models. The authors look at the changing dynamics of print collections, at the greater engagement with research and learning behaviors, and at trends in scholarly communication. The goal is…

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

A multivariate quadrature based moment method for LES based modeling of supersonic combustion

NASA Astrophysics Data System (ADS)

Donde, Pratik; Koo, Heeseok; Raman, Venkat

2012-07-01

The transported probability density function (PDF) approach is a powerful technique for large eddy simulation (LES) based modeling of scramjet combustors. In this approach, a high-dimensional transport equation for the joint composition-enthalpy PDF needs to be solved. Quadrature based approaches provide deterministic Eulerian methods for solving the joint-PDF transport equation. In this work, it is first demonstrated that the numerical errors associated with LES require special care in the development of PDF solution algorithms. The direct quadrature method of moments (DQMOM) is one quadrature-based approach developed for supersonic combustion modeling. This approach is shown to generate inconsistent evolution of the scalar moments. Further, gradient-based source terms that appear in the DQMOM transport equations are severely underpredicted in LES leading to artificial mixing of fuel and oxidizer. To overcome these numerical issues, a semi-discrete quadrature method of moments (SeQMOM) is formulated. The performance of the new technique is compared with the DQMOM approach in canonical flow configurations as well as a three-dimensional supersonic cavity stabilized flame configuration. The SeQMOM approach is shown to predict subfilter statistics accurately compared to the DQMOM approach.

Evolution of US DOE Performance Assessments Over 20 Years - 13597

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suttora, Linda C.; Seitz, Roger R.

2013-07-01

Performance assessments (PAs) have been used for many years for the analysis of post-closure hazards associated with a radioactive waste disposal facility and to provide a reasonable expectation of the ability of the site and facility design to meet objectives for the protection of members of the public and the environment. The use of PA to support decision-making for LLW disposal facilities has been mandated in United States Department of Energy (US DOE) directives governing radioactive waste management since 1988 (currently DOE Order 435.1, Radioactive Waste Management). Prior to that time, PAs were also used in a less formal role.more » Over the past 20+ years, the US DOE approach to conduct, review and apply PAs has evolved into an efficient, rigorous and mature process that includes specific requirements for continuous improvement and independent reviews. The PA process has evolved through refinement of a graded and iterative approach designed to help focus efforts on those aspects of the problem expected to have the greatest influence on the decision being made. Many of the evolutionary changes to the PA process are linked to the refinement of the PA maintenance concept that has proven to be an important element of US DOE PA requirements in the context of supporting decision-making for safe disposal of LLW. The PA maintenance concept is central to the evolution of the graded and iterative philosophy and has helped to drive the evolution of PAs from a deterministic compliance calculation into a systematic approach that helps to focus on critical aspects of the disposal system in a manner designed to provide a more informed basis for decision-making throughout the life of a disposal facility (e.g., monitoring, research and testing, waste acceptance criteria, design improvements, data collection, model refinements). A significant evolution in PA modeling has been associated with improved use of uncertainty and sensitivity analysis techniques to support efficient implementation of the graded and iterative approach. Rather than attempt to exactly predict the migration of radionuclides in a disposal unit, the best PAs have evolved into tools that provide a range of results to guide decision-makers in planning the most efficient, cost effective, and safe disposal of radionuclides. (authors)« less

Using Publish-Subscribe Messaging for System Status and Automation

NASA Technical Reports Server (NTRS)

Smith, Danford S.

2015-01-01

The NASA Goddard Mission Services Evolution Center (GMSEC) system is a message-based plug-and-play open system architecture used in many of NASA mission operations centers. This presentation will focus on the use of GMSEC standard messages to report and analyze the status of a system and enable the automation of the system's components. In GMSEC systems, each component reports its status using a keep-alive message and also publishes status and activities as log messages. In addition, the components can accept functional directive messages from the GMSEC message bus. Over the past several years, development teams have found ways to utilize these messages to create innovative display pages and increasingly sophisticated approaches to automation. This presentation will show the flexibility and value of the message-based approach to system awareness and automation.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

PubMed

Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

2012-03-01

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

The Inception, Evolution, and Current State of the Moral Development School of Lawrence Kohlberg.

ERIC Educational Resources Information Center

Cortese, Anthony J.

Tiryakian's "school" approach is used to analyze the evolution of Kohlberg's study of moral development over the past 25 years. The first part of the paper contrasts the paradigm approach (Kuhn 1970) to the schools approach in defining the development of the social sciences. Specifically, Kuhn's definition of a paradigm…

Emotional and Spiritual Quotient Approach Improve Biology Education Students’ Acceptance of Evolution Theory

NASA Astrophysics Data System (ADS)

Darussyamsu, R.; Fadilah, M.; Putri, D. H.

2018-04-01

Emotional and spiritual aspect is one of main factors that influence students’ acceptance of a theory. This study aim to measure university students’ acceptance of evolution by learns evolution using emotional and spiritual quotient (ESQ) approach. This is a quasi-experimental research using one shot case study design with the subject 36 biology educational students at Biology Department, Faculty of Mathematics and Natural Science, Universitas Negeri Padang. Data collected using the MATE instrument by Rutledge and Warden (2000) after the students learn evolution for eight meetings since January until March 2017. The result showed that by learning evolution theory combine with ESQ aspects increase students acceptance from very low become moderate acceptance. It concluded that ESQ aspects can improve students’ acceptance of evolution. Any criteria depend on it are discussed.

Forecasting Propagation and Evolution of CMEs in an Operational Setting: What Has Been Learned

NASA Technical Reports Server (NTRS)

Zheng, Yihua; Macneice, Peter; Odstrcil, Dusan; Mays, M. L.; Rastaetter, Lutz; Pulkkinen, Antti; Taktakishvili, Aleksandre; Hesse, Michael; Kuznetsova, M. Masha; Lee, Hyesook;

Evolution of Aging Theories: Why Modern Programmed Aging Concepts Are Transforming Medical Research.

PubMed

Goldsmith, Theodore C

2016-12-01

Programmed aging refers to the idea that senescence in humans and other organisms is purposely caused by evolved biological mechanisms to obtain an evolutionary advantage. Until recently, programmed aging was considered theoretically impossible because of the mechanics of the evolution process, and medical research was based on the idea that aging was not programmed. Theorists struggled for more than a century in efforts to develop non-programmed theories that fit observations, without obtaining a consensus supporting any non-programmed theory. Empirical evidence of programmed lifespan limitations continued to accumulate. More recently, developments, especially in our understanding of biological inheritance, have exposed major issues and complexities regarding the process of evolution, some of which explicitly enable programmed aging of mammals. Consequently, science-based opposition to programmed aging has dramatically declined. This progression has major implications for medical research, because the theories suggest that very different biological mechanisms are ultimately responsible for highly age-related diseases that now represent most research efforts and health costs. Most particularly, programmed theories suggest that aging per se is a treatable condition and suggest a second path toward treating and preventing age-related diseases that can be exploited in addition to the traditional disease-specific approaches. The theories also make predictions regarding the nature of biological aging mechanisms and therefore suggest research directions. This article discusses developments of evolutionary mechanics, the consequent programmed aging theories, and logical inferences concerning biological aging mechanisms. It concludes that major medical research organizations cannot afford to ignore programmed aging concepts in assigning research resources and directions.

Forecasting propagation and evolution of CMEs in an operational setting: What has been learned

NASA Astrophysics Data System (ADS)

Zheng, Yihua; Macneice, Peter; Odstrcil, Dusan; Mays, M. L.; Rastaetter, Lutz; Pulkkinen, Antti; Taktakishvili, Aleksandre; Hesse, Michael; Masha Kuznetsova, M.; Lee, Hyesook; Chulaki, Anna

2013-10-01

of the major types of solar eruption, coronal mass ejections (CMEs) not only impact space weather, but also can have significant societal consequences. CMEs cause intense geomagnetic storms and drive fast mode shocks that accelerate charged particles, potentially resulting in enhanced radiation levels both in ions and electrons. Human and technological assets in space can be endangered as a result. CMEs are also the major contributor to generating large amplitude Geomagnetically Induced Currents (GICs), which are a source of concern for power grid safety. Due to their space weather significance, forecasting the evolution and impacts of CMEs has become a much desired capability for space weather operations worldwide. Based on our operational experience at Space Weather Research Center at NASA Goddard Space Flight Center (http://swrc.gsfc.nasa.gov), we present here some of the insights gained about accurately predicting CME impacts, particularly in relation to space weather operations. These include: 1. The need to maximize information to get an accurate handle of three-dimensional (3-D) CME kinetic parameters and therefore improve CME forecast; 2. The potential use of CME simulation results for qualitative prediction of regions of space where solar energetic particles (SEPs) may be found; 3. The need to include all CMEs occurring within a 24 h period for a better representation of the CME interactions; 4. Various other important parameters in forecasting CME evolution in interplanetary space, with special emphasis on the CME propagation direction. It is noted that a future direction for our CME forecasting is to employ the ensemble modeling approach.

Subsea approach to work systems development

NASA Technical Reports Server (NTRS)

Gernhardt, M. L.; Frisbie, F. R.; Brown, C. E.

1988-01-01

Self-contained undersea working environments with applications to space station EVA environments are discussed. Physiological limitations include decompression, inert gas narcosis, high-pressure nervous system, gas toxicity, and thermal limitations. Work task requirements include drilling support, construction, inspection, and repair. Work systems include hyperbaric diving, atmospheric work systems, tele-operated work systems, and hybrid systems. Each type of work system is outlined in terms of work capabilities, special interface requirements, and limitations. Various operational philosophies are discussed. The evolution of work systems in the subsea industry has been the result of direct operational experience in a competitive market.

New Assumptions to Guide SETI Research

NASA Technical Reports Server (NTRS)

Colombano, S. P.

2018-01-01

The recent Kepler discoveries of Earth-like planets offer the opportunity to focus our attention on detecting signs of life and technology in specific planetary systems, but I feel we need to become more flexible in our assumptions. The reason is that, while it is still reasonable and conservative to assume that life is most likely to have originated in conditions similar to ours, the vast time differences in potential evolutions render the likelihood of "matching" technologies very slim. In light of these challenges I propose a more "aggressive"� approach to future SETI exploration in directions that until now have received little consideration.

Microstructural comparison of the kinematics of discrete and continuum dislocations models

NASA Astrophysics Data System (ADS)

Sandfeld, Stefan; Po, Giacomo

2015-12-01

The Continuum Dislocation Dynamics (CDD) theory and the Discrete Dislocation Dynamics (DDD) method are compared based on concise mathematical formulations of the coarse graining of discrete data. A numerical tool for converting from a discrete to a continuum representation of a given dislocation configuration is developed, which allows to directly compare both simulation approaches based on continuum quantities (e.g. scalar density, geometrically necessary densities, mean curvature). Investigating the evolution of selected dislocation configurations within analytically given velocity fields for both DDD and CDD reveals that CDD contains a surprising number of important microstructural details.

Genetic Differences Between Great Apes and Humans: Implications for Human Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varki, Ajit

2004-03-17

When considering protein sequences, humans are 99-100% identical to chimpanzees and bonobos, our closest evolutionary relatives. The evolution of humans (and the unique features of our species) from a common ancestor with these great apes involved many steps, influenced by interactions amongst factors of genetic, developmental, ecological, microbial, climatic, behavioral, cultural and social origin. The genetic factors can be approached by direct comparisons of human and great ape genomes, genes and gene products, and by elucidating biochemical and biological consequences of the differences. We have discovered multiple genetic and biochemical differences between humans and great apes, particularly in relationship tomore » a family of cell surface molecules called sialic acids. These differences have implications for the human condition, ranging from susceptibility or resistance to microbial pathogens; effects on endogenous receptors in the immune system; potential effects on placental signaling; the expression of oncofetal antigens in cancers; consequences of dietary intake of animal foods; and the development of the mammalian brain. This talk will provide an overview of these and other genetic differences between humans and great apes, with attention to differences potentially relevant to the evolution of humans.« less

Identification of a missing link in the evolution of an enzyme into a transcriptional regulator.

PubMed

Durante-Rodríguez, Gonzalo; Mancheño, José Miguel; Rivas, Germán; Alfonso, Carlos; García, José Luis; Díaz, Eduardo; Carmona, Manuel

2013-01-01

The evolution of transcriptional regulators through the recruitment of DNA-binding domains by enzymes is a widely held notion. However, few experimental approaches have directly addressed this hypothesis. Here we report the reconstruction of a plausible pathway for the evolution of an enzyme into a transcriptional regulator. The BzdR protein is the prototype of a subfamily of prokaryotic transcriptional regulators that controls the expression of genes involved in the anaerobic degradation of benzoate. We have shown that BzdR consists of an N-terminal DNA-binding domain connected through a linker to a C-terminal effector-binding domain that shows significant identity to the shikimate kinase (SK). The construction of active synthetic BzdR-like regulators by fusing the DNA-binding domain of BzdR to the Escherichia coli SKI protein strongly supports the notion that an ancestral SK domain could have been involved in the evolutionary origin of BzdR. The loss of the enzymatic activity of the ancestral SK domain was essential for it to evolve as a regulatory domain in the current BzdR protein. This work also supports the view that enzymes precede the emergence of the regulatory systems that may control their expression.

Evolutionary rates for multivariate traits: the role of selection and genetic variation

PubMed Central

Pitchers, William; Wolf, Jason B.; Tregenza, Tom; Hunt, John; Dworkin, Ian

2014-01-01

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. PMID:25002697

Molding the business end of neurotoxins by diversifying evolution.

PubMed

Kozminsky-Atias, Adi; Zilberberg, Noam

2012-02-01

A diverse range of organisms utilize neurotoxins that target specific ion channels and modulate their activity. Typically, toxins are clustered into several multigene families, providing an organism with the upper hand in the never-ending predator-prey arms race. Several gene families, including those encoding certain neurotoxins, have been subject to diversifying selection forces, resulting in rapid gene evolution. Here we sought a spatial pattern in the distribution of both diversifying and purifying selection forces common to neurotoxin gene families. Utilizing the mechanistic empirical combination model, we analyzed various toxin families from different phyla affecting various receptors and relying on diverse modes of action. Through this approach, we were able to detect clear correlations between the pharmacological surface of a toxin and rapidly evolving domains, rich in positively selected residues. On the other hand, patches of negatively selected residues were restricted to the nontoxic face of the molecule and most likely help in stabilizing the tertiary structure of the toxin. We thus propose a mutual evolutionary strategy of venomous animals in which adaptive molecular evolution is directed toward the toxin active surface. Furthermore, we propose that the binding domains of unstudied toxins could be readily predicted using evolutionary considerations.

Accounting for rate variation among lineages in comparative demographic analyses.

PubMed

Hope, Andrew G; Ho, Simon Y W; Malaney, Jason L; Cook, Joseph A; Talbot, Sandra L

2014-09-01

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Two fundamental questions about protein evolution.

PubMed

Penny, David; Zhong, Bojian

2015-12-01

Two basic questions are considered that approach protein evolution from different directions; the problems arising from using Markov models for the deeper divergences, and then the origin of proteins themselves. The real problem for the first question (going backwards in time) is that at deeper phylogenies the Markov models of sequence evolution must lose information exponentially at deeper divergences, and several testable methods are suggested that should help resolve these deeper divergences. For the second question (coming forwards in time) a problem is that most models for the origin of protein synthesis do not give a role for the very earliest stages of the process. From our knowledge of the importance of replication accuracy in limiting the length of a coding molecule, a testable hypothesis is proposed. The length of the code, the code itself, and tRNAs would all have prior roles in increasing the accuracy of RNA replication; thus proteins would have been formed only after the tRNAs and the length of the triplet code are already formed. Both questions lead to testable predictions. Copyright © 2014 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Deviation from the line of least resistance does not exclude genetic constraints: a comment on Berner et al. (2010).

PubMed

Hansen, Thomas F; Voje, Kjetil L

2011-06-01

Berner et al. (2010) found that freshwater adaptation of three-spined sticklebacks had not followed the direction of maximal evolvability. Based on this, they suggested that ancestral variance structure has not appreciably biased adaptive diversification. We reanalyze their data to show that evolution has happened in directions of much larger than average evolvability, and we conclude that their data are consistent with an influence of ancestral variational constraints. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Toward multiscale modelings of grain-fluid systems

NASA Astrophysics Data System (ADS)

Chareyre, Bruno; Yuan, Chao; Montella, Eduard P.; Salager, Simon

2017-06-01

Computationally efficient methods have been developed for simulating partially saturated granular materials in the pendular regime. In contrast, one hardly avoid expensive direct resolutions of 2-phase fluid dynamics problem for mixed pendular-funicular situations or even saturated regimes. Following previous developments for single-phase flow, a pore-network approach of the coupling problems is described. The geometry and movements of phases and interfaces are described on the basis of a tetrahedrization of the pore space, introducing elementary objects such as bridge, meniscus, pore body and pore throat, together with local rules of evolution. As firmly established local rules are still missing on some aspects (entry capillary pressure and pore-scale pressure-saturation relations, forces on the grains, or kinetics of transfers in mixed situations) a multi-scale numerical framework is introduced, enhancing the pore-network approach with the help of direct simulations. Small subsets of a granular system are extracted, in which multiphase scenario are solved using the Lattice-Boltzman method (LBM). In turns, a global problem is assembled and solved at the network scale, as illustrated by a simulated primary drainage.

Micromechanical modeling of short glass-fiber reinforced thermoplastics-Isotropic damage of pseudograins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kammoun, S.; Brassart, L.; Doghri, I.

A micromechanical damage modeling approach is presented to predict the overall elasto-plastic behavior and damage evolution in short fiber reinforced composite materials. The practical use of the approach is for injection molded thermoplastic parts reinforced with short glass fibers. The modeling is proceeded as follows. The representative volume element is decomposed into a set of pseudograins, the damage of which affects progressively the overall stiffness and strength up to total failure. Each pseudograin is a two-phase composite with aligned inclusions having same aspect ratio. A two-step mean-field homogenization procedure is adopted. In the first step, the pseudograins are homogenized individuallymore » according to the Mori-Tanaka scheme. The second step consists in a self-consistent homogenization of homogenized pseudograins. An isotropic damage model is applied at the pseudograin level. The model is implemented as a UMAT in the finite element code ABAQUS. Model is shown to reproduce the strength and the anisotropy (Lankford coefficient) during uniaxial tensile tests on samples cut under different directions relative to the injection flow direction.« less

Micromechanical modeling of short glass-fiber reinforced thermoplastics-Isotropic damage of pseudograins

NASA Astrophysics Data System (ADS)

Kammoun, S.; Brassart, L.; Robert, G.; Doghri, I.; Delannay, L.

2011-05-01

A micromechanical damage modeling approach is presented to predict the overall elasto-plastic behavior and damage evolution in short fiber reinforced composite materials. The practical use of the approach is for injection molded thermoplastic parts reinforced with short glass fibers. The modeling is proceeded as follows. The representative volume element is decomposed into a set of pseudograins, the damage of which affects progressively the overall stiffness and strength up to total failure. Each pseudograin is a two-phase composite with aligned inclusions having same aspect ratio. A two-step mean-field homogenization procedure is adopted. In the first step, the pseudograins are homogenized individually according to the Mori-Tanaka scheme. The second step consists in a self-consistent homogenization of homogenized pseudograins. An isotropic damage model is applied at the pseudograin level. The model is implemented as a UMAT in the finite element code ABAQUS. Model is shown to reproduce the strength and the anisotropy (Lankford coefficient) during uniaxial tensile tests on samples cut under different directions relative to the injection flow direction.

Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

PubMed Central

Pechmann, Sebastian; Frydman, Judith

2014-01-01

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability. We here examine factors that systematically promote non-conservative mutations at the proteome level. Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered. Similarly, whether and how molecular chaperones, which have been shown to buffer destabilizing mutations in individual proteins, generally provide robustness during proteome evolution remains unclear. To this end, we introduce an evolutionary parameter λ that directly estimates the rate of non-conservative substitutions. Our analysis of λ in Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens sequences reveals how co- and post-translationally acting chaperones differentially promote non-conservative substitutions in their substrates, likely through buffering of their destabilizing effects. We further find that λ serves well to quantify the evolution of intrinsically disordered proteins even though the unstructured, thus generally variable regions in proteins are often flanked by very conserved sequences. Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher λ at the expense of enhanced chaperone assistance. Our findings thus highlight an intricate interplay of molecular chaperones and protein disorder in the evolvability of protein networks. Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. We feel that the development of λ may be a valuable addition to the toolbox applied to understand the molecular basis of evolution. PMID:24968255

An adaptive sharing elitist evolution strategy for multiobjective optimization.

PubMed

Costa, Lino; Oliveira, Pedro

2003-01-01

Almost all approaches to multiobjective optimization are based on Genetic Algorithms (GAs), and implementations based on Evolution Strategies (ESs) are very rare. Thus, it is crucial to investigate how ESs can be extended to multiobjective optimization, since they have, in the past, proven to be powerful single objective optimizers. In this paper, we present a new approach to multiobjective optimization, based on ESs. We call this approach the Multiobjective Elitist Evolution Strategy (MEES) as it incorporates several mechanisms, like elitism, that improve its performance. When compared with other algorithms, MEES shows very promising results in terms of performance.

Toward an evolutionary-predictive foundation for creativity : Commentary on "Human creativity, evolutionary algorithms, and predictive representations: The mechanics of thought trials" by Arne Dietrich and Hilde Haider, 2014 (Accepted pending minor revisions for publication in Psychonomic Bulletin & Review).

PubMed

Gabora, Liane; Kauffman, Stuart

2016-04-01

Dietrich and Haider (Psychonomic Bulletin & Review, 21 (5), 897-915, 2014) justify their integrative framework for creativity founded on evolutionary theory and prediction research on the grounds that "theories and approaches guiding empirical research on creativity have not been supported by the neuroimaging evidence." Although this justification is controversial, the general direction holds promise. This commentary clarifies points of disagreement and unresolved issues, and addresses mis-applications of evolutionary theory that lead the authors to adopt a Darwinian (versus Lamarckian) approach. To say that creativity is Darwinian is not to say that it consists of variation plus selection - in the everyday sense of the term - as the authors imply; it is to say that evolution is occurring because selection is affecting the distribution of randomly generated heritable variation across generations. In creative thought the distribution of variants is not key, i.e., one is not inclined toward idea A because 60 % of one's candidate ideas are variants of A while only 40 % are variants of B; one is inclined toward whichever seems best. The authors concede that creative variation is partly directed; however, the greater the extent to which variants are generated non-randomly, the greater the extent to which the distribution of variants can reflect not selection but the initial generation bias. Since each thought in a creative process can alter the selective criteria against which the next is evaluated, there is no demarcation into generations as assumed in a Darwinian model. We address the authors' claim that reduced variability and individuality are more characteristic of Lamarckism than Darwinian evolution, and note that a Lamarckian approach to creativity has addressed the challenge of modeling the emergent features associated with insight.

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

PubMed Central

Brites, Daniela; Stucki, David; Evans, Joanna C.; Seldon, Ronnett; Heekes, Alexa; Mulder, Nicola; Nicol, Mark; Oni, Tolu; Mizrahi, Valerie; Warner, Digby F.; Parkhill, Julian; Gagneux, Sebastien; Martin, Darren P.; Wilkinson, Robert J.

2017-01-01

Abstract HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates. PMID:28369607

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

PubMed

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel; Wegmann, Daniel

2017-11-01

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Modeling evolution of the mind and cultures: emotional Sapir-Whorf hypothesis

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid I.

2009-05-01

Evolution of cultures is ultimately determined by mechanisms of the human mind. The paper discusses the mechanisms of evolution of language from primordial undifferentiated animal cries to contemporary conceptual contents. In parallel with differentiation of conceptual contents, the conceptual contents were differentiated from emotional contents of languages. The paper suggests the neural brain mechanisms involved in these processes. Experimental evidence and theoretical arguments are discussed, including mathematical approaches to cognition and language: modeling fields theory, the knowledge instinct, and the dual model connecting language and cognition. Mathematical results are related to cognitive science, linguistics, and psychology. The paper gives an initial mathematical formulation and mean-field equations for the hierarchical dynamics of both the human mind and culture. In the mind heterarchy operation of the knowledge instinct manifests through mechanisms of differentiation and synthesis. The emotional contents of language are related to language grammar. The conclusion is an emotional version of Sapir-Whorf hypothesis. Cultural advantages of "conceptual" pragmatic cultures, in which emotionality of language is diminished and differentiation overtakes synthesis resulting in fast evolution at the price of self doubts and internal crises are compared to those of traditional cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation. Multi-language, multi-ethnic society might combine the benefits of stability and fast differentiation. Unsolved problems and future theoretical and experimental directions are discussed.

Sexual selection on male size drives the evolution of male-biased sexual size dimorphism via the prolongation of male development.

PubMed

Rohner, Patrick T; Blanckenhorn, Wolf U; Puniamoorthy, Nalini

2016-06-01

Sexual size dimorphism (SSD) arises when the net effects of natural and sexual selection on body size differ between the sexes. Quantitative SSD variation between taxa is common, but directional intraspecific SSD reversals are rare. We combined micro- and macroevolutionary approaches to study geographic SSD variation in closely related black scavenger flies. Common garden experiments revealed stark intra- and interspecific variation: Sepsis biflexuosa is monomorphic across the Holarctic, while S. cynipsea (only in Europe) consistently exhibits female-biased SSD. Interestingly, S. neocynipsea displays contrasting SSD in Europe (females larger) and North America (males larger), a pattern opposite to the geographic reversal in SSD of S. punctum documented in a previous study. In accordance with the differential equilibrium model for the evolution of SSD, the intensity of sexual selection on male size varied between continents (weaker in Europe), whereas fecundity selection on female body size did not. Subsequent comparative analyses of 49 taxa documented at least six independent origins of male-biased SSD in Sepsidae, which is likely caused by sexual selection on male size and mediated by bimaturism. Therefore, reversals in SSD and the associated changes in larval development might be much more common and rapid and less constrained than currently assumed. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models.

PubMed

Foulkes, N S; Whitmore, D; Vallone, D; Bertolucci, C

2016-01-01

The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work. This is illustrated by the use of fish models for studying the function and evolution of the circadian clock. In this review we outline our current understanding of how fish clocks sense and respond to light and explain how this differs fundamentally from the situation with mammalian clocks. In addition, we present results from comparative studies involving two species of blind cavefish, Astyanax mexicanus and Phreatichthys andruzzii. This work reveals the consequences of evolution in perpetual darkness for the circadian clock and its regulation by light as well as for other mechanisms such as DNA repair, sleep, and metabolism which directly or indirectly are affected by regular exposure to sunlight. Major differences in the cave habitats inhabited by these two cavefish species have a clear impact on shaping the molecular and cellular adaptations to life in complete darkness. Copyright © 2016 Elsevier Inc. All rights reserved.

Using “Tender” x-ray ambient pressure x-Ray photoelectron spectroscopy as a direct probe of solid-liquid interface

DOE PAGES

Axnanda, Stephanus; Crumlin, Ethan J.; Mao, Baohua; ...

2015-05-07

We report a new method to probe the solid-liquid interface through the use of a thin liquid layer on a solid surface. An ambient pressure XPS (AP-XPS) endstation that is capable of detecting high kinetic energy photoelectrons (7 keV) at a pressure up to 110 Torr has been constructed and commissioned. Additionally, we have deployed a “dip & pull” method to create a stable nanometers-thick aqueous electrolyte on platinum working electrode surface. Combining the newly constructed AP-XPS system, “dip & pull” approach, with a “tender” X-ray synchrotron source (2 keV–7 keV), we are able to access the interface between liquidmore » and solid dense phases with photoelectrons and directly probe important phenomena occurring at the narrow solid-liquid interface region in an electrochemical system. Using this approach, we have performed electrochemical oxidation of the Pt electrode at an oxygen evolution reaction (OER) potential. Under this potential, we observe the formation of both Pt²⁺ and Pt⁴⁺ interfacial species on the Pt working electrode in situ. We believe this thin-film approach and the use of “tender” AP-XPS highlighted in this study is an innovative new approach to probe this key solid-liquid interface region of electrochemistry.« less

Using “Tender” x-ray ambient pressure x-Ray photoelectron spectroscopy as a direct probe of solid-liquid interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Axnanda, Stephanus; Crumlin, Ethan J.; Mao, Baohua

We report a new method to probe the solid-liquid interface through the use of a thin liquid layer on a solid surface. An ambient pressure XPS (AP-XPS) endstation that is capable of detecting high kinetic energy photoelectrons (7 keV) at a pressure up to 110 Torr has been constructed and commissioned. Additionally, we have deployed a “dip & pull” method to create a stable nanometers-thick aqueous electrolyte on platinum working electrode surface. Combining the newly constructed AP-XPS system, “dip & pull” approach, with a “tender” X-ray synchrotron source (2 keV–7 keV), we are able to access the interface between liquidmore » and solid dense phases with photoelectrons and directly probe important phenomena occurring at the narrow solid-liquid interface region in an electrochemical system. Using this approach, we have performed electrochemical oxidation of the Pt electrode at an oxygen evolution reaction (OER) potential. Under this potential, we observe the formation of both Pt²⁺ and Pt⁴⁺ interfacial species on the Pt working electrode in situ. We believe this thin-film approach and the use of “tender” AP-XPS highlighted in this study is an innovative new approach to probe this key solid-liquid interface region of electrochemistry.« less

Evolution of genetic architecture under directional selection.

PubMed

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.

Dynamical Models of Elliptical Galaxies in z = 0.5 Clusters. I. Data-Model Comparison and Evolution of Galaxy Rotation

NASA Astrophysics Data System (ADS)

van der Marel, Roeland P.; van Dokkum, Pieter G.

2007-10-01

We present spatially resolved stellar rotation velocity and velocity dispersion profiles from Keck/LRIS absorption-line spectra for 25 galaxies, mostly visually classified ellipticals, in three clusters at z~0.5. We interpret the kinematical data and HST photometry using oblate axisymmetric two-integral f(E,Lz) dynamical models based on the Jeans equations. This yields good fits, provided that the seeing and observational characteristics are carefully modeled. The fits yield for each galaxy the dynamical mass-to-light ratio (M/L) and a measure of the galaxy rotation rate. Paper II addresses the implied M/L evolution. Here we study the rotation-rate evolution by comparison to a sample of local elliptical galaxies of similar present-day luminosity. The brightest galaxies in the sample all rotate too slowly to account for their flattening, as is also observed at z=0. But the average rotation rate is higher at z~0.5 than locally. This may be due to a higher fraction of misclassified S0 galaxies (although this effect is insufficient to explain the observed strong evolution of the cluster S0 fraction with redshift). Alternatively, dry mergers between early-type galaxies may have decreased the average rotation rate over time. It is unclear whether such mergers are numerous enough in clusters to explain the observed trend quantitatively. Disk-disk mergers may affect the comparison through the so-called ``progenitor bias,'' but this cannot explain the direction of the observed rotation-rate evolution. Additional samples are needed to constrain possible environmental dependencies and cosmic variance in galaxy rotation rates. Either way, studies of the internal stellar dynamics of distant galaxies provide a valuable new approach for exploring galaxy evolution.

Determining the Interstellar Wind Longitudinal Inflow Evolution Using Pickup Ions in the Helium Focusing Cone

NASA Astrophysics Data System (ADS)

Spitzer, S. A.; Gilbert, J. A.; Lepri, S. T.

2017-12-01

We propose to determine the longitudinal inflow direction of the local interstellar medium through the Heliosphere. This longitudinal inflow direction directly correlates to the longitudinal direction of the helium focusing cone with respect to the Sun. We can calculate this direction by finding the He+ pickup ion density peak as mass spectrometers such as ACE/SWICS, Wind/STICS, and Helios/Micrometeoroid Detector and Analyzer pass through the focusing cone. Mapping from the location of this density peak to the Sun, around which the helium is focused, will directly yield the desired longitudinal direction. We will find this direction for each year since the first measurements in the 1970s through the present and thereby analyze its evolution over time. This poster outlines our proposed method and initial results.

Screening glycosynthase libraries with a fluoride chemosensor assay independently of enzyme specificity: identification of a transitional hydrolase to synthase mutant.

PubMed

Andrés, Eduardo; Aragunde, Hugo; Planas, Antoni

2014-03-01

Glycosynthases have become efficient tools for the enzymatic synthesis of oligosaccharides, glycoconjugates and polysaccharides. Enzyme-directed evolution approaches are applied to improve the performance of current glycosynthases and engineer specificity for non-natural substrates. However, simple and general screening methods are required since most of the reported assays are specific for each particular enzyme. In the present paper, we report a general screening assay that is independent of enzyme specificity, and implemented in an HTS (high-throughput screening) format for the screening of cell extracts in directed evolution experiments. Fluoride ion is a general by-product released in all glycosynthase reactions with glycosyl fluoride donors. The new assay is based on the use of a specific chemical sensor (a silyl ether of a fluorogenic methylumbelliferone) to transduce fluoride concentration into a fluorescence signal. As a proof-of-concept, it has been applied to a nucleophile saturation mutant library of Bacillus licheniformis 1,3-1,4-β-glucanase. Beyond the expected mutations at the glutamic acid (catalytic) nucleophile, other variants have been shown to acquire glycosynthase activity. Surprisingly, an aspartic acid for glutamic acid replacement renders a highly active glycosynthase, but still retains low hydrolase activity. It appears as an intermediate state between glycosyl hydrolase and glycosynthase.

The physical origin of the X-ray emission from SN 1987A

NASA Astrophysics Data System (ADS)

Miceli, M.; Orlando, S.; Petruk, O.

2017-10-01

We revisit the spectral analysis of the set of archive XMM-Newton observations of SN 1987A through our 3-D hydrodynamic model describing the whole evolution from the onset of the supernova to the full remnant development. For the first time the spectral analysis accounts for the single observations and for the evolution of the system self-consistently. We adopt a forward modeling approach which allows us to directly synthesize, from the model, X-ray spectra and images in different energy bands. We fold the synthetic observables through the XMM-Newton instrumental response and directly compare models and actual data. We find that our simulation provides an excellent fit to the data, by reproducing simultaneously X-ray fluxes, spectral features, and morphology of SN 1987A at all evolutionary stages. Our analysis enables us to obtain a deep insight on the physical origin of the observed multi-thermal emission, by revealing the contribution of shocked surrounding medium, dense clumps of the circumstellar ring, and ejecta to the total emission. We finally provide predictions for future observations (to be performed with XMM-Newton in the next future and with the forthcoming Athena X-ray telescope in approximately 10 years), showing the growing contribution of the ejecta X-ray emission.

Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution.

PubMed

Ahmad, Kareem M; Xiao, Yi; Soh, H Tom

2012-12-01

Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (K(d)) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.

Surface monitoring for pitting evolution into uniform corrosion on Cu-Ni-Zn ternary alloy in alkaline chloride solution: ex-situ LCM and in-situ SECM

NASA Astrophysics Data System (ADS)

Kong, Decheng; Dong, Chaofang; Zheng, Zhaoran; Mao, Feixiong; Xu, Aoni; Ni, Xiaoqing; Man, Cheng; Yao, Jizheng; Xiao, Kui; Li, Xiaogang

2018-05-01

The evolution of the corrosion process on Cu-Ni-Zn alloy in alkaline chloride solution was investigated by in-situ scanning electrochemical microscopy, X-ray photoelectron spectroscopy, and ex-situ laser confocal microscopy, and the effects of ambient temperature and polarization time were also discussed. The results demonstrated a higher pitting nucleation rate and lower pit growth rate at low temperature. The ratio of pit depth to mouth diameter decreased with increasing pit volume and temperature, indicating that pits preferentially propagate in the horizontal direction rather than the vertical direction owing to the presence of corrosion products and deposited copper. The surface current was uniform and stabilized at approximately 2.2 nA during the passive stage, whereas the current increased after the pits were formed with the maximum approaching 3 nA. Increasing the temperature led to an increase in porous corrosion products (CuO, Zn(OH)2, and Ni(OH)2) and significantly increased the rate of transition from pitting to uniform corrosion. Dezincification corrosion was detected by energy dispersive spectrometry, and a mechanism for pitting transition into uniform corrosion induced by dezincification at the grain boundaries is proposed.

Nonlinear derating of high-intensity focused ultrasound beams using Gaussian modal sums.

PubMed

Dibaji, Seyed Ahmad Reza; Banerjee, Rupak K; Soneson, Joshua E; Myers, Matthew R

2013-11-01

A method is introduced for using measurements made in water of the nonlinear acoustic pressure field produced by a high-intensity focused ultrasound transducer to compute the acoustic pressure and temperature rise in a tissue medium. The acoustic pressure harmonics generated by nonlinear propagation are represented as a sum of modes having a Gaussian functional dependence in the radial direction. While the method is derived in the context of Gaussian beams, final results are applicable to general transducer profiles. The focal acoustic pressure is obtained by solving an evolution equation in the axial variable. The nonlinear term in the evolution equation for tissue is modeled using modal amplitudes measured in water and suitably reduced using a combination of "source derating" (experiments in water performed at a lower source acoustic pressure than in tissue) and "endpoint derating" (amplitudes reduced at the target location). Numerical experiments showed that, with proper combinations of source derating and endpoint derating, direct simulations of acoustic pressure and temperature in tissue could be reproduced by derating within 5% error. Advantages of the derating approach presented include applicability over a wide range of gains, ease of computation (a single numerical quadrature is required), and readily obtained temperature estimates from the water measurements.

Quadrupole deformation ({beta},{gamma}) of light {Lambda} hypernuclei in a constrained relativistic mean field model: Shape evolution and shape polarization effect of the {Lambda} hyperon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu Bingnan; Zhao Enguang; Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator, Lanzhou 730000

2011-07-15

The shapes of light normal nuclei and {Lambda} hypernuclei are investigated in the ({beta},{gamma}) deformation plane by using a newly developed constrained relativistic mean field (RMF) model. As examples, the results of some C, Mg, and Si nuclei are presented and discussed in details. We found that for normal nuclei the present RMF calculations and previous Skyrme-Hartree-Fock models predict similar trends of the shape evolution with the neutron number increasing. But some quantitative aspects from these two approaches, such as the depth of the minimum and the softness in the {gamma} direction, differ a lot for several nuclei. For {Lambda}more » hypernuclei, in most cases, the addition of a {Lambda} hyperon alters slightly the location of the ground state minimum toward the direction of smaller {beta} and softer {gamma} in the potential energy surface E{approx}({beta},{gamma}). There are three exceptions, namely, {sub {Lambda}}{sup 13}C, {sub {Lambda}}{sup 23}C, and {sub {Lambda}}{sup 31}Si in which the polarization effect of the additional {Lambda} is so strong that the shapes of these three hypernuclei are drastically different from their corresponding core nuclei.« less

Bridging scales in the evolution of infectious disease life histories: theory.

PubMed

Day, Troy; Alizon, Samuel; Mideo, Nicole

2011-12-01

A significant goal of recent theoretical research on pathogen evolution has been to develop theory that bridges within- and between-host dynamics. The main approach used to date is one that nests within-host models of pathogen replication in models for the between-host spread of infectious diseases. Although this provides an elegant approach, it nevertheless suffers from some practical difficulties. In particular, the information required to satisfactorily model the mechanistic details of the within-host dynamics is not often available. Here, we present a theoretical approach that circumvents these difficulties by quantifying the relevant within-host factors in an empirically tractable way. The approach is closely related to quantitative genetic models for function-valued traits, and it also allows for the prediction of general characteristics of disease life history, including the timing of virulence, transmission, and host recovery. In a companion paper, we illustrate the approach by applying it to data from a model system of malaria. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Rate and State Friction Relation for Nanoscale Contacts: Thermally Activated Prandtl-Tomlinson Model with Chemical Aging

NASA Astrophysics Data System (ADS)

Tian, Kaiwen; Goldsby, David L.; Carpick, Robert W.

2018-05-01

Rate and state friction (RSF) laws are widely used empirical relationships that describe macroscale to microscale frictional behavior. They entail a linear combination of the direct effect (the increase of friction with sliding velocity due to the reduced influence of thermal excitations) and the evolution effect (the change in friction with changes in contact "state," such as the real contact area or the degree of interfacial chemical bonds). Recent atomic force microscope (AFM) experiments and simulations found that nanoscale single-asperity amorphous silica-silica contacts exhibit logarithmic aging (increasing friction with time) over several decades of contact time, due to the formation of interfacial chemical bonds. Here we establish a physically based RSF relation for such contacts by combining the thermally activated Prandtl-Tomlinson (PTT) model with an evolution effect based on the physics of chemical aging. This thermally activated Prandtl-Tomlinson model with chemical aging (PTTCA), like the PTT model, uses the loading point velocity for describing the direct effect, not the tip velocity (as in conventional RSF laws). Also, in the PTTCA model, the combination of the evolution and direct effects may be nonlinear. We present AFM data consistent with the PTTCA model whereby in aging tests, for a given hold time, static friction increases with the logarithm of the loading point velocity. Kinetic friction also increases with the logarithm of the loading point velocity at sufficiently high velocities, but at a different increasing rate. The discrepancy between the rates of increase of static and kinetic friction with velocity arises from the fact that appreciable aging during static contact changes the energy landscape. Our approach extends the PTT model, originally used for crystalline substrates, to amorphous materials. It also establishes how conventional RSF laws can be modified for nanoscale single-asperity contacts to provide a physically based friction relation for nanoscale contacts that exhibit chemical bond-induced aging, as well as other aging mechanisms with similar physical characteristics.

Evolved α-factor prepro-leaders for directed laccase evolution in Saccharomyces cerevisiae.

PubMed

Mateljak, Ivan; Tron, Thierry; Alcalde, Miguel

2017-11-01

Although the functional expression of fungal laccases in Saccharomyces cerevisiae has proven to be complicated, the replacement of signal peptides appears to be a suitable approach to enhance secretion in directed evolution experiments. In this study, twelve constructs were prepared by fusing native and evolved α-factor prepro-leaders from S. cerevisiae to four different laccases with low-, medium- and high-redox potential (PM1L from basidiomycete PM1; PcL from Pycnoporus cinnabarinus; TspC30L from Trametes sp. strain C30; and MtL from Myceliophthora thermophila). Microcultures of the prepro-leader:laccase fusions were grown in selective expression medium that used galactose as both the sole carbon source and as the inducer of expression so that the secretion and activity were assessed with low- and high-redox potential mediators in a high-throughput screening context. With total activity improvements as high as sevenfold over those obtained with the native α-factor prepro-leader, the evolved prepro-leader from PcL (α PcL ) most strongly enhanced secretion of the high- and medium-redox potential laccases PcL, PM1L and TspC30L in the microtiter format with an expression pattern driven by prepro-leaders in the order α PcL  > α PM 1L  ~ α native . By contrast, the pattern of the low-redox potential MtL was α native  > α PcL  > α PM 1L . When produced in flask with rich medium, the evolved prepro-leaders outperformed the α native signal peptide irrespective of the laccase attached, enhancing secretion over 50-fold. Together, these results highlight the importance of using evolved α-factor prepro-leaders for functional expression of fungal laccases in directed evolution campaigns. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Directed evolution of polymerase function by compartmentalized self-replication.

PubMed

Ghadessy, F J; Ong, J L; Holliger, P

2001-04-10

We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

NASA Astrophysics Data System (ADS)

Chodera, John D.; Noé, Frank

2010-09-01

Discrete-state Markov (or master equation) models provide a useful simplified representation for characterizing the long-time statistical evolution of biomolecules in a manner that allows direct comparison with experiments as well as the elucidation of mechanistic pathways for an inherently stochastic process. A vital part of meaningful comparison with experiment is the characterization of the statistical uncertainty in the predicted experimental measurement, which may take the form of an equilibrium measurement of some spectroscopic signal, the time-evolution of this signal following a perturbation, or the observation of some statistic (such as the correlation function) of the equilibrium dynamics of a single molecule. Without meaningful error bars (which arise from both approximation and statistical error), there is no way to determine whether the deviations between model and experiment are statistically meaningful. Previous work has demonstrated that a Bayesian method that enforces microscopic reversibility can be used to characterize the statistical component of correlated uncertainties in state-to-state transition probabilities (and functions thereof) for a model inferred from molecular simulation data. Here, we extend this approach to include the uncertainty in observables that are functions of molecular conformation (such as surrogate spectroscopic signals) characterizing each state, permitting the full statistical uncertainty in computed spectroscopic experiments to be assessed. We test the approach in a simple model system to demonstrate that the computed uncertainties provide a useful indicator of statistical variation, and then apply it to the computation of the fluorescence autocorrelation function measured for a dye-labeled peptide previously studied by both experiment and simulation.

Inferring processes of cultural transmission: the critical role of rare variants in distinguishing neutrality from novelty biases.

PubMed

O'Dwyer, James P; Kandler, Anne

2017-12-05

Neutral evolution assumes that there are no selective forces distinguishing different variants in a population. Despite this striking assumption, many recent studies have sought to assess whether neutrality can provide a good description of different episodes of cultural change. One approach has been to test whether neutral predictions are consistent with observed progeny distributions, recording the number of variants that have produced a given number of new instances within a specified time interval: a classic example is the distribution of baby names. Using an overlapping generations model, we show that these distributions consist of two phases: a power-law phase with a constant exponent of [Formula: see text], followed by an exponential cut-off for variants with very large numbers of progeny. Maximum-likelihood estimations of the model parameters provide a direct way to establish whether observed empirical patterns are consistent with neutral evolution. We apply our approach to a complete dataset of baby names from Australia. Crucially, we show that analyses based on only the most popular variants, as is often the case in studies of cultural evolution, can provide misleading evidence for underlying transmission hypotheses. While neutrality provides a plausible description of progeny distributions of abundant variants, rare variants deviate from neutrality. Further, we develop a simulation framework that allows the detection of alternative cultural transmission processes. We show that anti-novelty bias is able to replicate the complete progeny distribution of the Australian dataset.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown.

PubMed

Colston, Timothy J; Jackson, Colin R

2016-08-01

Vertebrates harbour microbes both internally and externally, and collectively, these microorganisms (the 'microbiome') contain genes that outnumber the host's genetic information 10-fold. The majority of the microorganisms associated with vertebrates are found within the gut, where they influence host physiology, immunity and development. The development of next-generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture-based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is a substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts, and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of nonmammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts, a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution. © 2016 John Wiley & Sons Ltd.

Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

Regional-Scale Salt Tectonics Modelling: Bench-Scale Validation and Extension to Field-Scale

NASA Astrophysics Data System (ADS)

Crook, A. J. L.; Yu, J. G.; Thornton, D. A.

2010-05-01

The role of salt in the evolution of the West African continental margin, and in particular its impact on hydrocarbon migration and trap formation, is an important research topic. It has attracted many researchers who have based their research on bench-scale experiments, numerical models and seismic observations. This research has shown that the evolution is very complex. For example, regional analogue bench-scale models of the Angolan margin (Fort et al., 2004) indicate a complex system with an upslope extensional domain with sealed tilted blocks, growth fault and rollover systems and extensional diapers, and a downslope contractional domain with squeezed diapirs, polyharmonic folds and thrust faults, and late-stage folding and thrusting. Numerical models have the potential to provide additional insight into the evolution of these salt driven passive margins. The longer-term aim is to calibrate regional-scale evolution models, and then to evaluate the effect of the depositional history on the current day geomechanical and hydrogeologic state in potential target hydrocarbon reservoir formations adjacent to individual salt bodies. To achieve this goal the burial and deformational history of the sediment must be modelled from initial deposition to the current-day state, while also accounting for the reaction and transport processes occurring in the margin. Accurate forward modeling is, however complex, and necessitates advanced procedures for the prediction of fault formation and evolution, representation of the extreme deformations in the salt, and for coupling the geomechanical, fluid flow and temperature fields. The evolution of the sediment due to a combination of mechanical compaction, chemical compaction and creep relaxation must also be represented. In this paper ongoing research on a computational approach for forward modelling complex structural evolution, with particular reference to passive margins driven by salt tectonics is presented. The approach is an extension of a previously published approach (Crook et al., 2006a, 2006b) that focused on predictive modelling of structure evolution in 2-D sandbox experiments, and in particular two extensional sand box experiments that exhibit complex fault development including a series of superimposed crestal collapse graben systems (McClay, 1990) . The formulation adopts a finite strain Lagrangian method, complemented by advanced localization prediction algorithms and robust and efficient automated adaptive meshing techniques. The sediment is represented by an elasto-viscoplastic constitutive model based on extended critical state concepts, which enables representation of the combined effect of mechanical and chemical compaction. This is achieved by directly coupling the evolution of the material state boundary surface with both the mechanically and chemically driven porosity change. Using these procedures the evolution of the geological structures arises naturally from the imposed boundary conditions without the requirement of seeding using initial imperfections. Simulations are presented for regional bench-scale models based on the analogue experiments presented by Fort et al. (2004), together with additional insights provided by the numerical models. It is shown that the behaviour observed in both the extensional and compressional zones of these analogue models arises naturally in the finite element simulations. Extension of these models to the field-scale is then discussed and several simulations are presented to highlight important issues related to practical field-scale numerical modelling.

The consecutive dry days to trigger rainfall over West Africa

NASA Astrophysics Data System (ADS)

Lee, J. H.

2018-01-01

In order to resolve contradictions in addressing a soil moisture-precipitation feedback mechanism over West Africa and to clarify the impact of antecedent soil moisture on subsequent rainfall evolution, we first validated various data sets (SMOS satellite soil moisture observations, NOAH land surface model, TRMM rainfall, CMORPH rainfall and HadGEM climate models) with the Analyses Multidisciplinaires de la Mousson Africaine (AMMA) field campaign data. Based on this analysis, it was suggested that biases of data sets might cause contradictions in studying mechanisms. Thus, by taking into account uncertainties in data, it was found that the approach of consecutive dry days (i.e. a relative comparison of time-series) showed consistency across various data sets, while the direct comparison approach for soil moisture state and rainfall did not. Thus, it was discussed that it may be difficult to directly relate rain with soil moisture as the absolute value, however, it may be reasonable to compare a temporal progress of the variables. Based upon the results consistently showing a positive relationship between the consecutive dry days and rainfall, this study supports a negative feedback often neglected by climate model structure. This approach is less sensitive to interpretation errors arising from systematic errors in data sets, as this measures a temporal gradient of soil moisture state.

Study of the microdoppler signature of a bicyclist for different directions of approach

NASA Astrophysics Data System (ADS)

Rodriguez-Hervas, Berta; Maile, Michael; Flores, Benjamin C.

2015-05-01

The successful implementation of autonomous driving in an urban setting depends on the ability of the environment perception system to correctly classify vulnerable road users such as pedestrians and bicyclists in dense, complex scenarios. Self-driving vehicles include sensor systems such as cameras, lidars, and radars to enable decision making. Among these systems, radars are particularly relevant due to their operational robustness under adverse weather and night light conditions. Classification of pedestrian and car in urban settings using automotive radar has been widely investigated, suggesting that micro-Doppler signatures are useful for target discrimination. Our objective is to analyze and study the micro-Doppler signature of bicyclists approaching a vehicle from different directions in order to establish the basis of a classification criterion to distinguish bicycles from other targets including clutter. The micro-Doppler signature is obtained by grouping individual reflecting points using a clustering algorithm and observing the evolution of all the points belonging to an object in the Doppler domain over time. A comparison is then made with simulated data that uses a kinematic model of bicyclists' movement. The suitability of the micro-Doppler bicyclist signature as a classification feature is determined by comparing it to those belonging to cars and pedestrians approaching the automotive radar system.

Direct dating of human fossils.

PubMed

Grün, Rainer

2006-01-01

The methods that can be used for the direct dating of human remains comprise of radiocarbon, U-series, electron spin resonance (ESR), and amino acid racemization (AAR). This review gives an introduction to these methods in the context of dating human bones and teeth. Recent advances in ultrafiltration techniques have expanded the dating range of radiocarbon. It now seems feasible to reliably date bones up to 55,000 years. New developments in laser ablation mass spectrometry permit the in situ analysis of U-series isotopes, thus providing a rapid and virtually non-destructive dating method back to about 300,000 years. This is of particular importance when used in conjunction with non-destructive ESR analysis. New approaches in AAR analysis may lead to a renaissance of this method. The potential and present limitations of these direct dating techniques are discussed for sites relevant to the reconstruction of modern human evolution, including Florisbad, Border Cave, Tabun, Skhul, Qafzeh, Vindija, Banyoles, and Lake Mungo. (c) 2006 Wiley-Liss, Inc.

Marine legislation--the ultimate 'horrendogram': international law, European directives & national implementation.

PubMed

Boyes, Suzanne J; Elliott, Michael

2014-09-15

The EU is a pre-eminent player in sustainable development, adopting more than 200 pieces of legislation that have direct repercussions for marine environmental policy and management. Over five decades, measures have aimed to protect the marine environment by tackling the impact of human activities, but maritime affairs have been dealt with by separate sectoral policies without fully integrating all relevant sectors. Such compartmentalisation has resulted in a patchwork of EU legislation and resultant national legislation leading to a piecemeal approach to marine protection. These are superimposed on international obligations emanating from UN and other bodies and are presented here as complex 'horrendograms' showing the complexity across vertical governance. These horrendograms have surprised marine experts despite them acknowledging the many uses and users of the marine environment. Encouragingly since 2000, the evolution in EU policy has progressed to more holistic directives and here we give an overview of this change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans.

PubMed

Sharma, Manmohan D; Hunt, John; Hosken, David J

2012-03-01

Natural and sexual selection are classically thought to oppose one another, and although there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. Here, we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (CHCs), a character subject to both modes of selection, in Drosophila simulans. Natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experimental evolution, the responses of male and female CHCs were assessed. The effects of natural and sexual selection differed greatly across the sexes. The responses of female CHCs were generally small, but CHCs evolved predominantly in the direction of natural selection. For males, profiles evolved via sexual and natural selection, as well as through the interaction between the two, with some male CHC components only evolving in the direction of natural selection when sexual selection was relaxed. These results indicate sex-specific responses to selection, and that sexual and natural selection act antagonistically for at least some combinations of CHCs. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

PubMed Central

Echave, Julian; Wilke, Claus O.

2018-01-01

For decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic misfolding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field. PMID:28301766

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

Space Station fluid management logistics

NASA Technical Reports Server (NTRS)

Dominick, Sam M.

1990-01-01

Viewgraphs and discussion on space station fluid management logistics are presented. Topics covered include: fluid management logistics - issues for Space Station Freedom evolution; current fluid logistics approach; evolution of Space Station Freedom fluid resupply; launch vehicle evolution; ELV logistics system approach; logistics carrier configuration; expendable fluid/propellant carrier description; fluid carrier design concept; logistics carrier orbital operations; carrier operations at space station; summary/status of orbital fluid transfer techniques; Soviet progress tanker system; and Soviet propellant resupply system observations.

Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era.

PubMed

Moroz, Leonid L

2015-12-01

The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Language and emotions: emotional Sapir-Whorf hypothesis.

PubMed

Perlovsky, Leonid

2009-01-01

An emotional version of Sapir-Whorf hypothesis suggests that differences in language emotionalities influence differences among cultures no less than conceptual differences. Conceptual contents of languages and cultures to significant extent are determined by words and their semantic differences; these could be borrowed among languages and exchanged among cultures. Emotional differences, as suggested in the paper, are related to grammar and mostly cannot be borrowed. The paper considers conceptual and emotional mechanisms of language along with their role in the mind and cultural evolution. Language evolution from primordial undifferentiated animal cries is discussed: while conceptual contents increase, emotional reduced. Neural mechanisms of these processes are suggested as well as their mathematical models: the knowledge instinct, the dual model connecting language and cognition, neural modeling fields. Mathematical results are related to cognitive science, linguistics, and psychology. Experimental evidence and theoretical arguments are discussed. Dynamics of the hierarchy-heterarchy of human minds and cultures is formulated using mean-field approach and approximate equations are obtained. The knowledge instinct operating in the mind heterarchy leads to mechanisms of differentiation and synthesis determining ontological development and cultural evolution. These mathematical models identify three types of cultures: "conceptual" pragmatic cultures in which emotionality of language is reduced and differentiation overtakes synthesis resulting in fast evolution at the price of uncertainty of values, self doubts, and internal crises; "traditional-emotional" cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation; and "multi-cultural" societies combining fast cultural evolution and stability. Unsolved problems and future theoretical and experimental directions are discussed.

Evolution Acceptance and Epistemological Beliefs of College Biology Students

ERIC Educational Resources Information Center

Borgerding, Lisa A.; Deniz, Hasan; Anderson, Elizabeth Shevock

2017-01-01

Evolutionary theory is central to biology, and scientifically accurate evolution instruction is promoted within national and state standards documents. Previous literature has identified students' epistemological beliefs as potential predictors of evolution acceptance. The present work seeks to explore more directly how student views of evolution…

Towards Complex Abiotic Systems for Chemical and Biological Sensing

DTIC Science & Technology

2009-11-01

such as phage display, cell surface display, and Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Other processes necessary to...Directed evolution by in vitro compartmentalization. Nat Methods 2006, 3, 561-570. l7Chelliserrykattil, J.; Ellington, A.D. Evolution of a T7 RNA

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

PubMed Central

Kazeev, Vladimir; Khammash, Mustafa; Nip, Michael; Schwab, Christoph

2014-01-01

The Chemical Master Equation (CME) is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks. Yet direct solutions of the CME have remained elusive. Although several approaches overcome the infinite dimensional nature of the CME through projections or other means, a common feature of proposed approaches is their susceptibility to the curse of dimensionality, i.e. the exponential growth in memory and computational requirements in the number of problem dimensions. We present a novel approach that has the potential to “lift” this curse of dimensionality. The approach is based on the use of the recently proposed Quantized Tensor Train (QTT) formatted numerical linear algebra for the low parametric, numerical representation of tensors. The QTT decomposition admits both, algorithms for basic tensor arithmetics with complexity scaling linearly in the dimension (number of species) and sub-linearly in the mode size (maximum copy number), and a numerical tensor rounding procedure which is stable and quasi-optimal. We show how the CME can be represented in QTT format, then use the exponentially-converging -discontinuous Galerkin discretization in time to reduce the CME evolution problem to a set of QTT-structured linear equations to be solved at each time step using an algorithm based on Density Matrix Renormalization Group (DMRG) methods from quantum chemistry. Our method automatically adapts the “basis” of the solution at every time step guaranteeing that it is large enough to capture the dynamics of interest but no larger than necessary, as this would increase the computational complexity. Our approach is demonstrated by applying it to three different examples from systems biology: independent birth-death process, an example of enzymatic futile cycle, and a stochastic switch model. The numerical results on these examples demonstrate that the proposed QTT method achieves dramatic speedups and several orders of magnitude storage savings over direct approaches. PMID:24626049

Darwin and Mendel: Evolution and Genetics

ERIC Educational Resources Information Center

Bizzo, Nelio; El-Hani, Charbel N.

2009-01-01

Many studies have shown that students' understanding of evolution is low and some sort of historical approach would be necessary in order to allow students to understand the theory of evolution. It is common to present Mendelian genetics to high school students prior to Biological Evolution, having in mind historical and epistemological…

Computationally efficient methods for modelling laser wakefield acceleration in the blowout regime

NASA Astrophysics Data System (ADS)

Cowan, B. M.; Kalmykov, S. Y.; Beck, A.; Davoine, X.; Bunkers, K.; Lifschitz, A. F.; Lefebvre, E.; Bruhwiler, D. L.; Shadwick, B. A.; Umstadter, D. P.; Umstadter

2012-08-01

Electron self-injection and acceleration until dephasing in the blowout regime is studied for a set of initial conditions typical of recent experiments with 100-terawatt-class lasers. Two different approaches to computationally efficient, fully explicit, 3D particle-in-cell modelling are examined. First, the Cartesian code vorpal (Nieter, C. and Cary, J. R. 2004 VORPAL: a versatile plasma simulation code. J. Comput. Phys. 196, 538) using a perfect-dispersion electromagnetic solver precisely describes the laser pulse and bubble dynamics, taking advantage of coarser resolution in the propagation direction, with a proportionally larger time step. Using third-order splines for macroparticles helps suppress the sampling noise while keeping the usage of computational resources modest. The second way to reduce the simulation load is using reduced-geometry codes. In our case, the quasi-cylindrical code calder-circ (Lifschitz, A. F. et al. 2009 Particle-in-cell modelling of laser-plasma interaction using Fourier decomposition. J. Comput. Phys. 228(5), 1803-1814) uses decomposition of fields and currents into a set of poloidal modes, while the macroparticles move in the Cartesian 3D space. Cylindrical symmetry of the interaction allows using just two modes, reducing the computational load to roughly that of a planar Cartesian simulation while preserving the 3D nature of the interaction. This significant economy of resources allows using fine resolution in the direction of propagation and a small time step, making numerical dispersion vanishingly small, together with a large number of particles per cell, enabling good particle statistics. Quantitative agreement of two simulations indicates that these are free of numerical artefacts. Both approaches thus retrieve the physically correct evolution of the plasma bubble, recovering the intrinsic connection of electron self-injection to the nonlinear optical evolution of the driver.

Dynamics of one-dimensional self-gravitating systems using Hermite-Legendre polynomials

NASA Astrophysics Data System (ADS)

Barnes, Eric I.; Ragan, Robert J.

2014-01-01

The current paradigm for understanding galaxy formation in the Universe depends on the existence of self-gravitating collisionless dark matter. Modelling such dark matter systems has been a major focus of astrophysicists, with much of that effort directed at computational techniques. Not surprisingly, a comprehensive understanding of the evolution of these self-gravitating systems still eludes us, since it involves the collective non-linear dynamics of many particle systems interacting via long-range forces described by the Vlasov equation. As a step towards developing a clearer picture of collisionless self-gravitating relaxation, we analyse the linearized dynamics of isolated one-dimensional systems near thermal equilibrium by expanding their phase-space distribution functions f(x, v) in terms of Hermite functions in the velocity variable, and Legendre functions involving the position variable. This approach produces a picture of phase-space evolution in terms of expansion coefficients, rather than spatial and velocity variables. We obtain equations of motion for the expansion coefficients for both test-particle distributions and self-gravitating linear perturbations of thermal equilibrium. N-body simulations of perturbed equilibria are performed and found to be in excellent agreement with the expansion coefficient approach over a time duration that depends on the size of the expansion series used.

Engineering C4 photosynthesis into C3 chassis in the synthetic biology age.

PubMed

Schuler, Mara L; Mantegazza, Otho; Weber, Andreas P M

2016-07-01

C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Detecting gene subnetworks under selection in biological pathways.

PubMed

Gouy, Alexandre; Daub, Joséphine T; Excoffier, Laurent

2017-09-19

Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data. We developed a method to analyse gene networks that is suitable to evidence polygenic selection. The general idea is to search biological pathways for subnetworks of genes that directly interact with each other and that present unusual evolutionary features. Subnetwork search is a typical combinatorial optimization problem that we solve using a simulated annealing approach. We have applied our methodology to find signals of adaptation to high-altitude in human populations. We show that this adaptation has a clear polygenic basis and is influenced by many genetic components. Our approach, implemented in the R package signet, improves on gene-level classical tests for selection by identifying both new candidate genes and new biological processes involved in adaptation to altitude. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A methodological approach to characterize the resilience of aquatic ecosystems with application to Lake Annecy, France

NASA Astrophysics Data System (ADS)

Pinault, J.-L.; Berthier, F.

2007-01-01

We propose a methodological approach to characterize the resilience of aquatic ecosystems with respect to the evolution of environmental parameters as well as their aptitude to adapt to forcings. This method that is applied to Lake Annecy, France, proceeds in three stages. First, according to the depth, variations of physicochemical parameters versus time are separated into three components related to (1) energy transfer through the surface of the lake, (2) the flow of rivers and springs that feed the lake, and (3) long-term evolution of the benthic zone as a consequence of mineral and organic matter loads. Second, dynamics of the lake are deduced by analyzing the physicochemical parameter components related to the three boundary conditions. Third, a stochastic process associated with the transfer models aims to characterize the resilience of the lakes according to forcings. For Lake Annecy, whose dynamics are representative of oligotrophic stratified lakes controlled by decarbonation processes where turnover and mixing occurring once a year in winter, the major consequence is the impoverishment of dissolved oxygen in deep water in autumn due to a temperature increase of the surface water in summer. The simulation raises relevant questions about whether a connection exists between physicochemical parameters and global warming, which should not induce harmful consequences on water quality and biodiversity in deep water. This methodological approach is general since it does not use any physical conceptual model to predict the hydrosystem behavior but uses directly observed data.

Evolution of psychology and counseling in infertility.

PubMed

Boivin, Jacky; Gameiro, Sofia

2015-08-01

Five key paradigm shifts are described to illustrate the evolution of psychology and counseling in infertility. The first paradigm shift was in the 1930s when psychosomatic concepts were introduced in obstetrics and gynecology as causal factors to explain why some couples could not conceive despite the absence of organic pathology. In the second shift, the nurse advocacy movement of the 1970s stimulated the investigation of the psychosocial consequences of infertility and promoted counseling to help couples grieve childlessness when medical treatments often could not help them conceive. The third shift occurred with the advent of IVF, which created a demand for mental health professionals in fertility clinics. Mental health professionals assessed the ability of couples to withstand the demands of this new high technology treatment as well as their suitability as potential parents. The fourth shift, in the 1990s, saw reproductive medicine embrace the principles of evidence-based medicine, which introduced a much more rigorous approach to medical practice (effectiveness and safety) that extended to psychosocial interventions. The most recent paradigm shift, in the new millennium, occurred with the realization that compliance with protracted fertility treatment depended on the adoption of an integrated approach to fertility care. An integrated approach could reduce treatment burden arising from multiple sources (i.e., patient, clinic, and treatment). This review describes these paradigm shifts and reflects on future clinical and research directions for mental health professionals. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p +p collisions at √{s } =510 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Alexander, J.; Alfred, M.; Andrieux, V.; Aoki, K.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Awes, T. C.; Ayuso, C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bai, X.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bathe, S.; Baublis, V.; Baumann, C.; Baumgart, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Black, D.; Blau, D. S.; Boer, M.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Butler, C.; Butsyk, S.; Campbell, S.; Canoa Roman, V.; Cervantes, R.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choi, S.; Christiansen, P.; Chujo, T.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Connors, M.; Cronin, N.; Crossette, N.; Csanád, M.; Csörgő, T.; Danley, T. W.; Datta, A.; Daugherity, M. S.; David, G.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Ding, L.; Dion, A.; Dixit, D.; Do, J. H.; D'Orazio, L.; Drapier, O.; Drees, A.; Drees, K. A.; Dumancic, M.; Durham, J. M.; Durum, A.; Elder, T.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Eyser, K. O.; Fadem, B.; Fan, W.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukao, Y.; Fukuda, Y.; Fusayasu, T.; Gainey, K.; Gal, C.; Gallus, P.; Garg, P.; Garishvili, A.; Garishvili, I.; Ge, H.; Giordano, F.; Glenn, A.; Gong, X.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guragain, H.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamilton, H. F.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haseler, T. O. S.; Hashimoto, K.; Hayano, R.; He, X.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hill, K.; Hollis, R. S.; Homma, K.; Hong, B.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Ichihara, T.; Ikeda, Y.; Imai, K.; Imazu, Y.; Imrek, J.; Inaba, M.; Iordanova, A.; Isenhower, D.; Isinhue, A.; Ito, Y.; Ivanishchev, D.; Jacak, B. V.; Jeon, S. J.; Jezghani, M.; Ji, Z.; Jia, J.; Jiang, X.; Johnson, B. M.; Joo, E.; Joo, K. S.; Jorjadze, V.; Jouan, D.; Jumper, D. S.; Kamin, J.; Kanda, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kapukchyan, D.; Kapustinsky, J.; Karthas, S.; Kawall, D.; Kazantsev, A. V.; Key, J. A.; Khachatryan, V.; Khandai, P. K.; Khanzadeev, A.; Kihara, K.; Kijima, K. M.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.-J.; Kim, H.-J.; Kim, M. H.; Kim, M.; Kim, Y.-J.; Kim, Y. K.; Kincses, D.; Kistenev, E.; Klatsky, J.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kofarago, M.; Komkov, B.; Koster, J.; Kotchetkov, D.; Kotov, D.; Krizek, F.; Kudo, S.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lallow, E. O.; Lebedev, A.; Lee, D. M.; Lee, G. H.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S.; Lee, S. H.; Leitch, M. J.; Leitgab, M.; Leung, Y. H.; Lewis, B.; Lewis, N. A.; Li, X.; Li, X.; Lim, S. H.; Liu, L. D.; Liu, M. X.; Loggins, V.-R.; Loggins, V.-R.; Lovasz, K.; Lynch, D.; Maguire, C. F.; Majoros, T.; Makdisi, Y. I.; Makek, M.; Malaev, M.; Manion, A.; Manko, V. I.; Mannel, E.; Masuda, H.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Mihalik, D. E.; Miller, A. J.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Mitsuka, G.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Mohapatra, S.; Montuenga, P.; Moon, T.; Morrison, D. P.; Morrow, S. I. M.; Moskowitz, M.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Mwai, A.; Nagae, T.; Nagai, K.; Nagamiya, S.; Nagashima, K.; Nagashima, T.; Nagle, J. L.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nattrass, C.; Netrakanti, P. K.; Nihashi, M.; Niida, T.; Nouicer, R.; Novák, T.; Novitzky, N.; Novotny, R.; Nyanin, A. S.; O'Brien, E.; Ogilvie, C. A.; Oide, H.; Okada, K.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Ottino, G. J.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, I. H.; Park, J. S.; Park, S.; Park, S. K.; Pate, S. F.; Patel, L.; Patel, M.; Peng, J.-C.; Peng, W.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perezlara, C. E.; Perry, J.; Petti, R.; Phipps, M.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Pun, A.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richardson, E.; Richford, D.; Rinn, T.; Riveli, N.; Roach, D.; Rolnick, S. D.; Rosati, M.; Rowan, Z.; Rubin, J. G.; Runchey, J.; Ryu, M. S.; Safonov, A. S.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sako, H.; Samsonov, V.; Sarsour, M.; Sato, K.; Sato, S.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sekiguchi, Y.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shaver, A.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shioya, T.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Singh, B. K.; Singh, C. P.; Singh, V.; Skolnik, M.; Slunečka, M.; Smith, K. L.; Snowball, M.; Solano, S.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Steinberg, P.; Stenlund, E.; Stepanov, M.; Ster, A.; Stoll, S. P.; Stone, M. R.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Syed, S.; Sziklai, J.; Takahara, A.; Takeda, A.; Taketani, A.; Tanaka, Y.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tarnai, G.; Tennant, E.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Tomášek, M.; Torii, H.; Towell, C. L.; Towell, M.; Towell, R.; Towell, R. S.; Tserruya, I.; Ueda, Y.; Ujvari, B.; van Hecke, H. W.; Vargyas, M.; Vazquez-Carson, S.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vrba, V.; Vukman, N.; Vznuzdaev, E.; Wang, X. R.; Wang, Z.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Whitaker, S.; Wolin, S.; Wong, C. P.; Woody, C. L.; Wysocki, M.; Xia, B.; Xu, C.; Xu, Q.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yamamoto, H.; Yanovich, A.; Yin, P.; Yokkaichi, S.; Yoo, J. H.; Yoon, I.; You, Z.; Younus, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zharko, S.; Zhou, S.; Zou, L.; Phenix Collaboration

2017-04-01

Dihadron and isolated direct photon-hadron angular correlations are measured in p +p collisions at √{s }=510 GeV . Correlations of charged hadrons of 0.7

Aspect-Oriented Model-Driven Software Product Line Engineering

NASA Astrophysics Data System (ADS)

Groher, Iris; Voelter, Markus

Software product line engineering aims to reduce development time, effort, cost, and complexity by taking advantage of the commonality within a portfolio of similar products. The effectiveness of a software product line approach directly depends on how well feature variability within the portfolio is implemented and managed throughout the development lifecycle, from early analysis through maintenance and evolution. This article presents an approach that facilitates variability implementation, management, and tracing by integrating model-driven and aspect-oriented software development. Features are separated in models and composed of aspect-oriented composition techniques on model level. Model transformations support the transition from problem to solution space models. Aspect-oriented techniques enable the explicit expression and modularization of variability on model, template, and code level. The presented concepts are illustrated with a case study of a home automation system.

Network-based recommendation algorithms: A review

NASA Astrophysics Data System (ADS)

Yu, Fei; Zeng, An; Gillard, Sébastien; Medo, Matúš

2016-06-01

Recommender systems are a vital tool that helps us to overcome the information overload problem. They are being used by most e-commerce web sites and attract the interest of a broad scientific community. A recommender system uses data on users' past preferences to choose new items that might be appreciated by a given individual user. While many approaches to recommendation exist, the approach based on a network representation of the input data has gained considerable attention in the past. We review here a broad range of network-based recommendation algorithms and for the first time compare their performance on three distinct real datasets. We present recommendation topics that go beyond the mere question of which algorithm to use-such as the possible influence of recommendation on the evolution of systems that use it-and finally discuss open research directions and challenges.

Spacelike matching to null infinity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zenginoglu, Anil; Tiglio, Manuel

2009-07-15

We present two methods to include the asymptotic domain of a background spacetime in null directions for numerical solutions of evolution equations so that both the radiation extraction problem and the outer boundary problem are solved. The first method is based on the geometric conformal approach, the second is a coordinate based approach. We apply these methods to the case of a massless scalar wave equation on a Kerr spacetime. Our methods are designed to allow existing codes to reach the radiative zone by including future null infinity in the computational domain with relatively minor modifications. We demonstrate the flexibilitymore » of the methods by considering both Boyer-Lindquist and ingoing Kerr coordinates near the black hole. We also confirm numerically predictions concerning tail decay rates for scalar fields at null infinity in Kerr spacetime due to Hod for the first time.« less

Forward jet and particle production at HERA

NASA Astrophysics Data System (ADS)

Adloff, C.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Bate, P.; Beck, M.; Beglarian, A.; Behnke, O.; Behrend, H.-J.; Beier, C.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Biddulph, P.; Bizot, J. C.; Boudry, V.; Braunschweig, W.; Brisson, V.; Brown, D. P.; Brückner, W.; Bruel, P.; Bruncko, D.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Chabert, E.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cvach, J.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davidsson, M.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Demirchyan, R.; Diaconu, C.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Donovan, K. T.; Dowell, J. D.; Droutskoi, A.; Ebert, J.; Eckerlin, G.; Eckstein, D.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Enzenberger, M.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Fleischer, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gerhards, R.; Ghazaryan, S.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haustein, V.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Hengstmann, S.; Henschel, H.; Heremans, R.; Herynek, I.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hurling, S.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacquet, M.; Jaffre, M.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kästli, H. K.; Kander, M.; Kant, D.; Kapichine, M.; Karlsson, M.; Karschnik, O.; Katzy, J.; Kaufmann, O.; Kausch, M.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, K.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Laforge, B.; Lahmann, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Lendermann, V.; Levonian, S.; Lindstroem, M.; List, B.; Lobo, G.; Lobodzinska, E.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martin, G.; Martyn, H.-U.; Martyniak, J.; Maxfield, S. J.; McMahon, S. J.; McMahon, T. R.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Mikochi, S.; Milstead, D.; Moeck, J.; Mohr, R.; Mohrdieck, S.; Moreau, F.; Morris, J. V.; Müller, D.; Müller, K.; Murín, P.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nikitin, D.; Nix, O.; Nowak, G.; Nunnemann, T.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panassik, V.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Rabbertz, K.; Rauschenberger, J.; Reimer, P.; Reisert, B.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Scheins, J.; Schleif, S.; Schleper, P.; Schmidt, D.; Schmidt, D.; Schoeffel, L.; Schröder, V.; Schultz-Coulon, H.-C.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Sirois, Y.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Spaskov, V.; Specka, A.; Spiekermann, J.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stiewe, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Swart, M.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Udluft, S.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Haecke, A.; Van Mechelen, P.; Vazdik, Y.; Villet, G.; Wacker, K.; Wallny, R.; Walter, T.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wittmann, E.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žáček, J.; Zálešák, J.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1999-01-01

Single particles and jets in deeply inelastic scattering at low x are measured with the H1 detector in the region away from the current jet and towards the proton remnant, known as the forward region. Hadronic final state measurements in this region are expected to be particularly sensitive to QCD evolution effects. Jet cross sections are presented as a function of Bjorken- x for forward jets produced with a polar angle to the proton direction, θjet, in the range 7° < θjet < 20°. Azimuthal correlations are studied between the forward jet and the scattered lepton. Charged and neutral single particle production in the forward region are measured as a function of Bjorken- x, in the range 5° < θ < 25°, for particle transverse momenta larger than 1 GeV. QCD based Monte Carlo predictions and analytical calculations based on BFKL, CCFM and DGLAP evolution are compared to the data. Predictions based on the DGLAP approach fail to describe the data, except for those which allow for a resolved photon contribution.

Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation

PubMed Central

Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

2015-01-01

Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of “melting pots in a supercomputer” is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments. PMID:26311304

Time evolution of photon-pulse propagation in scattering and absorbing media: The dynamic radiative transfer system

NASA Astrophysics Data System (ADS)

Georgakopoulos, A.; Politopoulos, K.; Georgiou, E.

2018-03-01

A new dynamic-system approach to the problem of radiative transfer inside scattering and absorbing media is presented, directly based on first-hand physical principles. This method, the Dynamic Radiative Transfer System (DRTS), employs a dynamical system formality using a global sparse matrix, which characterizes the physical, optical and geometrical properties of the material-volume of interest. The new system state is generated by the above time-independent matrix, using simple matrix-vector multiplication for each subsequent time step. DRTS is capable of calculating accurately the time evolution of photon propagation in media of complex structure and shape. The flexibility of DRTS allows the integration of time-dependent sources, boundary conditions, different media and several optical phenomena like reflection and refraction in a unified and consistent way. Various examples of DRTS simulation results are presented for ultra-fast light pulse 3-D propagation, demonstrating greatly reduced computational cost and resource requirements compared to other methods.

The Evolution of Holistic Processing of Faces

PubMed Central

Burke, Darren; Sulikowski, Danielle

2013-01-01

In this paper we examine the holistic processing of faces from an evolutionary perspective, clarifying what such an approach entails, and evaluating the extent to which the evidence currently available permits any strong conclusions. While it seems clear that the holistic processing of faces depends on mechanisms evolved to perform that task, our review of the comparative literature reveals that there is currently insufficient evidence (or sometimes insufficiently compelling evidence) to decide when in our evolutionary past such processing may have arisen. It is also difficult to assess what kinds of selection pressures may have led to evolution of such a mechanism, or even what kinds of information holistic processing may have originally evolved to extract, given that many sources of socially relevant face-based information other than identity depend on integrating information across different regions of the face – judgments of expression, behavioral intent, attractiveness, sex, age, etc. We suggest some directions for future research that would help to answer these important questions. PMID:23382721

Preparing tomorrow's behavioral medicine scientists and practitioners: a survey of future directions for education and training.

PubMed

Goldstein, Carly M; Minges, Karl E; Schoffman, Danielle E; Cases, Mallory G

2017-02-01

Behavioral medicine training is due for an overhaul given the rapid evolution of the field, including a tight funding climate, changing job prospects, and new research and industry collaborations. The purpose of the present study was to collect responses from trainee and practicing members of a multidisciplinary professional society about their perceptions of behavioral medicine training and their suggestions for changes to training for future behavioral medicine scientists and practitioners. A total of 162 faculty and 110 students (total n = 272) completed a web-based survey on strengths of their current training programs and ideas for changes. Using a mixed-methods approach, the survey findings are used to highlight seven key areas for improved preparation of the next generation of behavioral medicine scientists and practitioners, which are grant writing, interdisciplinary teamwork, advanced statistics and methods, evolving research program, publishable products from coursework, evolution and use of theory, and non-traditional career paths.

Visualizing decoupling in nanocrystalline alloys: A FORC-temperature analysis

NASA Astrophysics Data System (ADS)

Rivas, M.; Martínez-García, J. C.; Gorria, P.

2016-02-01

Devitrifying ferromagnetic amorphous precursors in the adequate conditions may give rise to disordered assemblies of densely packed nanocrystals with extraordinary magnetic softness well explained by the exchange coupling among multiple crystallites. Whether the magnetic exchange interaction is produced by direct contact or mediated by the intergranular amorphous matrix has a strong influence on the behaviour of the system above room temperature. Multi-phase amorphous-nanocrystalline systems dramatically harden when approaching the amorphous Curie temperature (TC) due to the hard grains decoupling. The study of the thermally induced decoupling of nanosized crystallites embedded in an amorphous matrix has been performed in this work by the first-order reversal curves (FORCs) analysis. We selected a Fe-rich amorphous alloy with TC = 330 K, in order to follow the evolution of the FORC diagrams obtained below and above such temperature in samples with different percentages of nanocrystalline phase. The existence of up to four regions exhibiting unlike magnetic behaviours is unambiguously determined from the temperature evolution of the FORC.

Spatio-Temporal Mining of PolSAR Satellite Image Time Series

NASA Astrophysics Data System (ADS)

Julea, A.; Meger, N.; Trouve, E.; Bolon, Ph.; Rigotti, C.; Fallourd, R.; Nicolas, J.-M.; Vasile, G.; Gay, M.; Harant, O.; Ferro-Famil, L.

2010-12-01

This paper presents an original data mining approach for describing Satellite Image Time Series (SITS) spatially and temporally. It relies on pixel-based evolution and sub-evolution extraction. These evolutions, namely the frequent grouped sequential patterns, are required to cover a minimum surface and to affect pixels that are sufficiently connected. These spatial constraints are actively used to face large data volumes and to select evolutions making sense for end-users. In this paper, a specific application to fully polarimetric SAR image time series is presented. Preliminary experiments performed on a RADARSAT-2 SITS covering the Chamonix Mont-Blanc test-site are used to illustrate the proposed approach.

2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

DOE Office of Scientific and Technical Information (OSTI.GOV)

ANTHONY DEAN

2009-07-24

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomicmore » approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.« less

Evolutionary and plastic responses to climate change in terrestrial plant populations

PubMed Central

Franks, Steven J; Weber, Jennifer J; Aitken, Sally N

2014-01-01

As climate change progresses, we are observing widespread changes in phenotypes in many plant populations. Whether these phenotypic changes are directly caused by climate change, and whether they result from phenotypic plasticity or evolution, are active areas of investigation. Here, we review terrestrial plant studies addressing these questions. Plastic and evolutionary responses to climate change are clearly occurring. Of the 38 studies that met our criteria for inclusion, all found plastic or evolutionary responses, with 26 studies showing both. These responses, however, may be insufficient to keep pace with climate change, as indicated by eight of 12 studies that examined this directly. There is also mixed evidence for whether evolutionary responses are adaptive, and whether they are directly caused by contemporary climatic changes. We discuss factors that will likely influence the extent of plastic and evolutionary responses, including patterns of environmental changes, species’ life history characteristics including generation time and breeding system, and degree and direction of gene flow. Future studies with standardized methodologies, especially those that use direct approaches assessing responses to climate change over time, and sharing of data through public databases, will facilitate better predictions of the capacity for plant populations to respond to rapid climate change. PMID:24454552

Defining a relationship between incident wave parameters and morphologic evolution of shoals on ebb tidal deltas using long term X-band radar observation from RIOS

NASA Astrophysics Data System (ADS)

Humberston, J. L.; McNinch, J.; Lippmann, T. C.

2016-12-01

The morphology of tidal inlet ebb-shoals varies dynamically over time, particularly in response to large wave events. Understanding which wave qualities most influence shoals' evolution would support advancements in sediment bypassing models as well as targeted maintenance dredging for hydrographic purposes. Unfortunately, shallow and rapidly changing bathymetry, turbid waters and ambiguous wave speeds resulting from multiple shoaling and de-shoaling areas limits many traditional surveying techniques from obtaining the spatial and temporal resolution necessary to effectively characterize shoal development. The Radar Inlet Observing System (RIOS) is a uniquely designed mobile X-band radar system that can be deployed to inlet environments and, using roof-mounted solar panels and an automatically triggered highly efficient diesel generator, run automated hourly collections and wirelessly stream data for up to several months at a time in nearly all weather and water conditions. During 2015 and early 2016, RIOS was deployed to St. Augustine Inlet, FL., New River Inlet, N.C., and Oregon Inlet, N.C. for periods of one to six months to allow for measureable shoal evolution. During deployments, ten minute collections (at 1 Hz) were conducted every hour and the data gridded to a 5m alongshore/cross-shore grid. Raw intensity returns were time-averaged and analyzed to define three metrics of shoal evolution: movement direction, movement velocity and inferred bathymetry. For each location and time period, wave frequencies, wave directions and significant wave heights were collected from the nearest wave-buoy. Time lapse videos of shoal positions were inspected and used in concert with cross-correlations values from each pair of shoal and wave parameters to determine the incident wave qualities most strongly relating to shoal evolution. Preliminary results suggest wave height, more than frequency, controls shoal movement. Wave direction and size collaboratively appear to direct the shoal's alongshore movement direction as well as general trends of morphologic evolution.

Retrovolution: HIV-driven evolution of cellular genes and improvement of anticancer drug activation.

PubMed

Rossolillo, Paola; Winter, Flore; Simon-Loriere, Etienne; Gallois-Montbrun, Sarah; Negroni, Matteo

2012-08-01

In evolution strategies aimed at isolating molecules with new functions, screening for the desired phenotype is generally performed in vitro or in bacteria. When the final goal of the strategy is the modification of the human cell, the mutants selected with these preliminary screenings may fail to confer the desired phenotype, due to the complex networks that regulate gene expression in higher eukaryotes. We developed a system where, by mimicking successive infection cycles with HIV-1 derived vectors containing the gene target of the evolution in their genome, libraries of gene mutants are generated in the human cell, where they can be directly screened. As a proof of concept we created a library of mutants of the human deoxycytidine kinase (dCK) gene, involved in the activation of nucleoside analogues used in cancer treatment, with the aim of isolating a variant sensitizing cancer cells to the chemotherapy compound Gemcitabine, to be used in gene therapy for anti-cancer approaches or as a poorly immunogenic negative selection marker for cell transplantation approaches. We describe the isolation of a dCK mutant, G12, inducing a 300-fold sensitization to Gemcitabine in cells originally resistant to the prodrug (Messa 10K), an effect 60 times stronger than the one induced by the wt enzyme. The phenotype is observed in different tumour cell lines irrespective of the insertion site of the transgene and is due to a change in specificity of the mutated kinase in favour of the nucleoside analogue. The mutations characterizing G12 are distant from the active site of the enzyme and are unpredictable on a rational basis, fully validating the pragmatic approach followed. Besides the potential interest of the G12 dCK variant for therapeutic purposes, the methodology developed is of interest for a large panel of applications in biotechnology and basic research.

Slowly switching between environments facilitates reverse evolution in small populations

NASA Astrophysics Data System (ADS)

Tan, Longzhi; Gore, Jeff

2011-03-01

The rate at which a physical process occurs usually changes the behavior of a system. In thermodynamics, the reversibility of a process generally increases when it occurs at an infinitely slow rate. In biological evolution, adaptations to a new environment may be reversed by evolution in the ancestral environment. Such fluctuating environments are ubiquitous in nature, although how the rate of switching affects reverse evolution is unknown. Here we use a computational approach to quantify evolutionary reversibility as a function of the rate of switching between two environments. For small population sizes, which travel on landscapes as random walkers, we find that both genotypic and phenotypic reverse evolution increase at slow switching rates. However, slow switching of environments decreases evolutionary reversibility for a greedy walker, corresponding to large populations (extensive clonal interference). We conclude that the impact of the switching rate for biological evolution is more complicated than other common physical processes, and that a quantitative approach may yield significant insight into reverse evolution.

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution.

PubMed

Baele, Guy; Lemey, Philippe; Vansteelandt, Stijn

2013-03-06

Accurate model comparison requires extensive computation times, especially for parameter-rich models of sequence evolution. In the Bayesian framework, model selection is typically performed through the evaluation of a Bayes factor, the ratio of two marginal likelihoods (one for each model). Recently introduced techniques to estimate (log) marginal likelihoods, such as path sampling and stepping-stone sampling, offer increased accuracy over the traditional harmonic mean estimator at an increased computational cost. Most often, each model's marginal likelihood will be estimated individually, which leads the resulting Bayes factor to suffer from errors associated with each of these independent estimation processes. We here assess the original 'model-switch' path sampling approach for direct Bayes factor estimation in phylogenetics, as well as an extension that uses more samples, to construct a direct path between two competing models, thereby eliminating the need to calculate each model's marginal likelihood independently. Further, we provide a competing Bayes factor estimator using an adaptation of the recently introduced stepping-stone sampling algorithm and set out to determine appropriate settings for accurately calculating such Bayes factors, with context-dependent evolutionary models as an example. While we show that modest efforts are required to roughly identify the increase in model fit, only drastically increased computation times ensure the accuracy needed to detect more subtle details of the evolutionary process. We show that our adaptation of stepping-stone sampling for direct Bayes factor calculation outperforms the original path sampling approach as well as an extension that exploits more samples. Our proposed approach for Bayes factor estimation also has preferable statistical properties over the use of individual marginal likelihood estimates for both models under comparison. Assuming a sigmoid function to determine the path between two competing models, we provide evidence that a single well-chosen sigmoid shape value requires less computational efforts in order to approximate the true value of the (log) Bayes factor compared to the original approach. We show that the (log) Bayes factors calculated using path sampling and stepping-stone sampling differ drastically from those estimated using either of the harmonic mean estimators, supporting earlier claims that the latter systematically overestimate the performance of high-dimensional models, which we show can lead to erroneous conclusions. Based on our results, we argue that highly accurate estimation of differences in model fit for high-dimensional models requires much more computational effort than suggested in recent studies on marginal likelihood estimation.

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution

PubMed Central

2013-01-01

Background Accurate model comparison requires extensive computation times, especially for parameter-rich models of sequence evolution. In the Bayesian framework, model selection is typically performed through the evaluation of a Bayes factor, the ratio of two marginal likelihoods (one for each model). Recently introduced techniques to estimate (log) marginal likelihoods, such as path sampling and stepping-stone sampling, offer increased accuracy over the traditional harmonic mean estimator at an increased computational cost. Most often, each model’s marginal likelihood will be estimated individually, which leads the resulting Bayes factor to suffer from errors associated with each of these independent estimation processes. Results We here assess the original ‘model-switch’ path sampling approach for direct Bayes factor estimation in phylogenetics, as well as an extension that uses more samples, to construct a direct path between two competing models, thereby eliminating the need to calculate each model’s marginal likelihood independently. Further, we provide a competing Bayes factor estimator using an adaptation of the recently introduced stepping-stone sampling algorithm and set out to determine appropriate settings for accurately calculating such Bayes factors, with context-dependent evolutionary models as an example. While we show that modest efforts are required to roughly identify the increase in model fit, only drastically increased computation times ensure the accuracy needed to detect more subtle details of the evolutionary process. Conclusions We show that our adaptation of stepping-stone sampling for direct Bayes factor calculation outperforms the original path sampling approach as well as an extension that exploits more samples. Our proposed approach for Bayes factor estimation also has preferable statistical properties over the use of individual marginal likelihood estimates for both models under comparison. Assuming a sigmoid function to determine the path between two competing models, we provide evidence that a single well-chosen sigmoid shape value requires less computational efforts in order to approximate the true value of the (log) Bayes factor compared to the original approach. We show that the (log) Bayes factors calculated using path sampling and stepping-stone sampling differ drastically from those estimated using either of the harmonic mean estimators, supporting earlier claims that the latter systematically overestimate the performance of high-dimensional models, which we show can lead to erroneous conclusions. Based on our results, we argue that highly accurate estimation of differences in model fit for high-dimensional models requires much more computational effort than suggested in recent studies on marginal likelihood estimation. PMID:23497171

Mr. Red in the American South: a response to Lisa Borgerding

NASA Astrophysics Data System (ADS)

Meadows, Lee

2017-03-01

This review essay affirms the work Mr. Red does with his students to support their learning about evolution and how his approach agrees with the realities of teaching evolution in the American South. It then shows how focusing on understanding, but not necessarily belief, adds to Mr. Red's apparent neutrality a complimentary pedagogical approach that legitimizes more strongly accepted science while at the same time attending to the deep conflict many rural students feel when they are asked to learn evolution.

Using Human Evolution to Teach Evolutionary Theory

ERIC Educational Resources Information Center

Besterman, Hugo; La Velle, Linda Baggott

2007-01-01

This paper discusses some traditional approaches to the teaching of evolutionary theory at pre-university level, criticising in particular some of the more commonly used models and exemplars. Curricular demands are described and an alternative approach is suggested, using the emerging story of human evolution. Recent discoveries help to illustrate…

An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome.

PubMed

Kawano, Yasuhiro; Neeley, Shane; Adachi, Kei; Nakai, Hiroyuki

2013-01-01

Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm, with which VP and AAP were co-evolved from random or native nucleotide sequences in silico. As a result, we demonstrate that these two heptapeptide motifs could exhibit high degeneracy if coded by separate nucleotide sequences, and elucidate how overlap-evoked co-evolutionary constraints play a role in making the VP and AAP heptapeptide sequences into the present shape. Specifically, we demonstrate that two valine (V) residues and β-strand propensity in QVKEVTQ are structurally important, the strongly negative and hydrophilic nature of KSKRSRR is functionally important, and overlap-evoked co-evolution imposes strong constraints on serine (S) residues in KSKRSRR, despite high degeneracy of the motifs in the absence of co-evolutionary constraints.

Dynamics of double-polarity subduction: application to the Western Mediterranean

NASA Astrophysics Data System (ADS)

Peral, Mireia; Zlotnik, Sergio; Fernandez, Manel; Vergés, Jaume; Jiménez-Munt, Ivone; Torne, Montserrat

2016-04-01

The evolution of the Western Mediterranean is a highly debated question by geologists and geophysicists. Even though most scientists agree in considering slab roll-back to be the driving mechanism of the tectonic evolution of this area, there is still no consensus about the initial setup and its time evolution. A recent model suggests a lateral change in subduction polarity of the Ligurian-Thetys oceanic domain to explain the formation and evolution of the Betic-Rif orogenic system and the associated Alboran back-arc basin. Such geodynamic scenario is also proposed for different converging regions. The aim of this study is to analyze the dynamic evolution of a double-polarity subduction process and its consequences in order to test the physical feasibility of this interaction and provide geometries and evolutions comparable to those proposed for the Western Mediterranean. The 3D numerical model is carried out via the Underworld framework. Tectonic plate behavior is described by equations of fluid dynamics in the presence of several different phases. Underworld solves a non-linear Stokes flow problem using Finite Elements combined with particle-in-cell approach, thus the discretization combines a standard Eulerian Finite Element mesh with Lagrangian particles to track the location of the phases. The final model consists of two oceanic plates with viscoplastic rheology subducting into the upper mantle in opposite direction and the problem is driven by Rayleigh-Taylor instability. We study the influence of the boundary conditions in the model evolution, and the slab deformation produced by the proximity between both plates. Moreover the case of asymmetric friction on the lateral sides of slabs is also considered. Simulations of single subduction models are used as a reference, to compare results and understand the influence of the second plate. We observe slight differences in the trench retreat velocity and the slab morphology near the contact area when plates are spaced less than 100 km.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective. Copyright © 2017 Elsevier B.V. All rights reserved.

Possible impact of global warming on the evolution of hemagglutinins from influenza a viruses.

PubMed

Yan, Shaomin; Wu, Guang

2011-02-01

To determine if global warming has an impact on the evolution of hemagglutinins from influenza A viruses, because both global warming and influenza pandemics/epidemics threaten the world. 4 706 hemagglutinins from influenza A viruses sampled from 1956 to 2009 were converted to a time-series to show their evolutionary process and compared with the global, northern hemisphere and southern hemisphere temperatures, to determine if their trends run in similar or opposite directions. Point-to-point comparisons between temperature and quantified hemagglutinins were performed for all species and for the major prevailing species. The comparisons show that the trends for both hemagglutinin evolution and temperature change run in a similar direction. Global warming has a consistent and progressive impact on the hemagglutinin evolution of influenza A viruses.

Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes.

PubMed

Ghadessy, Farid J; Holliger, Philipp

2007-01-01

Compartmentalized self-replication (CSR) is a novel method for the directed evolution of enzymes and, in particular, polymerases. In its simplest form, CSR consists of a simple feedback loop involving a polymerase that replicates only its own encoding gene (self-replication). Self-replication occurs in discrete, spatially separate, noncommunicating compartments formed by a heat-stable water-in-oil emulsion. Compartmentalization ensures the linkage of phenotype and genotype (i.e., it ensures that each polymerase replicates only its own encoding gene to the exclusion of those in the other compartments). As a result, adaptive gains by the polymerase directly (and proportionally) translate into genetic amplification of the encoding polymerase gene. CSR has proven to be a useful strategy for the directed evolution of polymerases directly from diverse repertoires of polymerase genes. In this chapter, we describe some of the CSR protocols used successfully to evolve variants of T. aquaticus Pol I (Taq) polymerase with novel and useful properties, such as increased thermostability or resistance to the potent inhibitor, heparin, from a repertoire of randomly mutated Taq polymerase genes.

Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions

NASA Astrophysics Data System (ADS)

Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.

2014-12-01

The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.

Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry.

PubMed

Duthie, A B; Bocedi, G; Germain, R R; Reid, J M

2018-01-01

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. 'degeneracy') potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry. © The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

TRIADS: A phase-resolving model for nonlinear shoaling of directional wave spectra

NASA Astrophysics Data System (ADS)

Sheremet, Alex; Davis, Justin R.; Tian, Miao; Hanson, Jeffrey L.; Hathaway, Kent K.

2016-03-01

We investigate the performance of TRIADS, a numerical implementation of a phase-resolving, nonlinear, spectral model describing directional wave evolution in intermediate and shallow water. TRIADS simulations of shoaling waves generated by Hurricane Bill, 2009 are compared to directional spectral estimates based on observations collected at the Field Research Facility of the US Army Corps Of Engineers, at Duck, NC. Both the ability of the model to capture the processes essential to the nonlinear wave evolution, and the efficiency of the numerical implementations are analyzed and discussed.

Microstructural Evolution in Intensively Melt Sheared Direct Chill Cast Al-Alloys

NASA Astrophysics Data System (ADS)

Jones, S.; Rao, A. K. Prasada; Patel, J. B.; Scamans, G. M.; Fan, Z.

The work presented here introduces the novel melt conditioned direct chill casting (MC-DC) technology, where intensive melt shearing is applied to the conventional direct-chill casting process. MC-DC casting can successfully produce high quality Al-alloy billets. The results obtained from 80 mm diameter billets cast at speed of 200 mm/min show that MC-DC casting of Al-alloys, substantially refines the microstructure and reduces macro-segregation. In this paper, we present the preliminary results and discuss microstructural evolution during MC-DC casting of Al-alloys.

Modeling for Matrix Multicracking Evolution of Cross-ply Ceramic-Matrix Composites Using Energy Balance Approach

NASA Astrophysics Data System (ADS)

Longbiao, Li

2015-12-01

The matrix multicracking evolution of cross-ply ceramic-matrix composites (CMCs) has been investigated using energy balance approach. The multicracking of cross-ply CMCs was classified into five modes, i.e., (1) mode 1: transverse multicracking; (2) mode 2: transverse multicracking and matrix multicracking with perfect fiber/matrix interface bonding; (3) mode 3: transverse multicracking and matrix multicracking with fiber/matrix interface debonding; (4) mode 4: matrix multicracking with perfect fiber/matrix interface bonding; and (5) mode 5: matrix multicracking with fiber/matrix interface debonding. The stress distributions of four cracking modes, i.e., mode 1, mode 2, mode 3 and mode 5, are analysed using shear-lag model. The matrix multicracking evolution of mode 1, mode 2, mode 3 and mode 5, has been determined using energy balance approach. The effects of ply thickness and fiber volume fraction on matrix multicracking evolution of cross-ply CMCs have been investigated.

Deformation dependence of proton decay rates and angular distributions in a time-dependent approach

NASA Astrophysics Data System (ADS)

Carjan, N.; Talou, P.; Strottman, D.

1998-12-01

A new, time-dependent, approach to proton decay from axially symmetric deformed nuclei is presented. The two-dimensional time-dependent Schrödinger equation for the interaction between the emitted proton and the rest of the nucleus is solved numerically for well defined initial quasi-stationary proton states. Applied to the hypothetical proton emission from excited states in deformed nuclei of 208Pb, this approach shows that the problem cannot be reduced to one dimension. There are in general more than one directions of emission with wide distributions around them, determined mainly by the quantum numbers of the initial wave function rather than by the potential landscape. The distribution of the "residual" angular momentum and its variation in time play a major role in the determination of the decay rate. In a couple of cases, no exponential decay was found during the calculated time evolution (2×10-21 sec) although more than half of the wave function escaped during that time.

Fine-tuning gene networks using simple sequence repeats

PubMed Central

Egbert, Robert G.; Klavins, Eric

2012-01-01

The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch’s behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis—suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks. PMID:22927382

Cultural Change: The How and the Why.

PubMed

Varnum, Michael E W; Grossmann, Igor

2017-11-01

More than half a century of cross-cultural research has demonstrated group-level differences in psychological and behavioral phenomena, from values to attention to neural responses. However, cultures are not static, with several specific changes documented for cultural products, practices, and values. How and why do societies change? Here we juxtapose theory and insights from cultural evolution and social ecology. Evolutionary approaches enable an understanding of the how of cultural change, suggesting transmission mechanisms by which the contents of culture may change. Ecological approaches provide insights into the why of cultural change: They identify specific environmental pressures, which evoke shifts in psychology and thereby enable greater precision in predictions of specific cultural changes based on changes in ecological conditions. Complementary insights from the ecological and cultural evolutionary approaches can jointly clarify the process by which cultures change. We end by discussing the relevance of cultural change research for the contemporary societal shifts and by highlighting several critical challenges and future directions for the emerging field of cross-temporal research on culture and psychology.

Towards natural language question generation for the validation of ontologies and mappings.

PubMed

Ben Abacha, Asma; Dos Reis, Julio Cesar; Mrabet, Yassine; Pruski, Cédric; Da Silveira, Marcos

2016-08-08

The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging. We propose a novel semi-automatic approach based on the generation of natural language (NL) questions to support the validation of ontologies and their evolution. The proposed approach includes the automatic generation, factorization and ordering of NL questions from medical ontologies. The final validation and correction is performed by submitting these questions to domain experts and automatically analyzing their feedback. We also propose a second approach for the validation of mappings impacted by ontology changes. The method exploits the context of the changes to propose correction alternatives presented as Multiple Choice Questions. This research provides a question optimization strategy to maximize the validation of ontology entities with a reduced number of questions. We evaluate our approach for the validation of three medical ontologies. We also evaluate the feasibility and efficiency of our mappings validation approach in the context of ontology evolution. These experiments are performed with different versions of SNOMED-CT and ICD9. The obtained experimental results suggest the feasibility and adequacy of our approach to support the validation of interconnected and evolving ontologies. Results also suggest that taking into account RDFS and OWL entailment helps reducing the number of questions and validation time. The application of our approach to validate mapping evolution also shows the difficulty of adapting mapping evolution over time and highlights the importance of semi-automatic validation.

Reconstruction of DNA sequences using genetic algorithms and cellular automata: towards mutation prediction?

PubMed

Mizas, Ch; Sirakoulis, G Ch; Mardiris, V; Karafyllidis, I; Glykos, N; Sandaltzopoulos, R

2008-04-01

Change of DNA sequence that fuels evolution is, to a certain extent, a deterministic process because mutagenesis does not occur in an absolutely random manner. So far, it has not been possible to decipher the rules that govern DNA sequence evolution due to the extreme complexity of the entire process. In our attempt to approach this issue we focus solely on the mechanisms of mutagenesis and deliberately disregard the role of natural selection. Hence, in this analysis, evolution refers to the accumulation of genetic alterations that originate from mutations and are transmitted through generations without being subjected to natural selection. We have developed a software tool that allows modelling of a DNA sequence as a one-dimensional cellular automaton (CA) with four states per cell which correspond to the four DNA bases, i.e. A, C, T and G. The four states are represented by numbers of the quaternary number system. Moreover, we have developed genetic algorithms (GAs) in order to determine the rules of CA evolution that simulate the DNA evolution process. Linear evolution rules were considered and square matrices were used to represent them. If DNA sequences of different evolution steps are available, our approach allows the determination of the underlying evolution rule(s). Conversely, once the evolution rules are deciphered, our tool may reconstruct the DNA sequence in any previous evolution step for which the exact sequence information was unknown. The developed tool may be used to test various parameters that could influence evolution. We describe a paradigm relying on the assumption that mutagenesis is governed by a near-neighbour-dependent mechanism. Based on the satisfactory performance of our system in the deliberately simplified example, we propose that our approach could offer a starting point for future attempts to understand the mechanisms that govern evolution. The developed software is open-source and has a user-friendly graphical input interface.

Morphodynamics of Planetary Deserts: A Laboratory Approach

NASA Astrophysics Data System (ADS)

Garcia, A.; Courrech Du Pont, S.; Rodriguez, S.

2014-12-01

Earth deserts show a rich variety of dune shapes from transverse to barchan, star and linear dunes depending on the history of wind regimes (strength and variability) and sand availability [1]. In desert, exposed to one wind direction, dunes perpendicular to the wind direction are found to be transverse or barchans, only sand availability plays a key role on their formation and evolution. However, the evolution time scale of such structures (several years) limits our investigation of their morphodynamics understanding. We use here, a laboratory experiment able to considerably reduce space and time scales by reproducing millimeter to centimeter subaqueous dunes by controlling environmental parameters such as type of wind (multi-winds, bimodal, quasi-bimodal or unidirectional wind) and amount of sediment [2,3]. This set up allows us to characterize more precisely the different modes of dune formation and long-term evolution, and to constrain the physics behind the morphogenesis and dynamics of dunes. Indeed, the formation, evolution and transition between the different dune modes are better understood and quantified thanks to a new setting experiment able to give a remote sediment source in continuous (closer to what happens in terrestrial desert): a sand distributor that controls the input sand flow. Firstly, in a one wind direction conditions, we managed to follow and quantify the growth of the instability of transverse dunes that break into barchans when the sand supply is low and reversely when the sand supply is higher, barchan fields evolve to bars dunes ending to form transverse. The next step will be to perform experiments under two winds conditions in order to better constrain the formation mode of linear dunes, depending also only on the input sand flux. Previous experiments shown that linear "finger" dunes can be triggered by the break of transverse dunes and then the elongating of one barchan's arm [4]. These studies can farther explain more precisely in different wind history and sand supply, these patterns state that should emerge and, by applying the relevant scale law, to apply this laboratory work to terrestrial and planetary (Mars and Titan) desert dynamics. [1] Bagnold R.A. (1941). [2] Hersen P. (2004). [3] Reffet E. (2010). [4] Courrech Du Pont S. et al. (2014).

Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule.

PubMed

Ledbetter, Michael P; Hwang, Tony W; Stovall, Gwendolyn M; Ellington, Andrew D

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. In vitro directed evolution (IVDE) frequently serves as a model system for the study of Darwinian evolution but produces noticeable phenotypic shifts in a matter of hours. An IVDE demonstration lab would serve to both directly demonstrate how Darwinian selection can act on a pool of variants and introduce students to an essential method of modern molecular biology. To produce an IVDE demonstration lab, continuous IVDE of a T500 ribozyme ligase population has been paired with a fluorescent strand displacement reporter system to visualize the selection of improved catalytic function. A ribozyme population is taken through rounds of isothermal amplification dependent on the self-ligation of a T7 promoter. As the population is selectively enriched with better ligase activity, the strand displacement system allows for the monitoring of the population's ligation rate. The strand displacement reporter system permits the detection of ligated ribozyme. Once ligated with the T7 promoter, the 5' end of the ribozyme displaces paired fluorophore-quencher oligonucleotides, in turn, generating visible signal upon UV light excitation. As the ligation rate of the population increases, due to the selection for faster ligating species, the fluorescent signal develops more rapidly. The pairing of the continuous isothermal system with the fluorescent reporting scheme allows any user, provided with minimal materials, to model the continuous directed evolution of a biomolecule. Copyright © 2013 Wiley-Liss, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galarraga, Haize; Warren, Robert J.; Lados, Diana A.

Electron beam melting (EBM) is a metal powder bed fusion additive manufacturing (AM) technology that is used to fabricate three-dimensional near-net-shaped parts directly from computer models. Ti-6Al-4V is the most widely used and studied alloy for this technology and is the focus of this work in its ELI (Extra Low Interstitial) variation. The mechanisms of microstructure formation, evolution, and its subsequent influence on mechanical properties of the alloy in as-fabricated condition have been documented by various researchers. In the present work, the thermal history resulting in the formation of the as-fabricated microstructure was analyzed and studied by a thermal simulation.more » Subsequently different heat treatments were performed based on three approaches in order to study the effects of heat treatments on the singular and exclusive microstructure formed during the EBM fabrication process. In the first approach, the effect of cooling rate after the solutionizing process was studied. In the second approach, the variation of α lath thickness during annealing treatment and correlation with mechanical properties was established. In the last approach, several solutionizing and aging experiments were conducted.« less

An evolutionary game approach for determination of the structural conflicts in signed networks

PubMed Central

Tan, Shaolin; Lü, Jinhu

2016-01-01

Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks. PMID:26915581

Nuclear astrophysics in the laboratory and in the universe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Champagne, A. E., E-mail: artc@physics.unc.edu; Iliadis, C.; Longland, R.

Nuclear processes drive stellar evolution and so nuclear physics, stellar models and observations together allow us to describe the inner workings of stars and their life stories. This Information on nuclear reaction rates and nuclear properties are critical ingredients in addressing most questions in astrophysics and often the nuclear database is incomplete or lacking the needed precision. Direct measurements of astrophysically-interesting reactions are necessary and the experimental focus is on improving both sensitivity and precision. In the following, we review recent results and approaches taken at the Laboratory for Experimental Nuclear Astrophysics (LENA, http://research.physics.unc.edu/project/nuclearastro/Welcome.html )

Active control of lateral leakage in thin-ridge SOI waveguide structures

NASA Astrophysics Data System (ADS)

Dalvand, Naser; Nguyen, Thach G.; Tummidi, Ravi S.; Koch, Thomas L.; Mitchell, Arnan

2011-12-01

We report on the design and simulation of a novel Silicon-On-Insulator waveguide structures which when excited with TM guided light, emit TE polarized radiation with controlled radiation characteristics[1]. The structures utilize parallel leaky waveguides of specific separations. The structures are simulated using a full-vector mode-matching approach which allows visualisation of the evolution of the propagating and radiating fields over the length of the waveguide structure. It is shown that radiation can be resonantly enhanced or suppressed in different directions depending on the choice of the phase of the excitation of the waveguide components. Steps toward practical demonstration are identified.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

Engineering Genetically Encoded FRET Sensors

PubMed Central

Lindenburg, Laurens; Merkx, Maarten

2014-01-01

Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening. PMID:24991940

Why is the VLT Very Efficient?

NASA Astrophysics Data System (ADS)

Comerón, F.

2009-09-01

The operations model of the ESO Very Large Telescope (VLT) heavily relies on a full-scale implementation of Service Mode observing. In this contribution we review the main features of ESO's approach to Service Mode at the VLT, we outline the advantages offered by this mode, and the challenges faced when implementing it given the wide diversity of instrumentation and instrument modes currently available at the VLT and the VLT Interferometer (VLTI). We give special emphasis to the part of this challenge directly derived from the evolution of the atmospheric conditions, which drive the short-term scheduling of the different scientific programmes competing for the available time.

A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution

PubMed Central

Rübben, Albert; Nordhoff, Ole

2013-01-01

Summary Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment. It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution. The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages. Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients. PMID:23336076

Characterization of an Indian sword: classic and noninvasive methods of investigation in comparison

NASA Astrophysics Data System (ADS)

Barzagli, E.; Grazzi, F.; Williams, A.; Edge, D.; Scherillo, A.; Kelleher, J.; Zoppi, M.

2015-04-01

The evolution of metallurgy in history is one of the most interesting topics in Archaeometry. The production of steel and its forging methods to make tools and weapons are topics of great interest in the field of the history of metallurgy. In the production of weapons, we find almost always the highest level of technology. These were generally produced by skilled craftsmen who used the best quality materials available. Indian swords are an outstanding example in this field and one of the most interesting classes of objects for the study of the evolution of metallurgy. This work presents the study of a Shamsheer (a sword with a curved blade with single edge) made available by the Wallace Collection in London. The purpose of this study was to determine the composition, the microstructure, the level and the direction of residual strain and their distribution in the blade. We have used two different approaches: the classical one (metallography) and a nondestructive technique (neutron diffraction): In this way, we can test differences and complementarities of these two techniques. To obtain a good characterization of artifacts studied by traditional analytical methods, an invasive approach is required. However, the most ancient objects are scarce in number, and the most interesting ones are usually in an excellent state of conservation, so it is unthinkable to apply techniques with a destructive approach. The analysis of blades that has been performed by metallographic microscopy has demonstrated the specificity of the production of this type of steel. However, metallographic analysis can give only limited information about the structural characteristics of these artifacts of high quality, and it is limited to the sampled areas. The best approach for nondestructive analysis is therefore to use neutron techniques.

GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites.

PubMed

Leinweber, Matthias; Fober, Thomas; Freisleben, Bernd

2018-01-01

In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations. Binary classification tests based on the ATP, NADH, and FAD protein subsets of CavBase, a database containing putative binding sites, show average classification rate improvements from about 92 percent (CPU) to 96 percent (GPU). Further experiments indicate that the proposed GPU-based labeled point cloud superpositioning approach can be superior to traditional protein comparison approaches based on sequence alignments.

BOOSTED TIDAL DISRUPTION BY MASSIVE BLACK HOLE BINARIES DURING GALAXY MERGERS FROM THE VIEW OF N -BODY SIMULATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shuo; Berczik, Peter; Spurzem, Rainer

Supermassive black hole binaries (SMBHBs) are productions of the hierarchical galaxy formation model. There are many close connections between a central SMBH and its host galaxy because the former plays very important roles on galaxy formation and evolution. For this reason, the evolution of SMBHBs in merging galaxies is a fundamental challenge. Since there are many discussions about SMBHB evolution in a gas-rich environment, we focus on the quiescent galaxy, using tidal disruption (TD) as a diagnostic tool. Our study is based on a series of numerical, large particle number, direct N -body simulations for dry major mergers. According tomore » the simulation results, the evolution can be divided into three phases. In phase I, the TD rate for two well separated SMBHs in a merging system is similar to that for a single SMBH in an isolated galaxy. After two SMBHs approach close enough to form a bound binary in phase II, the disruption rate can be enhanced by ∼2 orders of magnitude within a short time. This “boosted” disruption stage finishes after the SMBHB evolves to a compact binary system in phase III, corresponding to a reduction in disruption rate back to a level of a few times higher than in phase I. We also discuss how to correctly extrapolate our N -body simulation results to reality, and the implications of our results to observations.« less

Body size reductions in nonmammalian eutheriodont therapsids (Synapsida) during the end-Permian mass extinction.

PubMed

Huttenlocker, Adam K

2014-01-01

The extent to which mass extinctions influence body size evolution in major tetrapod clades is inadequately understood. For example, the 'Lilliput effect,' a common feature of mass extinctions, describes a temporary decrease in body sizes of survivor taxa in post-extinction faunas. However, its signature on existing patterns of body size evolution in tetrapods and the persistence of its impacts during post-extinction recoveries are virtually unknown, and rarely compared in both geologic and phylogenetic contexts. Here, I evaluate temporal and phylogenetic distributions of body size in Permo-Triassic therocephalian and cynodont therapsids (eutheriodonts) using a museum collections-based approach and time series model fitting on a regional stratigraphic sequence from the Karoo Basin, South Africa. I further employed rank order correlation tests on global age and clade rank data from an expanded phylogenetic dataset, and performed evolutionary model testing using Brownian (passive diffusion) models. Results support significant size reductions in the immediate aftermath of the end-Permian mass extinction (ca. 252.3 Ma) consistent with some definitions of Lilliput effects. However, this temporal succession reflects a pattern that was underscored largely by Brownian processes and constructive selectivity. Results also support two recent contentions about body size evolution and mass extinctions: 1) active, directional evolution in size traits is rare over macroevolutionary time scales and 2) geologically brief size reductions may be accomplished by the ecological removal of large-bodied species without rapid originations of new small-bodied clades or shifts from long-term evolutionary patterns.

A historical study to understand students’ current difficulties about RMS values

NASA Astrophysics Data System (ADS)

Khantine-Langlois, Françoise; Munier, Valérie

2016-07-01

Several studies show that students experience more and more difficulties managing the measurements of electrical values in alternating current and that they have trouble making links between theory and practice. They find it difficult to give meaning to root mean square (RMS; or effective) values, which are not understood as average values and are confused with instantaneous values. This shows that students do not clearly differentiate variable and direct currents. In this paper we try, with a historical study and a study of teaching the concept of RMS values, to understand students’ difficulties with this concept. In the first part we present an epistemological analysis of the concept of RMS values, showing that it is multifaceted and can be approached from different points of view. In the second part we analyse the evolution of French secondary school curricula and textbooks from the explicit introduction of variable currents to today, questioning the links between the evolution of the curricula and the evolution of the place of science and technology in our societies. We point out that the evolution of the curricula is linked to the social context and to the connections between science, technology and society, and also to the relationship with mathematics curricula. We show that alternating current is introduced earlier in the curriculum but has gradually lost all phenomenological description. This study allows us to better understand students’ difficulties and to discuss some implications for teaching.

Evolutionary dynamics of collective action in spatially structured populations.

PubMed

Peña, Jorge; Nöldeke, Georg; Lehmann, Laurent

2015-10-07

Many models proposed to study the evolution of collective action rely on a formalism that represents social interactions as n-player games between individuals adopting discrete actions such as cooperate and defect. Despite the importance of spatial structure in biological collective action, the analysis of n-player games games in spatially structured populations has so far proved elusive. We address this problem by considering mixed strategies and by integrating discrete-action n-player games into the direct fitness approach of social evolution theory. This allows to conveniently identify convergence stable strategies and to capture the effect of population structure by a single structure coefficient, namely, the pairwise (scaled) relatedness among interacting individuals. As an application, we use our mathematical framework to investigate collective action problems associated with the provision of three different kinds of collective goods, paradigmatic of a vast array of helping traits in nature: "public goods" (both providers and shirkers can use the good, e.g., alarm calls), "club goods" (only providers can use the good, e.g., participation in collective hunting), and "charity goods" (only shirkers can use the good, e.g., altruistic sacrifice). We show that relatedness promotes the evolution of collective action in different ways depending on the kind of collective good and its economies of scale. Our findings highlight the importance of explicitly accounting for relatedness, the kind of collective good, and the economies of scale in theoretical and empirical studies of the evolution of collective action. Copyright © 2015 Elsevier Ltd. All rights reserved.

EcoEvo-MAPS: An Ecology and Evolution Assessment for Introductory through Advanced Undergraduates

ERIC Educational Resources Information Center

Summers, Mindi M.; Couch, Brian A.; Knight, Jennifer K.; Brownell, Sara E.; Crowe, Alison J.; Semsar, Katharine; Wright, Christian D.; Smith, Michelle K.

2018-01-01

A new assessment tool, Ecology and Evolution--Measuring Achievement and Progression in Science or EcoEvo-MAPS, measures student thinking in ecology and evolution during an undergraduate course of study. EcoEvo-MAPS targets foundational concepts in ecology and evolution and uses a novel approach that asks students to evaluate a series of…

Organizational Learning and the Learning Organization: Reviewing Evolution for Prospecting the Future

ERIC Educational Resources Information Center

Rebelo, Teresa Manuela; Gomes, Adelino Duarte

2008-01-01

Purpose: The purpose of this article is to analyse the evolution of the concepts of organizational learning and the learning organization and propose guidelines for the future. Design/methodology/approach: The evolution of organizational learning and the learning organization is analysed in the light of the three-stage model of the evolution of…

Spore: Spawning Evolutionary Misconceptions?

NASA Astrophysics Data System (ADS)

Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

2010-10-01

The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

The spread of a novel behavior in wild chimpanzees: New insights into the ape cultural mind.

PubMed

Gruber, Thibaud; Poisot, Timothée; Zuberbühler, Klaus; Hoppitt, William; Hobaiter, Catherine

2015-01-01

For years, the animal culture debate has been dominated by the puzzling absence of direct evidence for social transmission of behavioral innovations in the flagship species of animal culture, the common chimpanzee. Although social learning of novel behaviors has been documented in captivity, critics argue that these findings lack ecological validity and therefore may not be relevant for understanding the evolution of culture. For the wild, it is possible that group-specific behavioral differences emerge because group members respond individually to unspecified environmental differences, rather than learning from each other. In a recent paper, we used social network analyses in wild chimpanzees (Pan troglodytes schweinfurthii) to provide direct evidence for social transmission of a behavioral innovation, moss-sponging, to extract water from a tree hole. Here, we discuss the implications of our findings and how our new methodological approach could help future studies of social learning and culture in wild apes.

Vibration effect on the Soret-induced convection of ternary mixture in a rectangular cavity heated from below

NASA Astrophysics Data System (ADS)

Lyubimova, T. P.; Zubova, N. A.

2017-06-01

This paper presents the results of numerical simulation of the Soret-induced convection of ternary mixture in the rectangular cavity elongated in horizontal direction in gravity field. The cavity has rigid impermeable boundaries. It is heated from the bellow and undergoes translational linearly polarized vibrations of finite amplitude and frequency in the horizontal direction. The problem is solved by finite difference method in the framework of full unsteady non-linear approach. The procedure of diagonalization of the molecular diffusion coefficient matrix is applied, allowing to eliminate cross-diffusion components in the equations and to reduce the number of the governing parameters. The calculations are performed for model ternary mixture with positive separation ratios of the components. The data on the vibration effect on temporal evolution of instantaneous and average fields and integral characteristics of the flow and heat and mass transfer at different levels of gravity are obtained.

A kinetic model for the characteristic surface morphologies of thin films by directional vapor deposition

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Huang, Po-Yu

2017-12-01

In order to simulate a process of directional vapor deposition, in this study, a numerical approach was applied to model the growth and evolution of surface morphologies for the crystallographic structures of thin films. The critical factors affecting the surface morphologies in a deposition process, such as the crystallographic symmetry, anisotropic interfacial energy, shadowing effect, and deposition rate, were all enclosed in the theoretical model. By altering the parameters of crystallographic symmetry in the structures, the faceted nano-columns with rectangular and hexagonal shapes were established in the simulation results. Furthermore, for revealing the influences of the anisotropic strength and the deposition rate theoretically on the crystallographic structure formations, various parameters adjusted in the numerical calculations were also investigated. Not only the morphologies but also the surface roughnesses for different processing conditions were distinctly demonstrated with the quantitative analysis of the simulations.

Dispersion stability in carbon nanotube modified polymers and its effect on the fracture toughness

NASA Astrophysics Data System (ADS)

Mirjalili, Vahid; Yourdkhani, Mostafa; Hubert, Pascal

2012-08-01

In this paper, the dispersion stability of multiwall carbon nanotubes (MWNTs) mixed with an epoxy resin is studied. An instrumented optical microscope with a hot stage was used to study the evolution of the carbon nanotubes (CNTs) dispersion during the cure of the resin. A new image processing approach is then introduced to quantify dispersion and identify the source of dispersion degradation during the cure. The results showed that the reduction of the resin viscosity at temperatures greater than 100 °C caused an irreversible re-agglomeration of the CNTs in the matrix. It was shown that the fine-tuning of the ratio and type of curing agent as well as the curing temperature directly affect the dispersion stability of MWNTs in the epoxy polymer. The dispersion quality was then directly correlated to the fracture toughness of the modified resin and a maximum of 20% improvement was achieved.

Phase and amplitude analysis in time-frequency space--application to voluntary finger movement.

PubMed

Ginter, J; Blinowska, K J; Kamiński, M; Durka, P J

2001-09-30

Two methods operating in time-frequency space were applied to analysis of EEG activity accompanying voluntary finger movements. The first one, based on matching pursuit approach provided high-resolution distributions of power in time-frequency space. The phenomena of event related desynchronization (ERD) and synchronization (ERS) were investigated without the need of band-pass filtering. Time evolution of mu- and beta-components was observed in a detailed way. The second method was based on a multichannel autoregressive model (MVAR) adapted for investigation of short-time changes in EEG signal. The direction and spectral content of the EEG activity propagation was estimated by means of short-time directed transfer function (SDTF). The evidence of 'cross-talk' between different areas of motor and sensory cortex was found. The earlier known phenomena, connected with voluntary movements, were confirmed and a new evidence concerning focal ERD/surround ERS and beta activity post-movement synchronization was found.

Rainfall: State of the Science

NASA Astrophysics Data System (ADS)

Testik, Firat Y.; Gebremichael, Mekonnen

Rainfall: State of the Science offers the most up-to-date knowledge on the fundamental and practical aspects of rainfall. Each chapter, self-contained and written by prominent scientists in their respective fields, provides three forms of information: fundamental principles, detailed overview of current knowledge and description of existing methods, and emerging techniques and future research directions. The book discusses • Rainfall microphysics: raindrop morphodynamics, interactions, size distribution, and evolution • Rainfall measurement and estimation: ground-based direct measurement (disdrometer and rain gauge), weather radar rainfall estimation, polarimetric radar rainfall estimation, and satellite rainfall estimation • Statistical analyses: intensity-duration-frequency curves, frequency analysis of extreme events, spatial analyses, simulation and disaggregation, ensemble approach for radar rainfall uncertainty, and uncertainty analysis of satellite rainfall products The book is tailored to be an indispensable reference for researchers, practitioners, and graduate students who study any aspect of rainfall or utilize rainfall information in various science and engineering disciplines.

A Unified Estimation Framework for State-Related Changes in Effective Brain Connectivity.

PubMed

Samdin, S Balqis; Ting, Chee-Ming; Ombao, Hernando; Salleh, Sh-Hussain

2017-04-01

This paper addresses the critical problem of estimating time-evolving effective brain connectivity. Current approaches based on sliding window analysis or time-varying coefficient models do not simultaneously capture both slow and abrupt changes in causal interactions between different brain regions. To overcome these limitations, we develop a unified framework based on a switching vector autoregressive (SVAR) model. Here, the dynamic connectivity regimes are uniquely characterized by distinct vector autoregressive (VAR) processes and allowed to switch between quasi-stationary brain states. The state evolution and the associated directed dependencies are defined by a Markov process and the SVAR parameters. We develop a three-stage estimation algorithm for the SVAR model: 1) feature extraction using time-varying VAR (TV-VAR) coefficients, 2) preliminary regime identification via clustering of the TV-VAR coefficients, 3) refined regime segmentation by Kalman smoothing and parameter estimation via expectation-maximization algorithm under a state-space formulation, using initial estimates from the previous two stages. The proposed framework is adaptive to state-related changes and gives reliable estimates of effective connectivity. Simulation results show that our method provides accurate regime change-point detection and connectivity estimates. In real applications to brain signals, the approach was able to capture directed connectivity state changes in functional magnetic resonance imaging data linked with changes in stimulus conditions, and in epileptic electroencephalograms, differentiating ictal from nonictal periods. The proposed framework accurately identifies state-dependent changes in brain network and provides estimates of connectivity strength and directionality. The proposed approach is useful in neuroscience studies that investigate the dynamics of underlying brain states.

A flowgraph model for bladder carcinoma

PubMed Central

2014-01-01

Background Superficial bladder cancer has been the subject of numerous studies for many years, but the evolution of the disease still remains not well understood. After the tumor has been surgically removed, it may reappear at a similar level of malignancy or progress to a higher level. The process may be reasonably modeled by means of a Markov process. However, in order to more completely model the evolution of the disease, this approach is insufficient. The semi-Markov framework allows a more realistic approach, but calculations become frequently intractable. In this context, flowgraph models provide an efficient approach to successfully manage the evolution of superficial bladder carcinoma. Our aim is to test this methodology in this particular case. Results We have built a successful model for a simple but representative case. Conclusion The flowgraph approach is suitable for modeling of superficial bladder cancer. PMID:25080066

UAV survey of a Thyrrenian micro-tidal beach for shoreline evolution update

NASA Astrophysics Data System (ADS)

Benassai, Guido; Pugliano, Giovanni; Di Paola, Gianluigi; Mucerino, Luigi

2015-04-01

Coastal geomorphology requires increasingly accurate topographic information of the beach systems to perform reliable simulation of coastal erosion, flooding phenomena, and coastal vulnerability assessment. Among the range of terrestrial and aerial methods available to produce such a dataset, this study tests the utility of low-altitude aerial imageries collected by Unmanned Aerial Vehicle (UAV). The image-based approach was selected whilst searching for a rapid, inexpensive, and highly automated method, able to produce 3D information from unstructured aerial images. In particular, it was used to generate a high-resolution Digital Surface Model (DSM) of the micro-tidal beach of Serapo - Gaeta (LT) in order to obtain recent update of erosional/accretional trends already established through historical shoreline evolution. A UAV exacopter (fig. 1a) was used, weighing about 2500g, carrying on board a GPS and multi-directional accelerometer to ensure a recovery of the beach features (fig. 1b) through a sweep with constant speed, direction and altitude. The on-board camera was a Canon 16M pixels, with fixed and constant focal takeoff in order to perform the 3D cloud points. Six adjacent strips were performed for the survey realization with pictures taken every second in sequence, in order to allow a minimum 80% overlap. A direct on site survey was also carried out with a DGPS for the placement of GPS markers and the geo-referencing of the final product (fig. 1c). Each flight with constant speed, direction and altitude recorded from 500 to 800 shots. The height of flight was dictated by the scale of the final report, an altitude of 100m was used for the beach survey. The topographic survey on the ground for the placement of the control points was performed with the Trimble R6 DGPS in RTK mode. The long-term shoreline evolution was obtained by a sixty-year historical shoreline time-series, through the analysis of a number of aerial photographs dating from 1954 to 2013. The shoreline change analysis was performed using the ArcGis 9.3 extension Digital Shoreline Analysis System (DSAS), v. 3.2 (Thieler et al., 2005). Transects orthogonal to the shoreline were generated at 100m intervals along the 1,4 km stretch of beach studied. The DSAS allowed the calculation of the rates of erosion/accretion between points, on the basis of the distance between them and the elapsed time, assuming changes to be linear processes. The rate of change of shoreline positions was evaluated at 14 points. The availability of shoreline data of the years 1954, 2000, 2006, 2008 and 2013 allowed to obtain the shoreline evolution trend in the last 60 years. Moreover, the UAV survey allowed to update the shoreline evolution and to obtain the volume of sediment lost by erosion, in order to suggest the locations and the amount of possible replenishments.

Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis

PubMed Central

Hurford, Amy; Ellison, Amy R.

2017-01-01

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy when hosts are large-bodied, when variation in host body size is large, and in cooler environments. We then explore these predictions using a newly updated database of over 20 000 fish–macroparasite associations. Within the database we see some evidence supporting these predictions, but also highlight mismatches between theory and data. By combining these two approaches, we establish a theoretical basis for interpreting empirical data on parasites' host specificity and identify key areas for future work that will help untangle the drivers of parasite host-generalism. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289257

Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis.

PubMed

Walker, Josephine G; Hurford, Amy; Cable, Jo; Ellison, Amy R; Price, Stephen J; Cressler, Clayton E

2017-05-05

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists-infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy when hosts are large-bodied, when variation in host body size is large, and in cooler environments. We then explore these predictions using a newly updated database of over 20 000 fish-macroparasite associations. Within the database we see some evidence supporting these predictions, but also highlight mismatches between theory and data. By combining these two approaches, we establish a theoretical basis for interpreting empirical data on parasites' host specificity and identify key areas for future work that will help untangle the drivers of parasite host-generalism.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Authors.

An Enhanced Differential Evolution Algorithm Based on Multiple Mutation Strategies.

PubMed

Xiang, Wan-li; Meng, Xue-lei; An, Mei-qing; Li, Yin-zhen; Gao, Ming-xia

2015-01-01

Differential evolution algorithm is a simple yet efficient metaheuristic for global optimization over continuous spaces. However, there is a shortcoming of premature convergence in standard DE, especially in DE/best/1/bin. In order to take advantage of direction guidance information of the best individual of DE/best/1/bin and avoid getting into local trap, based on multiple mutation strategies, an enhanced differential evolution algorithm, named EDE, is proposed in this paper. In the EDE algorithm, an initialization technique, opposition-based learning initialization for improving the initial solution quality, and a new combined mutation strategy composed of DE/current/1/bin together with DE/pbest/bin/1 for the sake of accelerating standard DE and preventing DE from clustering around the global best individual, as well as a perturbation scheme for further avoiding premature convergence, are integrated. In addition, we also introduce two linear time-varying functions, which are used to decide which solution search equation is chosen at the phases of mutation and perturbation, respectively. Experimental results tested on twenty-five benchmark functions show that EDE is far better than the standard DE. In further comparisons, EDE is compared with other five state-of-the-art approaches and related results show that EDE is still superior to or at least equal to these methods on most of benchmark functions.

Evolutionary rates for multivariate traits: the role of selection and genetic variation.

PubMed

Pitchers, William; Wolf, Jason B; Tregenza, Tom; Hunt, John; Dworkin, Ian

2014-08-19

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (Δz(-)=Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz(-)) as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The evolution of utility functions and psychological altruism.

PubMed

Clavien, Christine; Chapuisat, Michel

2016-04-01

Numerous studies show that humans tend to be more cooperative than expected given the assumption that they are rational maximizers of personal gain. As a result, theoreticians have proposed elaborated formal representations of human decision-making, in which utility functions including "altruistic" or "moral" preferences replace the purely self-oriented "Homo economicus" function. Here we review mathematical approaches that provide insights into the mathematical stability of alternative utility functions. Candidate utility functions may be evaluated with help of game theory, classical modeling of social evolution that focuses on behavioral strategies, and modeling of social evolution that focuses directly on utility functions. We present the advantages of the latter form of investigation and discuss one surprisingly precise result: "Homo economicus" as well as "altruistic" utility functions are less stable than a function containing a preference for the common welfare that is only expressed in social contexts composed of individuals with similar preferences. We discuss the contribution of mathematical models to our understanding of human other-oriented behavior, with a focus on the classical debate over psychological altruism. We conclude that human can be psychologically altruistic, but that psychological altruism evolved because it was generally expressed towards individuals that contributed to the actor's fitness, such as own children, romantic partners and long term reciprocators. Copyright © 2015 Elsevier Ltd. All rights reserved.

Current status of endovascular catheter robotics.

PubMed

Lumsden, Alan B; Bismuth, Jean

2018-06-01

In this review, we will detail the evolution of endovascular therapy as the basis for the development of catheter-based robotics. In parallel, we will outline the evolution of robotics in the surgical space and how the convergence of technology and the entrepreneurs who push this evolution have led to the development of endovascular robots. The current state-of-the-art and future directions and potential are summarized for the reader. Information in this review has been drawn primarily from our personal clinical and preclinical experience in use of catheter robotics, coupled with some ground-breaking work reported from a few other major centers who have embraced the technology's capabilities and opportunities. Several case studies demonstrating the unique capabilities of a precisely controlled catheter are presented. Most of the preclinical work was performed in the advanced imaging and navigation laboratory. In this unique facility, the interface of advanced imaging techniques and robotic guidance is being explored. Although this procedure employs a very high-tech approach to navigation inside the endovascular space, we have conveyed the kind of opportunities that this technology affords to integrate 3D imaging and 3D control. Further, we present the opportunity of semi-autonomous motion of these devices to a target. For the interventionist, enhanced precision can be achieved in a nearly radiation-free environment.

The self-preservation of dissipation elements in homogeneous isotropic decaying turbulence

NASA Astrophysics Data System (ADS)

Gauding, Michael; Danaila, Luminita; Varea, Emilien

2017-11-01

The concept of self-preservation has played an important role in shaping the understanding of turbulent flows. The assumption of complete self-preservation imposes certain constrains on the dynamics of the flow, allowing to express statistics by choosing an appropriate unique length scale. Another approach in turbulence research is to study the dynamics of geometrical objects, like dissipation elements (DE). DE appear as coherent space-filling structures in turbulent scalar fields and can be parameterized by the linear length between their ending points. This distance is a natural length scale that provides information about the local structure of turbulence. In this work, the evolution of DE in decaying turbulence is investigated from a self-preservation perspective. The analysis is based on data obtained from direct numerical simulations (DNS). The temporal evolution of DE is governed by a complex process, involving cutting and reconnection events, which change the number and consequently also the length of DE. An analysis of the evolution equation for the probability density function of the length of DE is carried out and leads to specific constraints for the self-preservation of DE, which are justified from DNS. Financial support was provided by Labex EMC3 (under the Grant VAVIDEN), Normandy Region and FEDER.

Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

PubMed Central

Sharov, Alexei A.; Igamberdiev, Abir U.

2014-01-01

In the era of the Extended Evolutionary Synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a “nomothetical” approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of “repeated polymorphic sets” (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioural capacities. Meyen's theory is compatible with Darwin's natural selection; however Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviours) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations. PMID:25072709

Sandbox rheometry: Co-evolution of stress and strain in Riedel- and Critical Wedge-experiments

NASA Astrophysics Data System (ADS)

Ritter, Malte C.; Santimano, Tasca; Rosenau, Matthias; Leever, Karen; Oncken, Onno

2018-01-01

Analogue sandbox experiments have been used for a long time to understand tectonic processes, because they facilitate detailed measurements of deformation at a spatio-temporal resolution unachievable from natural data. Despite this long history, force measurements to further characterise the mechanical evolution in analogue sandbox experiments have only emerged recently. Combined continuous measurements of forces and deformation in such experiments, an approach here referred to as "sandbox rheometry", are a new tool that may help to better understand work budgets and force balances for tectonic systems and to derive constitutive laws for regional scale deformation. In this article we present an experimental device that facilitates precise measurements of boundary forces and surface deformation at high temporal and spatial resolution. We demonstrate its capabilities in two classical experiments: one of strike-slip deformation (the Riedel set-up) and one of compressional accretionary deformation (the Critical Wedge set-up). In these we are able to directly observe a correlation between strain weakening and strain localisation that had previously only been inferred, namely the coincidence of the maximum localisation rate with the onset of weakening. Additionally, we observe in the compressional experiment a hysteresis of localisation with respect to the mechanical evolution that reflects the internal structural complexity of an accretionary wedge.

Evolution determines how global warming and pesticide exposure will shape predator-prey interactions with vector mosquitoes.

PubMed

Tran, Tam T; Janssens, Lizanne; Dinh, Khuong V; Op de Beeck, Lin; Stoks, Robby

2016-07-01

How evolution may mitigate the effects of global warming and pesticide exposure on predator-prey interactions is directly relevant for vector control. Using a space-for-time substitution approach, we addressed how 4°C warming and exposure to the pesticide endosulfan shape the predation on Culex pipiens mosquitoes by damselfly predators from replicated low- and high-latitude populations. Although warming was only lethal for the mosquitoes, it reduced predation rates on these prey. Possibly, under warming escape speeds of the mosquitoes increased more than the attack efficiency of the predators. Endosulfan imposed mortality and induced behavioral changes (including increased filtering and thrashing and a positional shift away from the bottom) in mosquito larvae. Although the pesticide was only lethal for the mosquitoes, it reduced predation rates by the low-latitude predators. This can be explained by the combination of the evolution of a faster life history and associated higher vulnerabilities to the pesticide (in terms of growth rate and lowered foraging activity) in the low-latitude predators and pesticide-induced survival selection in the mosquitoes. Our results suggest that predation rates on mosquitoes at the high latitude will be reduced under warming unless predators evolve toward the current low-latitude phenotype or low-latitude predators move poleward.

The Radial Metallicity Gradients in the Milky Way Thick Disk as Fossil Signatures of a Primordial Chemical Distribution

NASA Astrophysics Data System (ADS)

Curir, A.; Serra, A. L.; Spagna, A.; Lattanzi, M. G.; Re Fiorentin, P.; Diaferio, A.

2014-04-01

In this Letter we examine the evolution of the radial metallicity gradient induced by secular processes, in the disk of an N-body Milky Way-like galaxy. We assign a [Fe/H] value to each particle of the simulation according to an initial, cosmologically motivated, radial chemical distribution and let the disk dynamically evolve for ~6 Gyr. This direct approach allows us to take into account only the effects of dynamical evolution and to gauge how and to what extent they affect the initial chemical conditions. The initial [Fe/H] distribution increases with R in the inner disk up to R ≈ 10 kpc and decreases for larger R. We find that the initial chemical profile does not undergo major transformations after ~6 Gyr of dynamical evolution. The final radial chemical gradients predicted by the model in the solar neighborhood are positive and of the same order as those recently observed in the Milky Way thick disk. We conclude that (1) the spatial chemical imprint at the time of disk formation is not washed out by secular dynamical processes and (2) the observed radial gradient may be the dynamical relic of a thick disk originated from a stellar population showing a positive chemical radial gradient in the inner regions.

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language

PubMed Central

Scharff, Constance; Petri, Jana

2011-01-01

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the ‘evo-devo’ conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this ‘deep homology’. Recently, ‘evo-devo’ has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can ‘descend with modification’. PMID:21690130

Transverse instabilities of stripe domains in magnetic thin films with perpendicular magnetic anisotropy

NASA Astrophysics Data System (ADS)

Ruth, Max E.; Iacocca, Ezio; Kevrekidis, Panayotis G.; Hoefer, Mark A.

2018-03-01

Stripe domains are narrow, elongated, reversed regions that exist in magnetic materials with perpendicular magnetic anisotropy. They appear as a pair of domain walls that can exhibit topology with a nonzero chirality. Recent experimental and numerical investigations identify an instability of stripe domains along the long direction as a means of nucleating isolated magnetic skyrmions. Here, the onset and nonlinear evolution of transverse instabilities for a dynamic stripe domain known as the bion stripe are investigated. Both nontopological and topological variants of the bion stripe are shown to exhibit a long-wavelength transverse instability with different characteristic features. In the former, small transverse variations in the stripe's width lead to a neck instability that eventually pinches the nontopological stripe into a chain of two-dimensional breathers composed of droplet soliton pairs. In the latter case, small variations in the stripe's center result in a snake instability whose topological structure leads to the nucleation of dynamic magnetic skyrmions and antiskyrmions as well as perimeter-modulated droplets. Quantitative, analytical predictions for both the early, linear evolution and the long-time, nonlinear evolution are achieved using an averaged Lagrangian approach that incorporates both exchange (dispersion) and anisotropy (nonlinearity). The method of analysis is general and can be applied to other filamentary structures.

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language.

PubMed

Scharff, Constance; Petri, Jana

2011-07-27

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the 'evo-devo' conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this 'deep homology'. Recently, 'evo-devo' has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can 'descend with modification'.