The evolution of fairness through spite

PubMed Central

Forber, Patrick; Smead, Rory

2014-01-01

The presence of apparently irrational fair play in the ultimatum game remains a focal point for studies in the evolution of social behaviour. We investigate the role of negative assortment in the evolution of fair play in the ultimatum game. Spite—social behaviour that inflicts harm with no direct benefit to the actor—can evolve when it is disproportionally directed at individuals playing different strategies. The introduction of negative assortment alters the dynamics in a way that increases the chance fairness evolves, but at a cost: spite also evolves. Fairness is usually linked to cooperation and prosocial behaviour, but this study shows that it may have evolutionary links to harmful antisocial behaviour. PMID:24523265

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.

Beyond directed evolution - semi-rational protein engineering and design

PubMed Central

Lutz, Stefan

2010-01-01

Over the last two decades, directed evolution has transformed the field of protein engineering. The advances in understanding protein structure and function, in no insignificant part a result of directed evolution studies, are increasingly empowering scientists and engineers to device more effective methods for manipulating and tailoring biocatalysts. Abandoning large combinatorial libraries, the focus has shifted to small, functionally-rich libraries and rational design. A critical component to the success of these emerging engineering strategies are computational tools for the evaluation of protein sequence datasets and the analysis of conformational variations of amino acids in proteins. Highlighting the opportunities and limitations of such approaches, this review focuses on recent engineering and design examples that require screening or selection of small libraries. PMID:20869867

Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution

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

Moretti, Rocco; Chang, Aram; Peltier-Pain, Pauline

2012-03-15

Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates. These mutations have been shown to improve activities over 10-fold for several targeted substrates, including non-native pyrimidine- and purine-based NTPs as well as non-native d- and l-sugars (both a- and b-isomers). This study highlights the first broadly applicable high throughput sugar-1-phosphate nucleotidyltransferase screen and the firstmore » proof of concept for the directed evolution of this enzyme class toward the identification of uniquely permissive RmlA variants.« less

Directed evolution: an approach to engineer enzymes.

PubMed

Kaur, Jasjeet; Sharma, Rohit

2006-01-01

Directed evolution is being used increasingly in industrial and academic laboratories to modify and improve commercially important enzymes. Laboratory evolution is thought to make its biggest contribution in explorations of non-natural functions, by allowing us to distinguish the properties nurtured by evolution. In this review we report the significant advances achieved with respect to the methods of biocatalyst improvement and some critical properties and applications of the modified enzymes. The application of directed evolution has been elaborately demonstrated for protein solubility, stability and catalytic efficiency. Modification of certain enzymes for their application in enantioselective catalysis has also been elucidated. By providing a simple and reliable route to enzyme improvement, directed evolution has emerged as a key technology for enzyme engineering and biocatalysis.

A review of the irradiation evolution of dispersed oxide nanoparticles in the b.c.c. Fe-Cr system: Current understanding and future directions

NASA Astrophysics Data System (ADS)

Wharry, Janelle P.; Swenson, Matthew J.; Yano, Kayla H.

2017-04-01

Thus far, a number of studies have investigated the irradiation evolution of oxide nanoparticles in b.c.c. Fe-Cr based oxide dispersion strengthened (ODS) alloys. But given the inconsistent experimental conditions, results have been widely variable and inconclusive. Crystal structure and chemistry changes differ from experiment to experiment, and the total nanoparticle volume fraction has been observed to both increase and decrease. Furthermore, there has not yet been a comprehensive review of the archival literature. In this paper, we summarize the existing studies on nanoparticle irradiation evolution. We note significant observations with respect to oxide nanoparticle crystallinity, composition, size, and number density. We discuss four possible contributing mechanisms for nanoparticle evolution: ballistic dissolution, Ostwald ripening, irradiation-enhanced diffusion, and homogeneous nucleation. Finally, we propose future directions to achieve a more comprehensive understanding of irradiation effects on oxide nanoparticles in ODS alloys.

Modeling of microstructure evolution in direct metal laser sintering: A phase field approach

NASA Astrophysics Data System (ADS)

Nandy, Jyotirmoy; Sarangi, Hrushikesh; Sahoo, Seshadev

2017-02-01

Direct Metal Laser Sintering (DMLS) is a new technology in the field of additive manufacturing, which builds metal parts in a layer by layer fashion directly from the powder bed. The process occurs within a very short time period with rapid solidification rate. Slight variations in the process parameters may cause enormous change in the final build parts. The physical and mechanical properties of the final build parts are dependent on the solidification rate which directly affects the microstructure of the material. Thus, the evolving of microstructure plays a vital role in the process parameters optimization. Nowadays, the increase in computational power allows for direct simulations of microstructures during materials processing for specific manufacturing conditions. In this study, modeling of microstructure evolution of Al-Si-10Mg powder in DMLS process was carried out by using a phase field approach. A MATLAB code was developed to solve the set of phase field equations, where simulation parameters include temperature gradient, laser scan speed and laser power. The effects of temperature gradient on microstructure evolution were studied and found that with increase in temperature gradient, the dendritic tip grows at a faster rate.

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

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.

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.

The 25 kW power module evolution study. Part 3: Conceptual designs for power module evolution. Volume 1: Power module evolution

NASA Technical Reports Server (NTRS)

1979-01-01

Candidate power module confugurations which will directly support an evolutionary scenario allowing growth from 25 kW to 100 kW are described. The growth rationale is structured to support a nominal scenario for sortie mission support to the POrbiter and to free-flying payloads during the 1983 to 1990 era.

Expanding the metabolic engineering toolbox with directed evolution.

PubMed

Abatemarco, Joseph; Hill, Andrew; Alper, Hal S

2013-12-01

Cellular systems can be engineered into factories that produce high-value chemicals from renewable feedstock. Such an approach requires an expanded toolbox for metabolic engineering. Recently, protein engineering and directed evolution strategies have started to play a growing and critical role within metabolic engineering. This review focuses on the various ways in which directed evolution can be applied in conjunction with metabolic engineering to improve product yields. Specifically, we discuss the application of directed evolution on both catalytic and non-catalytic traits of enzymes, on regulatory elements, and on whole genomes in a metabolic engineering context. We demonstrate how the goals of metabolic pathway engineering can be achieved in part through evolving cellular parts as opposed to traditional approaches that rely on gene overexpression and deletion. Finally, we discuss the current limitations in screening technology that hinder the full implementation of a metabolic pathway-directed evolution approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

The Stochastic Evolution of a Protocell: The Gillespie Algorithm in a Dynamically Varying Volume

PubMed Central

Carletti, T.; Filisetti, A.

2012-01-01

We propose an improvement of the Gillespie algorithm allowing us to study the time evolution of an ensemble of chemical reactions occurring in a varying volume, whose growth is directly related to the amount of some specific molecules, belonging to the reactions set. This allows us to study the stochastic evolution of a protocell, whose volume increases because of the production of container molecules. Several protocell models are considered and compared with the deterministic models. PMID:22536297

Prospects for the Study of Evolution in the Deep Biosphere

PubMed Central

Biddle, Jennifer F.; Sylvan, Jason B.; Brazelton, William J.; Tully, Benjamin J.; Edwards, Katrina J.; Moyer, Craig L.; Heidelberg, John F.; Nelson, William C.

2012-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org). PMID:22319515

Prospects for the study of evolution in the deep biosphere.

PubMed

Biddle, Jennifer F; Sylvan, Jason B; Brazelton, William J; Tully, Benjamin J; Edwards, Katrina J; Moyer, Craig L; Heidelberg, John F; Nelson, William C

2011-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

Human genetics: measuring the raw material of evolution.

PubMed

Armour, John A L

2009-09-15

By direct sequencing of two Y chromosomes inherited from the same paternal ancestor, a landmark study has derived a good direct estimate for the rate of base substitution mutations on the human Y chromosome.

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.

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

Cis-regulatory Elements and Human Evolution

PubMed Central

Siepel, Adam

2014-01-01

Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider “new frontiers” in this field stemming from recent research on transcriptional regulation. PMID:25218861

Integration of ambient seismic noise monitoring, displacement and meteorological measurements to infer the temperature-controlled long-term evolution of a complex prone-to-fall cliff

NASA Astrophysics Data System (ADS)

Colombero, C.; Baillet, L.; Comina, C.; Jongmans, D.; Larose, E.; Valentin, J.; Vinciguerra, S.

2018-06-01

Monitoring the temporal evolution of resonance frequencies and velocity changes detected from ambient seismic noise recordings can help in recognizing reversible and irreversible modifications within unstable rock volumes. With this aim, the long-term ambient seismic noise data set acquired at the potentially unstable cliff of Madonna delSasso (NW Italian Alps) was analysed in this study, using both spectral analysis and cross-correlation techniques. Noise results were integrated and compared with direct displacement measurements and meteorological data, to understand the long-term evolution of the cliff. No irreversible modifications in the stability of the site were detected over the monitored period. Conversely, daily and seasonal air temperature fluctuations were found to control resonance frequency values, amplitudes and directivities and to induce reversible velocity changes within the fractured rock mass. The immediate modification in the noise parameters due to temperature fluctuations was interpreted as the result of rock mass thermal expansion and contraction, inducing variations in the contact stiffness along the fractures isolating two unstable compartments. Differences with previous case studies were highlighted in the long-term evolution of noise spectral amplitudes and directivities, due to the complex 3-D fracture setting of the site and to the combined effects of the two unstable compartments.

Thermal plasticity of growth and development varies adaptively among alternative developmental pathways.

PubMed

Kivelä, Sami M; Svensson, Beatrice; Tiwe, Alma; Gotthard, Karl

2015-09-01

Polyphenism, the expression of discrete alternative phenotypes, is often a consequence of a developmental switch. Physiological changes induced by a developmental switch potentially affect reaction norms, but the evolution and existence of alternative reaction norms remains poorly understood. Here, we demonstrate that, in the butterfly Pieris napi (Lepidoptera: Pieridae), thermal reaction norms of several life history traits vary adaptively among switch-induced alternative developmental pathways of diapause and direct development. The switch was affected both by photoperiod and temperature, ambient temperature during late development having the potential to override earlier photoperiodic cues. Directly developing larvae had higher development and growth rates than diapausing ones across the studied thermal gradient. Reaction norm shapes also differed between the alternative developmental pathways, indicating pathway-specific selection on thermal sensitivity. Relative mass increments decreased linearly with increasing temperature and were higher under direct development than diapause. Contrary to predictions, population phenology did not explain trait variation or thermal sensitivity, but our experimental design probably lacks power for finding subtle phenology effects. We demonstrate adaptive differentiation in thermal reaction norms among alternative phenotypes, and suggest that the consequences of an environmentally dependent developmental switch primarily drive the evolution of alternative thermal reaction norms in P. napi. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

On the instability of wave-fields with JONSWAP spectra to inhomogeneous disturbances, and the consequent long-time evolution

NASA Astrophysics Data System (ADS)

Ribal, A.; Stiassnie, M.; Babanin, A.; Young, I.

2012-04-01

The instability of two-dimensional wave-fields and its subsequent evolution in time are studied by means of the Alber equation for narrow-banded random surface-waves in deep water subject to inhomogeneous disturbances. A linear partial differential equation (PDE) is obtained after applying an inhomogeneous disturbance to the Alber's equation and based on the solution of this PDE, the instability of the ocean wave surface is studied for a JONSWAP spectrum, which is a realistic ocean spectrum with variable directional spreading and steepness. The steepness of the JONSWAP spectrum depends on γ and α which are the peak-enhancement factor and energy scale of the spectrum respectively and it is found that instability depends on the directional spreading, α and γ. Specifically, if the instability stops due to the directional spreading, increase of the steepness by increasing α or γ can reactivate it. This result is in qualitative agreement with the recent large-scale experiment and new theoretical results. In the instability area of α-γ plane, a long-time evolution has been simulated by integrating Alber's equation numerically and recurrent evolution is obtained which is the stochastic counterpart of the Fermi-Pasta-Ulam recurrence obtained for the cubic Schrödinger equation.

Meta-analysis suggests choosy females get sexy sons more than "good genes".

PubMed

Prokop, Zofia M; Michalczyk, Łukasz; Drobniak, Szymon M; Herdegen, Magdalena; Radwan, Jacek

2012-09-01

Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

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.

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

Influence of particle shape on the microstructure evolution and the mechanical properties of granular materials

NASA Astrophysics Data System (ADS)

Tian, Jianqiu; Liu, Enlong; Jiang, Lian; Jiang, Xiaoqiong; Sun, Yi; Xu, Ran

2018-06-01

In order to study the influence of particle shape on the microstructure evolution and the mechanical properties of granular materials, a two-dimensional DEM analysis of samples with three particle shapes, including circular particles, triangular particles, and elongated particles, is proposed here to simulate the direct shear tests of coarse-grained soils. For the numerical test results, analyses are conducted in terms of particle rotations, fabric evolution, and average path length evolution. A modified Rowe's stress-dilatancy equation is also proposed and successfully fitted onto simulation data.

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

PubMed

Reznick, D N; Ghalambor, C K

2001-01-01

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Age of acquisition predicts rate of lexical evolution.

PubMed

Monaghan, Padraic

2014-12-01

The processes taking place during language acquisition are proposed to influence language evolution. However, evidence demonstrating the link between language learning and language evolution is, at best, indirect, constituting studies of laboratory-based artificial language learning studies or computational simulations of diachronic change. In the current study, a direct link between acquisition and evolution is established, showing that for two hundred fundamental vocabulary items, the age at which words are acquired is a predictor of the rate at which they have changed in studies of language evolution. Early-acquired words are more salient and easier to process than late-acquired words, and these early-acquired words are also more stably represented within the community's language. Analysing the properties of these early-acquired words potentially provides insight into the origins of communication, highlighting features of words that have been ultra-conserved in language. Copyright © 2014 Elsevier B.V. All rights reserved.

Evolution of ethnocentrism on undirected and directed Barabási-Albert networks

NASA Astrophysics Data System (ADS)

Lima, F. W. S.; Hadzibeganovic, Tarik; Stauffer, Dietrich

2009-12-01

Using Monte Carlo simulations, we study the evolution of contingent cooperation and ethnocentrism in the one-shot game. Interactions and reproduction among computational agents are simulated on undirected and directed Barabási-Albert (BA) networks. We first replicate the Hammond-Axelrod model of in-group favoritism on a square lattice and then generalize this model on undirected and directed BA networks for both asexual and sexual reproduction cases. Our simulations demonstrate that irrespective of the mode of reproduction, the ethnocentric strategy becomes common even though cooperation is individually costly and mechanisms such as reciprocity or conformity are absent. Moreover, our results indicate that the spread of favoritism towards similar others highly depends on the network topology and the associated heterogeneity of the studied population.

Endothermic decompositions of inorganic monocrystalline thin plates. II. Displacement rate modulation of the reaction front

NASA Astrophysics Data System (ADS)

Bertrand, G.; Comperat, M.; Lallemant, M.

1980-09-01

Copper sulfate pentahydrate dehydration into trihydrate was investigated using monocrystalline platelets with (110) crystallographic orientation. Temperature and pressure conditions were selected so as to obtain elliptical trihydrate domains. The study deals with the evolution, vs time, of elliptical domain dimensions and the evolution, vs water vapor pressure, of the {D}/{d} ratio of ellipse axes and on the other hand of the interface displacement rate along a given direction. The phenomena observed are not basically different from those yielded by the overall kinetic study of the solid sample. Their magnitude, however, is modulated depending on displacement direction. The results are analyzed within the scope of our study of endothermic decomposition of solids.

Electromagnetic induction heating for single crystal graphene growth: morphology control by rapid heating and quenching

NASA Astrophysics Data System (ADS)

Wu, Chaoxing; Li, Fushan; Chen, Wei; Veeramalai, Chandrasekar Perumal; Ooi, Poh Choon; Guo, Tailiang

2015-03-01

The direct observation of single crystal graphene growth and its shape evolution is of fundamental importance to the understanding of graphene growth physicochemical mechanisms and the achievement of wafer-scale single crystalline graphene. Here we demonstrate the controlled formation of single crystal graphene with varying shapes, and directly observe the shape evolution of single crystal graphene by developing a localized-heating and rapid-quenching chemical vapor deposition (CVD) system based on electromagnetic induction heating. Importantly, rational control of circular, hexagonal, and dendritic single crystalline graphene domains can be readily obtained for the first time by changing the growth condition. Systematic studies suggest that the graphene nucleation only occurs during the initial stage, while the domain density is independent of the growth temperatures due to the surface-limiting effect. In addition, the direct observation of graphene domain shape evolution is employed for the identification of competing growth mechanisms including diffusion-limited, attachment-limited, and detachment-limited processes. Our study not only provides a novel method for morphology-controlled graphene synthesis, but also offers fundamental insights into the kinetics of single crystal graphene growth.

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

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.

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

Evosystem Services: Rapid Evolution and the Provision of Ecosystem Services.

PubMed

Rudman, Seth M; Kreitzman, Maayan; Chan, Kai M A; Schluter, Dolph

2017-06-01

Evolution is recognized as the source of all organisms, and hence many ecosystem services. However, the role that contemporary evolution might play in maintaining and enhancing specific ecosystem services has largely been overlooked. Recent advances at the interface of ecology and evolution have demonstrated how contemporary evolution can shape ecological communities and ecosystem functions. We propose a definition and quantitative criteria to study how rapid evolution affects ecosystem services (here termed contemporary evosystem services) and present plausible scenarios where such services might exist. We advocate for the direct measurement of contemporary evosystem services to improve understanding of how changing environments will alter resource availability and human well-being, and highlight the potential utility of managing rapid evolution for future ecosystem services. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anatomy and evolution of heterocercal tail in lamniform sharks.

PubMed

Kim, Sun H; Shimada, Kenshu; Rigsby, Cynthia K

2013-03-01

Lamniformes is a small shark group consisting of 15 extant species with remarkably diverse lifestyles and a wide range in heterocercal tail morphology. The caudal fin morphology must be related to their lifestyle because the tail is a main locomotive structure in sharks, but such relationships have remained largely uninvestigated. Here, the morphology-lifestyle relationship in lamniforms is examined through phylogenetic mapping. This study suggests that, within Lamniformes, caudal fins with a more horizontally directed curvature of the vertebral column are plesiomorphic, whereas those with a large dorsally directed curvature of the vertebral column are apomorphic. It also shows that caudal fins with posteriorly directed hypochordal rays are plesiomorphic, and that those with ventrally directed hypochordal rays are apomorphic within Lamniformes. Four basic caudal fin types are recognized in lamniforms on the basis of these skeletal variables in which one corollary is that the evolution of external morphology of caudal fin does not necessarily correspond to the evolution of its skeletal anatomy. This study also demonstrates that specific lifestyles seen in different lamniforms are indeed correlative with different caudal fin types in which a less asymmetrical heterocercal tail is a derived feature in lamniforms that evolved for fast swimming to capture fast swimming prey. Copyright © 2013 Wiley Periodicals, Inc.

The evolution of costly mate choice against segregation distorters.

PubMed

Manser, Andri; Lindholm, Anna K; Weissing, Franz J

2017-12-01

The evolution of female preference for male genetic quality remains a controversial topic in sexual selection research. One well-known problem, known as the lek paradox, lies in understanding how variation in genetic quality is maintained in spite of natural selection and sexual selection against low-quality alleles. Here, we theoretically investigate a scenario where females pay a direct fitness cost to avoid males carrying an autosomal segregation distorter. We show that preference evolution is greatly facilitated under such circumstances. Because the distorter is transmitted in a non-Mendelian fashion, it can be maintained in the population despite directional sexual selection. The preference helps females avoid fitness costs associated with the distorter. Interestingly, we find that preference evolution is limited if the choice allele induces a very strong preference or if distortion is very strong. Moreover, the preference can only persist in the presence of a signal that reliably indicates a male's distorter genotype. Hence, even in a system where the lek paradox does not play a major role, costly preferences can only spread under specific circumstances. We discuss the importance of distorter systems for the evolution of costly female choice and potential implications for the use of artificial distorters in pest control. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

Directed evolution: tailoring biocatalysts for industrial applications.

PubMed

Kumar, Ashwani; Singh, Suren

2013-12-01

Current challenges and promises of white biotechnology encourage protein engineers to use a directed evolution approach to generate novel and useful biocatalysts for various sets of applications. Different methods of enzyme engineering have been used in the past in an attempt to produce enzymes with improved functions and properties. Recent advancement in the field of random mutagenesis, screening, selection and computational design increased the versatility and the rapid development of enzymes under strong selection pressure with directed evolution experiments. Techniques of directed evolution improve enzymes fitness without understanding them in great detail and clearly demonstrate its future role in adapting enzymes for use in industry. Despite significant advances to date regarding biocatalyst improvement, there still remains a need to improve mutagenesis strategies and development of easy screening and selection tools without significant human intervention. This review covers fundamental and major development of directed evolution techniques, and highlights the advances in mutagenesis, screening and selection methods with examples of enzymes developed by using these approaches. Several commonly used methods for creating molecular diversity with their advantages and disadvantages including some recently used strategies are also discussed.

Evolution of magnetic flux ropes associated with flux transfer events and interplanetary magnetic clouds

NASA Technical Reports Server (NTRS)

Wei, C. Q.; Lee, L. C.; Wang, S.; Akasofu, S.-I.

1991-01-01

Spacecraft observations suggest that flux transfer events and interplanetary magnetic clouds may be associated with magnetic flux ropes which are magnetic flux tubes containing helical magnetic field lines. In the magnetic flux ropes, the azimuthal magnetic field is superposed on the axial field. The time evolution of a localized magnetic flux rope is studied. A two-dimensional compressible MHD simulation code with a cylindrical symmetry is developed to study the wave modes associated with the evolution of flux ropes. It is found that in the initial phase both the fast magnetosonic wave and the Alfven wave are developed in the flux rope. After this initial phase, the Alfven wave becomes the dominant wave mode for the evolution of the magnetic flux rope and the radial expansion velocity of the flux rope is found to be negligible. Numerical results further show that even for a large initial azimuthal component of the magnetic field, the propagation velocity along the axial direction of the flux rope remains the Alfven velocity. It is also found that the localized magnetic flux rope tends to evolve into two separate magnetic ropes propagating in opposite directions. The simulation results are used to study the evolution of magnetic flux ropes associated with flux transfer events observed at the earth's dayside magnetopause and magnetic clouds in the interplanetary space.

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.

Engineering Biosynthesis of Non-ribosomal Peptides and Polyketides by Directed Evolution.

PubMed

Rui, Zhe; Zhang, Wenjun

2016-01-01

Non-ribosomal peptides (NRPs) and polyketides (PKs) play key roles in pharmaceutical industry due to their promising biological activities. The structural complexity of NRPs and PKs, however, creates significant synthetic challenges for producing these natural products and their analogues by purely chemical means. Alternatively, difficult syntheses can be achieved by using biosynthetic enzymes with improved efficiency and altered selectivity that are acquired from directed evolution. Key to the successful directed evolution is the methodology of screening/selection. This review summarizes the screening/selection strategies that have been employed to improve or modify the functions of non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), in the hope of triggering the wide adoption of the directed evolution approaches in the engineered biosynthesis of NRPs and PKs for drug discovery.

The search for life's origins: Progress and future directions in planetary biology and chemical evolution

NASA Technical Reports Server (NTRS)

1990-01-01

The current state is reviewed of the study of chemical evolution and planetary biology and the probable future is discussed of the field, at least for the near term. To this end, the report lists the goals and objectives of future research and makes detailed, comprehensive recommendations for accomplishing them, emphasizing those issues that were inadequately discussed in earlier Space Studies Board reports.

Directed evolution of an endoinulinase from Talaromyces purpureogenus toward efficient production of inulooligosaccharides.

PubMed

Afriat-Jurnou, Livnat; Cohen, Rami; Paluy, Irina; Ben-Adiva, Ran; Yadid, Itamar

2018-02-01

Inulinases are fructofuranosyl hydrolases that target the β-2,1 linkage of inulin and hydrolyze it into fructose, glucose and inulooligosaccharides (IOS), the latter are of growing interest as dietary fibers. Inulinases from various microorganisms have been purified, characterized and produced for industrial applications. However, there remains a need for inulinases with increased catalytic activity and better production yields to improve the hydrolysis process and fulfill the growing industrial demands for specific fibers. In this study, we used directed enzyme evolution to increase the yield and activity of an endoinulinase enzyme originated from the filamentous fungus Talaromyces purpureogenus (Penicillium purpureogenum ATCC4713). Our directed evolution approach yielded variants showing up to fivefold improvements in soluble enzyme production compared to the starting point which enabled high-yield production of highly purified recombinant enzyme. The distribution of the enzymatic reaction products demonstrated that after 24 h of incubation, the main product (57%) had a degree of polymerization of 3 (DP3). To the best of our knowledge, this is the first application of directed enzyme evolution to improve inulooligosaccharide production. The approach enabled the screening of large genetic libraries within short time frames and facilitated screening for improved enzymatic activities and properties, such as substrate specificity, product range, thermostability and pH optimum. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Experimental Evolution with Caenorhabditis Nematodes

PubMed Central

Teotónio, Henrique; Estes, Suzanne; Phillips, Patrick C.; Baer, Charles F.

2017-01-01

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host–pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative. PMID:28592504

Sex Ratio Bias Leads to the Evolution of Sex Role Reversal in Honey Locust Beetles.

PubMed

Fritzsche, Karoline; Booksmythe, Isobel; Arnqvist, Göran

2016-09-26

The reversal of conventional sex roles was enigmatic to Darwin, who suggested that it may evolve when sex ratios are female biased [1]. Here we present direct evidence confirming Darwin's hypothesis. We investigated mating system evolution in a sex-role-reversed beetle (Megabruchidius dorsalis) using experimental evolution under manipulated sex ratios and food regimes. In female-biased populations, where reproductive competition among females was intensified, females evolved to be more attractive and the sex roles became more reversed. Interestingly, female-specific mating behavior evolved more rapidly than male-specific mating behavior. We show that sexual selection due to reproductive competition can be strong in females and can target much the same traits as in males of species with conventional mating systems. Our study highlights two central points: the role of ecology in directing sexual selection and the role that females play in mating system evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Amino acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small library Thoroughly or a Large Library Sparsely?

PubMed Central

Muñoz, Enrique

2015-01-01

We compare the results obtained from searching a smaller library thoroughly versus searching a more diverse, larger library sparsely. We study protein evolution with reduced amino acid alphabets, by simulating directed evolution experiments at three different alphabet sizes: 20, 5 and 2. We employ a physical model for evolution, the generalized NK model, that has proved successful in modeling protein evolution, antibody evolution, and T cell selection. We find that antibodies with higher affinity are found by searching a library with a larger alphabet sparsely than by searching a smaller library thoroughly, even with well-designed reduced libraries. We find ranked amino acid usage frequencies in agreement with observations of the CDR-H3 variable region of human antibodies. PMID:18375453

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

Selection on skewed characters and the paradox of stasis.

PubMed

Bonamour, Suzanne; Teplitsky, Céline; Charmantier, Anne; Crochet, Pierre-André; Chevin, Luis-Miguel

2017-11-01

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modeling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold's (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson-Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate sample sizes. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date - repeatedly described as more evolutionarily stable than expected - so this skewness should be accounted for when investigating evolutionary dynamics in the wild. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The evolution and consequences of sex-specific reproductive variance.

PubMed

Mullon, Charles; Reuter, Max; Lehmann, Laurent

2014-01-01

Natural selection favors alleles that increase the number of offspring produced by their carriers. But in a world that is inherently uncertain within generations, selection also favors alleles that reduce the variance in the number of offspring produced. If previous studies have established this principle, they have largely ignored fundamental aspects of sexual reproduction and therefore how selection on sex-specific reproductive variance operates. To study the evolution and consequences of sex-specific reproductive variance, we present a population-genetic model of phenotypic evolution in a dioecious population that incorporates previously neglected components of reproductive variance. First, we derive the probability of fixation for mutations that affect male and/or female reproductive phenotypes under sex-specific selection. We find that even in the simplest scenarios, the direction of selection is altered when reproductive variance is taken into account. In particular, previously unaccounted for covariances between the reproductive outputs of different individuals are expected to play a significant role in determining the direction of selection. Then, the probability of fixation is used to develop a stochastic model of joint male and female phenotypic evolution. We find that sex-specific reproductive variance can be responsible for changes in the course of long-term evolution. Finally, the model is applied to an example of parental-care evolution. Overall, our model allows for the evolutionary analysis of social traits in finite and dioecious populations, where interactions can occur within and between sexes under a realistic scenario of reproduction.

The Evolution and Consequences of Sex-Specific Reproductive Variance

PubMed Central

Mullon, Charles; Reuter, Max; Lehmann, Laurent

2014-01-01

Natural selection favors alleles that increase the number of offspring produced by their carriers. But in a world that is inherently uncertain within generations, selection also favors alleles that reduce the variance in the number of offspring produced. If previous studies have established this principle, they have largely ignored fundamental aspects of sexual reproduction and therefore how selection on sex-specific reproductive variance operates. To study the evolution and consequences of sex-specific reproductive variance, we present a population-genetic model of phenotypic evolution in a dioecious population that incorporates previously neglected components of reproductive variance. First, we derive the probability of fixation for mutations that affect male and/or female reproductive phenotypes under sex-specific selection. We find that even in the simplest scenarios, the direction of selection is altered when reproductive variance is taken into account. In particular, previously unaccounted for covariances between the reproductive outputs of different individuals are expected to play a significant role in determining the direction of selection. Then, the probability of fixation is used to develop a stochastic model of joint male and female phenotypic evolution. We find that sex-specific reproductive variance can be responsible for changes in the course of long-term evolution. Finally, the model is applied to an example of parental-care evolution. Overall, our model allows for the evolutionary analysis of social traits in finite and dioecious populations, where interactions can occur within and between sexes under a realistic scenario of reproduction. PMID:24172130

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

Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics.

PubMed

Culumber, Zachary W

2014-02-01

The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.

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.

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

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

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.

Characterization of Inclusions in Evolution of Sodium Sulfate Using Terahertz Time-domain Spectroscopy.

PubMed

Bao, Rima; Wu, Zhikui; Li, Hao; Wang, Fang; Miao, Xinyang; Feng, Chengjing

2017-01-01

The study of fluid inclusion is one of the important means to understanding the evolution of mineral crystals, and can therefore provide original information of mineral evolution. In the process of evolution, outside factors such as temperature and pressure, directly affect the number and size of inclusions, and thus are related to the properties of crystals. In this paper, terahertz time-domain spectroscopy (THz-TDS) was used to detect sodium sulfate crystals with different growth temperatures, and absorption coefficient spectra of the samples were obtained. It is suggested that the evolution of sodium sulfate could be divided into two stages, and 80°C was the turning point. X-ray diffraction (XRD) and polarizing microscopy were used to support this conclusion. The research showed that THz-TDS could characterize the evolution of mineral crystals, and it had a unique advantage in terms of crystal evolution.

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.

Directed evolution of an angiopoietin-2 ligand trap by somatic hypermutation and cell surface display.

PubMed

Brindle, Nicholas P J; Sale, Julian E; Arakawa, Hiroshi; Buerstedde, Jean-Marie; Nuamchit, Teonchit; Sharma, Shikha; Steele, Kathryn H

2013-11-15

Tie2 is a receptor tyrosine kinase that is essential for the development and maintenance of blood vessels through binding the soluble ligands angiopoietin 1 (Ang1) and 2 (Ang2). Ang1 is constitutively produced by perivascular cells and is protective of the adult vasculature. Ang2 plays an important role in blood vessel formation and is normally expressed during development. However, its re-expression in disease states, including cancer and sepsis, results in destabilization of blood vessels contributing to the pathology of these conditions. Ang2 is thus an attractive therapeutic target. Here we report the directed evolution of a ligand trap for Ang2 by harnessing the B cell somatic hypermutation machinery and coupling this to selectable cell surface display of a Tie2 ectodomain. Directed evolution produced an unexpected combination of mutations resulting in loss of Ang1 binding but maintenance of Ang2 binding. A soluble form of the evolved ectodomain binds Ang2 but not Ang1. Furthermore, the soluble evolved ectodomain blocks Ang2 effects on endothelial cells without interfering with Ang1 activity. Our study has created a novel Ang2 ligand trap and provided proof of concept for combining surface display and exogenous gene diversification in B cells for evolution of a non-immunoglobulin target.

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.

Language evolution in the laboratory.

PubMed

Scott-Phillips, Thomas C; Kirby, Simon

2010-09-01

The historical origins of natural language cannot be observed directly. We can, however, study systems that support language and we can also develop models that explore the plausibility of different hypotheses about how language emerged. More recently, evolutionary linguists have begun to conduct language evolution experiments in the laboratory, where the emergence of new languages used by human participants can be observed directly. This enables researchers to study both the cognitive capacities necessary for language and the ways in which languages themselves emerge. One theme that runs through this work is how individual-level behaviours result in population-level linguistic phenomena. A central challenge for the future will be to explore how different forms of information transmission affect this process. 2010 Elsevier Ltd. All rights reserved.

Dissipative structures, machines, and organisms: A perspective

NASA Astrophysics Data System (ADS)

Kondepudi, Dilip; Kay, Bruce; Dixon, James

2017-10-01

Self-organization in nonequilibrium systems resulting in the formation of dissipative structures has been studied in a variety of systems, most prominently in chemical systems. We present a study of a voltage-driven dissipative structure consisting of conducting beads immersed in a viscous medium of oil. In this simple system, we observed remarkably complex organism-like behavior. The dissipative structure consists of a tree structure that spontaneously forms and moves like a worm and exhibits many features characteristic of living organisms. The complex motion of the beads driven by the applied field, the dipole-dipole interaction between the beads, and the hydrodynamic flow of the viscous medium result in a time evolution of the tree structure towards states of lower resistance or higher dissipation and thus higher rates of entropy production. The resulting end-directed evolution manifests as the tree moving to locations seeking higher current, the current that sustains its structure and dynamics. The study of end-directed evolution in the dissipative structure gives us a means to distinguish the fundamental difference between machines and organisms and opens a path for the formulation of physics of organisms.

ISSOL Meeting, 7th, Barcelona, Spain, July 4-9, 1993. [Abstracts only

NASA Technical Reports Server (NTRS)

Ferris, James P. (Editor)

1994-01-01

The journal issue consists of abstracts presented at the International Society for the Study of the Origins of Life (ISSOL) conference. Topics include research on biological and chemical evolution including prebiotic evolution: cosmic and terrestrial; mechanisms of abiogenesis including synthesis and reactions of biomonomers; and analysis of cometary matter and its possible relationship to organic compounds on Earth. Theories and research on origins of ribonucleic acids (RNA), deoxyribonucleic acid (DNA), and other amino acids and complex proteins including their autocatalysis, replication, and translation are presented. Abiotic synthesis of biopolymers, mechanisms of the Genetic Code, precellular membrane systems and energetics are considered. Earth planetary evolution including early microfossils and geochemical conditions and simulations to study these conditions are discussed. The role of chirality in precellular evolution and the taxonomy and phylogeny of very simple organisms are reported. Past and future explorations in exobiology and space research directed toward study of the origins of life and solar system evolution are described.

The effects of self-interstitial clusters on cascade defect evolution beyond the primary damage state

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

Heinisch, H.L.

1997-04-01

The intracascade evolution of the defect distributions of cascades in copper is investigated using stochastic annealing simulations applied to cascades generated with molecular dynamics (MD). The temperature and energy dependencies of annihilation, clustering and free defect production are determined for individual cascades. The annealing simulation results illustrate the strong influence on intracascade evolution of the defect configuration existing in the primary damage state. Another factor significantly affecting the evolution of the defect distribution is the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. This phenomenon introduces a cascade energy dependence of defect evolution that is apparentmore » only beyond the primary damage state, amplifying the need for further study of the annealing phase of cascade evolution and for performing many more MD cascade simulations at higher energies.« less

Step-induced deconstruction and step-height evolution of the Au(110) surface

NASA Astrophysics Data System (ADS)

Romahn, U.; von Blanckenhagen, P.; Kroll, C.; Göpel, W.

1993-05-01

We use temperature-dependent high-resolution low-energy electron diffraction and spot-profile analysis low-energy electron diffraction to study the Au(110) surface at room temperature up to 786 K. The experimental data were analyzed within the framework of the kinematic theory. Oscillations were determined of the positions of half order and fundamental Bragg peaks as well as of the full width at half maximum of the specular peak as a function of perpendicular momentum transfer. Evidence of mono- atomic steps occurring in the [001] direction was found below and around the (2×1)-->(1×1) transition at Tc. Above Tc, the surface gets smoother in the [001] direction; at the roughening temperature, TR, the evolution of multiple-height steps starts in both symmetry directions.

The tectonic evolution of the southeastern Terceira Rift/São Miguel region (Azores)

NASA Astrophysics Data System (ADS)

Weiß, B. J.; Hübscher, C.; Lüdmann, T.

2015-07-01

The eastern Azores Archipelago with São Miguel being the dominant subaerial structure is located at the intersection of an oceanic rift (Terceira Rift) with a major transform fault (Gloria Fault) representing the westernmost part of the Nubian-Eurasian plate boundary. The evolution of islands, bathymetric highs and basin margins involves strong volcanism, but the controlling geodynamic and tectonic processes are currently under debate. In order to study this evolution, multibeam bathymetry and marine seismic reflection data were collected to image faults and stratigraphy. The basins of the southeastern Terceira Rift are rift valleys whose southwestern and northeastern margins are defined by few major normal faults and several minor normal faults, respectively. Since São Miguel in between the rift valleys shows an unusual W-E orientation, it is supposed to be located on a leaky transform. South of the island and separated by a N120° trending graben system, the Monacco Bank represents a N160° oriented flat topped volcanic ridge dominated by tilted fault blocks. Up to six seismic units are interpreted for each basin. Although volcanic ridges hamper a direct linking of depositional strata between the rift and adjacent basins, the individual seismic stratigraphic units have distinct characteristics. Using these units to provide a consistent relative chrono-stratigraphic scheme for the entire study area, we suggest that the evolution of the southeastern Terceira Rift occurred in two stages. Considering age constrains from previous studies, we conclude that N140° structures developed orthogonal to the SW-NE direction of plate-tectonic extension before ~ 10 Ma. The N160° trending volcanic ridges and faults developed later as the plate tectonic spreading direction changed to WSW-ENE. Hence, the evolution of the southeastern Terceira Rift domain is predominantly controlled by plate kinematics and lithospheric stress forming a kind of a re-organized rift system.

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

The search for and analysis of direct samples of early Solar System aqueous fluids.

PubMed

Zolensky, Michael E; Bodnar, Robert J; Yurimoto, Hisayoshi; Itoh, Shoichi; Fries, Marc; Steele, Andrew; Chan, Queenie H-S; Tsuchiyama, Akira; Kebukawa, Yoko; Ito, Motoo

2017-05-28

We describe the current state of the search for direct, surviving samples of early, inner Solar System fluids-fluid inclusions in meteorites. Meteoritic aqueous fluid inclusions are not rare, but they are very tiny and their characterization is at the state of the art for most analytical techniques. Meteoritic fluid inclusions offer us a unique opportunity to study early Solar System brines in the laboratory. Inclusion-by-inclusion analyses of the trapped fluids in carefully selected samples will, in the immediate future, provide us detailed information on the evolution of fluids as they interacted with anhydrous solid materials. Thus, real data can replace calculated fluid compositions in thermochemical calculations of the evolution of water and aqueous reactions in comets, asteroids, moons and the terrestrial planets.This article is part of the themed issue 'The origin, history and role of water in the evolution of the inner Solar System'. © 2017 The Author(s).

Temporal evolution of a Current Sheet with Initial Finite Perturbations by Three-dimensional MHD Simulations

NASA Astrophysics Data System (ADS)

Yokoyama, Takaaki

Temporal evolution of a current sheet with initial perturbations is studied by using the threedimensional resistive magnetohydrodynamic (MHD) simulations. The magnetic reconnection is considered to be the main engine of the energy rele ase in solar flares. The structure of the diffusion region is, however, not stil l understood under the circumstances with enormously large magnetic Reynolds num ber as the solar corona. In particular, the relationship between the flare's macroscopic physics and the microscopic ones are unclear. It is generally believed that the MHD turbulence s hould play a role in the intermediate scale. The initial current sheet is in an approximately hydromagnetic equilibrium with anti-parallel magnetic field in the y-direction. We imposed a finite-amplitude perturbations (=50ee what happens. Special attention is paid upon the evolution of a three-dimens ional structure in the direction along the initial electric current (z-direction ). Our preliminary results are as follows: (1) In the early phase of the evolut ion, high wavenumber modes in the z-direction are excited and grow. (2) Many "X "-type neutral points (lines) are generated along the magnetic neutral line (pla ne) in the current sheet. When they evolve into the non-linear phase, three-dime nsional structures in the z-direction also evolve. The spatial scale in the z-di rection seems to be almost comparable with that in the xy-plane. (3) The energy release rate is reduced in case of 3D simulations compared with 2D ones probably because of the reduction of the inflow cross sections by the formation of pattc hy structures in the current sheet.

No evidence for directional evolution of body mass in herbivorous theropod dinosaurs

PubMed Central

Zanno, Lindsay E.; Makovicky, Peter J.

2013-01-01

The correlation between large body size and digestive efficiency has been hypothesized to have driven trends of increasing mass in herbivorous clades by means of directional selection. Yet, to date, few studies have investigated this relationship from a phylogenetic perspective, and none, to our knowledge, with regard to trophic shifts. Here, we reconstruct body mass in the three major subclades of non-avian theropod dinosaurs whose ecomorphology is correlated with extrinsic evidence of at least facultative herbivory in the fossil record—all of which also achieve relative gigantism (more than 3000 kg). Ordinary least-squares regressions on natural log-transformed mean mass recover significant correlations between increasing mass and geological time. However, tests for directional evolution in body mass find no support for a phylogenetic trend, instead favouring passive models of trait evolution. Cross-correlation of sympatric taxa from five localities in Asia reveals that environmental influences such as differential habitat sampling and/or taphonomic filtering affect the preserved record of dinosaurian body mass in the Cretaceous. Our results are congruent with studies documenting that behavioural and/or ecological factors may mitigate the benefit of increasing mass in extant taxa, and suggest that the hypothesis can be extrapolated to herbivorous lineages across geological time scales. PMID:23193135

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.

It's not all about us: evolution and maintenance of Cryptococcus virulence requires selection outside the human host.

PubMed

Gerstein, Aleeza C; Nielsen, Kirsten

2017-04-01

Cryptococcus is predominantly an AIDS-related pathogen that causes significant morbidity and mortality in immunocompromised patients. Research studies have historically focused on understanding how the organism causes human disease through the use of in vivo and in vitro model systems to identify virulence factors. Cryptococcus is not an obligate pathogen, however, as human-human transmission is either absent or rare. Selection in the environment must thus be invoked to shape the evolution of this taxa, and directly influences genotypic and trait diversity. Importantly, the evolution and maintenance of pathogenicity must also stem directly from environmental selection. To that end, here we examine abiotic and biotic stresses in the environment, and discuss how they could shape the factors that are commonly identified as important virulence traits. We identify a number of important unanswered questions about Cryptococcus diversity and evolution that are critical for understanding this deadly pathogen, and discuss how implementation of modern sampling and genomic tools could be utilized to answer these questions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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.

Nonlinear evolution of three-dimensional instabilities of thin and thick electron scale current sheets: Plasmoid formation and current filamentation

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

Jain, Neeraj; Büchner, Jörg; Max Planck Institute for Solar System Research, Justus-Von-Liebig-Weg-3, Göttingen

Nonlinear evolution of three dimensional electron shear flow instabilities of an electron current sheet (ECS) is studied using electron-magnetohydrodynamic simulations. The dependence of the evolution on current sheet thickness is examined. For thin current sheets (half thickness =d{sub e}=c/ω{sub pe}), tearing mode instability dominates. In its nonlinear evolution, it leads to the formation of oblique current channels. Magnetic field lines form 3-D magnetic spirals. Even in the absence of initial guide field, the out-of-reconnection-plane magnetic field generated by the tearing instability itself may play the role of guide field in the growth of secondary finite-guide-field instabilities. For thicker current sheetsmore » (half thickness ∼5 d{sub e}), both tearing and non-tearing modes grow. Due to the non-tearing mode, current sheet becomes corrugated in the beginning of the evolution. In this case, tearing mode lets the magnetic field reconnect in the corrugated ECS. Later thick ECS develops filamentary structures and turbulence in which reconnection occurs. This evolution of thick ECS provides an example of reconnection in self-generated turbulence. The power spectra for both the thin and thick current sheets are anisotropic with respect to the electron flow direction. The cascade towards shorter scales occurs preferentially in the direction perpendicular to the electron flow.« less

Synthesizing perspectives on the evolution of cooperation within and between species.

PubMed

Barker, Jessica L; Bronstein, Judith L; Friesen, Maren L; Jones, Emily I; Reeve, H Kern; Zink, Andrew G; Frederickson, Megan E

2017-04-01

Cooperation is widespread both within and between species, but are intraspecific and interspecific cooperation fundamentally similar or qualitatively different phenomena? This review evaluates this question, necessary for a general understanding of the evolution of cooperation. First, we outline three advantages of cooperation relative to noncooperation (acquisition of otherwise inaccessible goods and services, more efficient acquisition of resources, and buffering against variability), and predict when individuals should cooperate with a conspecific versus a heterospecific partner to obtain these advantages. Second, we highlight five axes along which heterospecific and conspecific partners may differ: relatedness and fitness feedbacks, competition and resource use, resource-generation abilities, relative evolutionary rates, and asymmetric strategy sets and outside options. Along all of these axes, certain asymmetries between partners are more common in, but not exclusive to, cooperation between species, especially complementary resource use and production. We conclude that cooperation within and between species share many fundamental qualities, and that differences between the two systems are explained by the various asymmetries between partners. Consideration of the parallels between intra- and interspecific cooperation facilitates application of well-studied topics in one system to the other, such as direct benefits within species and kin-selected cooperation between species, generating promising directions for future research. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

High strength-of-ties and low mobility enable the evolution of third-party punishment

PubMed Central

Roos, Patrick; Gelfand, Michele; Nau, Dana; Carr, Ryan

2014-01-01

As punishment can be essential to cooperation and norm maintenance but costly to the punisher, many evolutionary game-theoretic studies have explored how direct punishment can evolve in populations. Compared to direct punishment, in which an agent acts to punish another for an interaction in which both parties were involved, the evolution of third-party punishment (3PP) is even more puzzling, because the punishing agent itself was not involved in the original interaction. Despite significant empirical studies of 3PP, little is known about the conditions under which it can evolve. We find that punishment reputation is not, by itself, sufficient for the evolution of 3PP. Drawing on research streams in sociology and psychology, we implement a structured population model and show that high strength-of-ties and low mobility are critical for the evolution of responsible 3PP. Only in such settings of high social-structural constraint are punishers able to induce self-interested agents toward cooperation, making responsible 3PP ultimately beneficial to individuals as well as the collective. Our results illuminate the conditions under which 3PP is evolutionarily adaptive in populations. Responsible 3PP can evolve and induce cooperation in cases where other mechanisms alone fail to do so. PMID:24335985

The evolution of dorsal-ventral patterning mechanisms in insects.

PubMed

Lynch, Jeremy A; Roth, Siegfried

2011-01-15

The gene regulatory network (GRN) underpinning dorsal-ventral (DV) patterning of the Drosophila embryo is among the most thoroughly understood GRNs, making it an ideal system for comparative studies seeking to understand the evolution of development. With the emergence of widely applicable techniques for testing gene function, species with sequenced genomes, and multiple tractable species with diverse developmental modes, a phylogenetically broad and molecularly deep understanding of the evolution of DV axis formation in insects is feasible. Here, we review recent progress made in this field, compare our emerging molecular understanding to classical embryological experiments, and suggest future directions of inquiry.

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.

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,...

Unpredictable evolution in a 30-year study of Darwin's finches.

PubMed

Grant, Peter R; Grant, B Rosemary

2002-04-26

Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.

Gamma-ray luminosity and photon index evolution of FSRQ blazars and contribution to the gamma-ray background

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

Singal, J.; Ko, A.; Petrosian, V., E-mail: jsingal@richmond.edu

We present the redshift evolutions and distributions of the gamma-ray luminosity and photon spectral index of flat spectrum radio quasar (FSRQ) type blazars, using non-parametric methods to obtain the evolutions and distributions directly from the data. The sample we use for analysis consists of almost all FSRQs observed with a greater than approximately 7σ detection threshold in the first-year catalog of the Fermi Gamma-ray Space Telescope's Large Area Telescope, with redshifts as determined from optical spectroscopy by Shaw et al. We find that FSQRs undergo rapid gamma-ray luminosity evolution, but negligible photon index evolution, with redshift. With these evolutions accountedmore » for we determine the density evolution and luminosity function of FSRQs and calculate their total contribution to the extragalactic gamma-ray background radiation, resolved and unresolved, which is found to be 16(+10/–4)%, in agreement with previous studies.« less

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.

A self-triggered picoinjector in microfluidics

NASA Astrophysics Data System (ADS)

Yang, Yiming; Liu, Songsheng; Jia, Chunping; Mao, Hongju; Jin, Qinghui; Zhao, Jianlong; Zhou, Hongbo

2016-12-01

Droplet-based microfluidics has recently emerged as a potential platform for studies of single-cell, directed evolution, and genetic sequencing. In droplet-based microfluidics, adding reagents into drops is one of the most important functions. In this paper, we develop a new self-triggered picoinjector to add controlled volumes of reagent into droplets at kilohertz rates. In the picoinjector, the reagent injecting is triggered by the coming droplet itself, without needing a droplet detection module. Meanwhile, the dosing volume can be precisely controlled. These features make the system more practical and reliable. We expect the new picoinjector will find important applications of droplet-based microfluidics in automated biological assay, directed evolution, enzyme assay, and so on.

Relaxation of herbivore-mediated selection drives the evolution of genetic covariances between plant competitive and defense traits.

PubMed

Uesugi, Akane; Connallon, Tim; Kessler, André; Monro, Keyne

2017-06-01

Insect herbivores are important mediators of selection on traits that impact plant defense against herbivory and competitive ability. Although recent experiments demonstrate a central role for herbivory in driving rapid evolution of defense and competition-mediating traits, whether and how herbivory shapes heritable variation in these traits remains poorly understood. Here, we evaluate the structure and evolutionary stability of the G matrix for plant metabolites that are involved in defense and allelopathy in the tall goldenrod, Solidago altissima. We show that G has evolutionarily diverged between experimentally replicated populations that evolved in the presence versus the absence of ambient herbivory, providing direct evidence for the evolution of G by natural selection. Specifically, evolution in an herbivore-free habitat altered the orientation of G, revealing a negative genetic covariation between defense- and competition-related metabolites that is typically masked in herbivore-exposed populations. Our results may be explained by predictions of classical quantitative genetic theory, as well as the theory of acquisition-allocation trade-offs. The study provides compelling evidence that herbivory drives the evolution of plant genetic architecture. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

E-learning process maturity level: a conceptual framework

NASA Astrophysics Data System (ADS)

Rahmah, A.; Santoso, H. B.; Hasibuan, Z. A.

2018-03-01

ICT advancement is a sure thing with the impact influencing many domains, including learning in both formal and informal situations. It leads to a new mindset that we should not only utilize the given ICT to support the learning process, but also improve it gradually involving a lot of factors. These phenomenon is called e-learning process evolution. Accordingly, this study attempts to explore maturity level concept to provide the improvement direction gradually and progression monitoring for the individual e-learning process. Extensive literature review, observation, and forming constructs are conducted to develop a conceptual framework for e-learning process maturity level. The conceptual framework consists of learner, e-learning process, continuous improvement, evolution of e-learning process, technology, and learning objectives. Whilst, evolution of e-learning process depicted as current versus expected conditions of e-learning process maturity level. The study concludes that from the e-learning process maturity level conceptual framework, it may guide the evolution roadmap for e-learning process, accelerate the evolution, and decrease the negative impact of ICT. The conceptual framework will be verified and tested in the future study.

A behavioral perspective on fishing-induced evolution.

PubMed

Uusi-Heikkilä, Silva; Wolter, Christian; Klefoth, Thomas; Arlinghaus, Robert

2008-08-01

The potential for excessive and/or selective fishing to act as an evolutionary force has been emphasized recently. However, most studies have focused on evolution of life-history traits in response to size-selective harvesting. Here we draw attention to fishing-induced evolution of behavioral and underlying physiological traits. We contend that fishing-induced selection directly acting on behavioral rather than on life-history traits per se can be expected in all fisheries that operate with passive gears such as trapping, angling and gill-netting. Recent artificial selection experiments in the nest-guarding largemouth bass Micropterus salmoides suggest that fishing-induced evolution of behavioral traits that reduce exposure to fishing gear might be maladaptive, potentially reducing natural recruitment. To improve understanding and management of fisheries-induced evolution, we encourage greater application of methods from behavioral ecology, physiological ecology and behavioral genetics.

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

Study on Capturing Functional Requirements of the New Product Based on Evolution

NASA Astrophysics Data System (ADS)

Liu, Fang; Song, Liya; Bai, Zhonghang; Zhang, Peng

In order to exist in an increasingly competitive global marketplace, it is important for corporations to forecast the evolutionary direction of new products rapidly and effectively. Most products in the world are developed based on the design of existing products. In the product design, capturing functional requirements is a key step. Function is continuously evolving, which is driven by the evolution of needs and technologies. So the functional requirements of new product can be forecasted based on the functions of existing product. Eight laws of function evolution are put forward in this paper. The process model of capturing the functional requirements of new product based on function evolution is proposed. An example illustrates the design process.

Quantum gates by periodic driving.

PubMed

Shi, Z C; Wang, W; Yi, X X

2016-02-25

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions-it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation.

Dental microwear in relation to changes in the direction of mastication during the evolution of Myodonta (Rodentia, Mammalia)

NASA Astrophysics Data System (ADS)

Charles, Cyril; Jaeger, Jean-Jacques; Michaux, Jacques; Viriot, Laurent

2007-01-01

Observations of dental microwear are used to analyse the correlation between changes in molar tooth crown morphology and the direction of masticatory movement during the evolution of Myodonta (Rodentia, Mammalia). The studied sample includes 36 specimens representing both superfamilies of Myodonta (Muroidea and Dipodoidea) spanning 16 dipodoid and 9 muroid species. Microscopic scratches on occlusal surfaces resulting from contact between opposite teeth during mastication are analysed. Using these features, we determine the direction of masticatory movements. Microwear patterns display diverse orientations among Dipodoidea: oblique in Sicistinae, Euchoreutinae and Zapodinae, propalinal in Dipodinae and intermediary in Allactaginae. Similarly, Muroidea exhibit the following orientations: oblique in Cricetinae and propalinal in Arvicolinae, Cricetomyinae, Gerbillinae and Murinae. These various chewing types illustrate different evolutionary grades within the superfamilies. Acquisition of the antero-posterior masticatory movement in Dipodoidea is related to flattening of the molar occlusal surface. However, in some muroid subfamilies, this direction of mastication is associated with low-crowned and cuspidate molars (Cricetomyinae, Murinae).

A robust protocol for directed aryl sulfotransferase evolution toward the carbohydrate building block GlcNAc.

PubMed

Islam, Shohana; Mate, Diana M; Martínez, Ronny; Jakob, Felix; Schwaneberg, Ulrich

2018-05-01

Bacterial aryl sulfotransferases (AST) utilize p-nitrophenylsulfate (pNPS) as a phenolic donor to sulfurylate typically a phenolic acceptor. Interest in aryl sulfotransferases is growing because of their broad variety of acceptors and cost-effective sulfuryl-donors. For instance, aryl sulfotransferase A (ASTA) from Desulfitobacterium hafniense was recently reported to sulfurylate d-glucose. In this study, a directed evolution protocol was developed and validated for aryl sulfotransferase B (ASTB). Thereby the well-known pNPS quantification system was advanced to operate efficiently as a continuous screening system in 96-well MTP format with a true coefficient of variation of 14.3%. A random mutagenesis library (SeSaM library) of ASTB was screened (1,760 clones) to improve sulfurylation of the carbohydrate building block N-acetylglucosamine (GlcNAc). The beneficial variant ASTB-V1 (Val579Asp) showed an up to 3.4-fold increased specific activity toward GlcNAc when compared to ASTB-WT. HPLC- and MS-analysis confirmed ASTB-V1's increased GlcNAc monosulfurylation (2.4-fold increased product formation) representing the validation of the first successful directed evolution round of an AST for a saccharide substrate. © 2017 Wiley Periodicals, Inc.

The tectonometamorphic evolution of the Apuseni Mountains (Romania): Geodynamic constraints for the evolution of the Alps-Carpathians-Dinaride system of orogens

NASA Astrophysics Data System (ADS)

Reiser, Martin; Schuster, Ralf; Fügenschuh, Bernhard

2015-04-01

New structural, thermobarometric and geochronological data allow integrating kinematics, timing and intensity of tectonic phases into a geodynamic model of the Apuseni Mountain, which provides new constraints for the evolution of the Alps-Carpathians-Dinaride system of orogens. Strong differences in terms of deformation directions between Early and Late Cretaceous events provide new constraints on the regional geodynamic evolution during the Cretaceous. Geochronological and structural data evidence a Late Jurassic emplacement of the South Apuseni Ophiolites on top of the Biharia Nappe System (Dacia Mega-Unit), situated in an external position at the European margin. Following the emplacement of the ophiolites, three compressive deformation phases affected the Apuseni Mountains during Alpine orogeny: a) NE-directed in-sequence nappe stacking and regional metamorphic overprinting under amphibolite-facies conditions during the Early Cretaceous ("Austrian Phase"), b) NW-directed thrusting and folding, associated with greenschist-facies overprinting, during the early Late Cretaceous ("Turonian Phase") and c) E-W internal folding together with brittle thrusting during the latest Cretaceous ("Laramian Phase"). Major tectonic unroofing and exhumation at the transition from Early to Late Cretaceous times is documented through new Sm-Nd Grt, Ar-Ar Ms and Rb-Sr Bt ages from the study area and resulted in a complex thermal structure with strong lateral and vertical thermal gradients. Nappe stacking and medium-grade metamorphic overprinting during the Early Cretaceous exhibits striking parallels between the evolution of the Tisza-Dacia Mega-Units and the Austroalpine Nappes (ALCAPA Mega-Unit) and evidences a close connection. However, Late Cretaceous tectonic events in the study area exhibit strong similarities with the Dinarides. Thus, the Apuseni Mountains represent the "missing link" between the Early Cretaceous Meliata subduction (associated with obduction of ophiolites) and the Neotethys subduction during Late Cretaceous times.

Two-Fold Anisotropy Governs Morphological Evolution and Stress Generation in Sodiated Black Phosphorus for Sodium Ion Batteries.

PubMed

Chen, Tianwu; Zhao, Peng; Guo, Xu; Zhang, Sulin

2017-04-12

Phosphorus represents a promising anode material for sodium ion batteries owing to its extremely high theoretical capacity. Recent in situ transmission electron microscopy studies evidenced anisotropic swelling in sodiated black phosphorus, which may find an origin from the two intrinsic anisotropic properties inherent to the layered structure of black phosphorus: sodium diffusional directionality and insertion strain anisotropy. To understand the morphological evolution and stress generation in sodiated black phosphorus, we develop a chemo-mechanical model by incorporating the intrinsic anisotropic properties into the large elasto-plastic deformation. Our modeling results reveal that the apparent morphological evolution in sodiated black phosphorus is critically controlled by the coupled effect of the two intrinsic anisotropic properties. In particular, sodium diffusional directionality generates sharp interphases along the [010] and [001] directions, which constrain anisotropic development of the insertion strain. The coupled effect renders distinctive stress-generation and fracture mechanisms when sodiation starts from different crystal facets. In addition to providing a powerful modeling framework for sodiation and lithiation of layered structures, our findings shed significant light on the sodiation-induced chemo-mechanical degradation of black phosphorus as a promising anode for the next-generation sodium ion batteries.

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.

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.

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…

Thermal Evolution of a Failed Flux Rope Eruption Revealed by Temperature Maps

NASA Astrophysics Data System (ADS)

Song, H.; Zhang, J.; CHEN, Y.

2013-12-01

Flux rope is generally considered to be the fundamental magnetic configuration of a coronal mass ejection (CME). Recent observations suggest that hot channel or blob structures during the eruptions be the direct observational manifestation of flux ropes. In this study, we report our analysis of thermal evolution of a failed solar eruption with an apparent flux rope embedded. The thermal structure of the eruption is revealed through differential emission measure (DEM) analysis technique, which shows detailed temperature maps in both high spatial resolution and high temperature resolution based on SDO/AIA observations. Our results show that the flux rope exists in the corona before the eruption, and its temperature can quickly rise to over 10 MK within one minute of the eruption. The correlation study between the flux rope temperature and the soft x-ray flux suggests that the flux rope should be heated through the direct thermal energy release of magnetic reconnection. Further, we study the kinematic evolution process of the flux rope, in an effort to find the physical mechanism that prevents the magnetic rope eruption to become a full coronal mass ejection. This kind of study using temperature maps might reveal where and when magnetic reconnection takes place during solar eruptions.

An appraisal of the enzyme stability-activity trade-off.

PubMed

Miller, Scott R

2017-07-01

A longstanding idea in evolutionary physiology is that an enzyme cannot jointly optimize performance at both high and low temperatures due to a trade-off between stability and activity. Although a stability-activity trade-off has been observed for well-characterized examples, such a trade-off is not imposed by any physical chemical constraint. To better understand the pervasiveness of this trade-off, I investigated the stability-activity relationship for comparative biochemical studies of purified orthologous enzymes identified by a literature search. The nature of this relationship varied greatly among studies. Notably, studies of enzymes with low mean synonymous nucleotide sequence divergence were less likely to exhibit the predicted negative correlation between stability and activity. Similarly, a survey of directed evolution investigations of the stability-activity relationship indicated that these traits are often uncoupled among nearly identical yet phenotypically divergent enzymes. This suggests that the presumptive trade-off often reported for investigations of enzymes with high mean sequence divergence may in some cases instead be a consequence of the degeneration over time of enzyme function in unselected environments, rather than a direct effect of thermal adaptation. The results caution against the general assertion of a stability-activity trade-off during enzyme adaptation. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

PubMed Central

Ballouz, Sara; Francis, Andrew R.; Lan, Ruiting; Tanaka, Mark M.

2010-01-01

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters. PMID:20168992

Strain transfer through film-substrate interface and surface curvature evolution during a tensile test

NASA Astrophysics Data System (ADS)

He, Wei; Han, Meidong; Goudeau, Philippe; Bourhis, Eric Le; Renault, Pierre-Olivier; Wang, Shibin; Li, Lin-an

2018-03-01

Uniaxial tensile tests on polyimide-supported thin metal films are performed to respectively study the macroscopic strain transfer through an interface and the surface curvature evolution. With a dual digital image correlation (DIC) system, the strains of the film and the substrate can be simultaneously measured in situ during the tensile test. For the true strains below 2% (far beyond the films' elastic limit), a complete longitudinal strain transfer is present irrespective of the film thickness, residual stresses and microstructure. By means of an optical surface profiler, the three-dimensional (3D) topography of film surface can be obtained during straining. As expected, the profile of the specimen center remains almost flat in the tensile direction. Nevertheless, a relatively significant curvature evolution (of the same order with the initial curvature induced by residual stresses) is observed along the transverse direction as a result of a Poisson's ratio mismatch between the film and the substrate. Furthermore, finite element method (FEM) has been performed to simulate the curvature evolution considering the geometric nonlinearity and the perfect strain transfer at the interface, which agrees well with the experimental results.

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

First steps in experimental cancer evolution

PubMed Central

Taylor, Tiffany B; Johnson, Louise J; Jackson, Robert W; Brockhurst, Michael A; Dash, Philip R

2013-01-01

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research. PMID:23745144

Probing galaxy growth through metallicity scaling relations over the past 12 Gyr of cosmic history

NASA Astrophysics Data System (ADS)

Sanders, Ryan; MOSDEF team

2018-01-01

A primary goal of galaxy evolution studies is to understand the processes governing the growth of the baryonic content of galaxies over cosmic history. Observations of galaxy metallicity scaling relations and their evolution with redshift, in combination with chemical evolution models, provide unique insight into the interplay between star formation, gas accretion, and feedback/outflows. I present measurements of the stellar mass-gas phase metallicity relation and its evolution over the past 12 Gyr from z~0 to z~3.5, utilizing data from the Mosfire Deep Evolution Field survey that uniquely provides rest-frame optical spectra of >1000 uniformly-selected galaxies at z=1.3-3.8. We find evolution towards lower metallicity at fixed stellar mass with increasing redshift that is consistent with current cosmological simulations including chemical evolution, with a large evolution of ~0.3 dex from z~0 to z~2.5 and minor evolution of <0.1 dex from z~2.5 to z~3.5. We unambiguously confirm the existence of star-formation rate dependence of the mass-metallicity relation at high redshift for the first time. A clear view of cosmic chemical evolution requires accounting for systematic biases in galaxy metallicity measurements at both low and high redshifts. We use a set of empirically-based models to correct for diffuse ionized gas contamination that biases metallicity estimates from z~0 global galaxy spectra. Evolving properties of ionized gas such as electron density, ionization parameter, hardness of the ionizing spectrum, and chemical abundance patterns may render locally-calibrated metallicity estimators unreliable at high redshifts. Using strong-line ratios alone, it is extremely difficult to break degenerate solutions between pure metallicity evolution and additional evolution of the ionization parameter and/or shape of the ionizing spectrum. Temperature-sensitive auroral-line measurements provide a way to directly and independently measure metallicities, breaking these degeneracies. We present measurements of auroral [OIII]4363 and direct-method metallicities at z>2, and discuss the potential of current and next-generation observational facilities to obtain statistical auroral-line samples at high redshifts.

Evolution of group-wise cooperation: Is direct reciprocity insufficient?

PubMed

Kurokawa, Shun; Ihara, Yasuo

2017-02-21

Group-wise cooperation, or cooperation among three or more individuals, is an integral part of human societies. It is likely that group-wise cooperation also played a crucial role in the survival of early hominins, who were confronted with novel environmental challenges, long before the emergence of Homo sapiens. However, previous theoretical and empirical studies, focusing mainly on modern humans, have tended to suggest that evolution of cooperation in sizable groups cannot be explained by simple direct reciprocity and requires some additional mechanisms (reputation, punishment, etc.), which are cognitively too demanding for early hominins. As a partial resolution of the paradox, our recent analysis of a stochastic evolutionary model, which considers the effect of random drift, has revealed that evolution of group-wise cooperation is more likely to occur in larger groups when an individual's share of the benefit produced by one cooperator does not decrease with increasing group size (i.e., goods are non-rivalrous). In this paper, we further extend our previous analysis to explore possible consequences of introducing rare mistakes in behavior or imperfect information about behavior of others on the model outcome. Analyses of the extended models show that evolution of group-wise cooperation can be facilitated by large group size even when individuals intending to cooperate sometimes fail to do so or when all the information about the past behavior of group members is not available. We argue, therefore, that evolution of cooperation in sizable groups does not necessarily require other mechanisms than direct reciprocity if the goods to be produced via group-wise cooperation are non-rivalrous. Copyright © 2016 Elsevier Ltd. 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.

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.

The origin and dynamic evolution of chemical information transfer

PubMed Central

Steiger, Sandra; Schmitt, Thomas; Schaefer, H. Martin

2011-01-01

Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general. PMID:21177681

Characteristic Evolution and Matching

NASA Astrophysics Data System (ADS)

Winicour, Jeffrey

2012-01-01

I review the development of numerical evolution codes for general relativity based upon the characteristic initial-value problem. Progress in characteristic evolution is traced from the early stage of 1D feasibility studies to 2D-axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black-hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black-hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to extend such simulations to null infinity where the waveform from the binary inspiral and merger can be unambiguously computed. This has now been accomplished by Cauchy-characteristic extraction, where data for the characteristic evolution is supplied by Cauchy data on an extraction worldtube inside the artificial outer boundary. The ultimate application of characteristic evolution is to eliminate the role of this outer boundary by constructing a global solution via Cauchy-characteristic matching. Progress in this direction is discussed.

Trace elements at the intersection of marine biological and geochemical evolution

USGS Publications Warehouse

Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

2016-01-01

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

The importance of ecological costs for the evolution of plant defense against herbivory.

PubMed

van Velzen, Ellen; Etienne, Rampal S

2015-05-07

Plant defense against herbivory comes at a cost, which can be either direct (reducing resources available for growth and reproduction) or indirect (through reducing ecological performance, for example intraspecific competitiveness). While direct costs have been well studied in theoretical models, ecological costs have received almost no attention. In this study we compare models with a direct trade-off (reduced growth rate) to models with an ecological trade-off (reduced competitive ability), using a combination of adaptive dynamics and simulations. In addition, we study the dependence of the level of defense that can evolve on the type of defense (directly by reducing consumption, or indirectly by inducing herbivore mortality (toxicity)), and on the type of herbivore against which the plant is defending itself (generalists or specialists). We find three major results: First, for both direct and ecological costs, defense only evolves if the benefit to the plant is direct (through reducing consumption). Second, the type of cost has a major effect on the evolutionary dynamics: direct costs always lead to a single optimal strategy against herbivores, but ecological costs can lead to branching and the coexistence of non-defending and defending plants; however, coexistence is only possible when defending against generalist herbivores. Finally, we find that fast-growing plants invest less than slow-growing plants when defending against generalist herbivores, as predicted by the Resource Availability Hypothesis, but invest more than slow-growing plants when defending against specialists. Our results clearly show that assumptions about ecological interactions are crucial for understanding the evolution of defense against herbivores. Copyright © 2015 Elsevier Ltd. All rights reserved.

Adaptive Evolution of Mitochondrial Energy Metabolism Genes Associated with Increased Energy Demand in Flying Insects

PubMed Central

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects. PMID:24918926

Crack classification and evolution in anisotropic shale during cyclic loading tests by acoustic emission

NASA Astrophysics Data System (ADS)

Wang, Miaomiao; Tan, Chengxuan; Meng, Jing; Yang, Baicun; Li, Yuan

2017-08-01

Characterization and evolution of the cracking mode in shale formation is significant, as fracture networks are an important element in shale gas exploitation. In this study we determine the crack modes and evolution in anisotropic shale under cyclic loading using the acoustic emission (AE) parameter-analysis method based on the average frequency and RA (rise-time/amplitude) value. Shale specimens with bedding-plane orientations parallel and perpendicular to the axial loading direction were subjected to loading cycles with increasing peak values until failure occurred. When the loading was parallel to the bedding plane, most of the cracks at failure were shear cracks, while tensile cracks were dominant in the specimens that were loaded normal to the bedding direction. The evolution of the crack mode in the shale specimens observed in the loading-unloading sequence except for the first cycle can be divided into three stages: (I) no or several cracks (AE events) form as a result of the Kaiser effect, (II) tensile and shear cracks increase steadily at nearly equal proportions, (III) tensile cracks and shear cracks increase abruptly, with more cracks forming in one mode than in the other. As the dominant crack motion is influenced by the bedding, the failure mechanism is discussed based on the evolution of the different crack modes. Our conclusions can increase our understanding of the formation mechanism of fracture networks in the field.

Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

PubMed

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

Characteristics of temporal evolution of particle density and electron temperature in helicon discharge

NASA Astrophysics Data System (ADS)

Yang, Xiong; Cheng, Mousen; Guo, Dawei; Wang, Moge; Li, Xiaokang

2017-10-01

On the basis of considering electrochemical reactions and collision relations in detail, a direct numerical simulation model of a helicon plasma discharge with three-dimensional two-fluid equations was employed to study the characteristics of the temporal evolution of particle density and electron temperature. With the assumption of weak ionization, the Maxwell equations coupled with the plasma parameters were directly solved in the whole computational domain. All of the partial differential equations were solved by the finite element solver in COMSOL MultiphysicsTM with a fully coupled method. In this work, the numerical cases were calculated with an Ar working medium and a Shoji-type antenna. The numerical results indicate that there exist two distinct modes of temporal evolution of the electron and ground atom density, which can be explained by the ion pumping effect. The evolution of the electron temperature is controlled by two schemes: electromagnetic wave heating and particle collision cooling. The high RF power results in a high peak electron temperature while the high gas pressure leads to a low steady temperature. In addition, an OES experiment using nine Ar I lines was conducted using a modified CR model to verify the validity of the results by simulation, showing that the trends of temporal evolution of electron density and temperature are well consistent with the numerically simulated ones.

Testing of some assumptions about biodegradability in soil as measured by carbon dioxide evolution

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

El-Din Sharabi, N.; Bartha, R.

1993-04-01

The Toxic Substance Control Act calls for a premanufacturing review of novel chemical substances including their biodegradability. Carbon dioxide evolution, using non-labeled carbon or [sup 14]C, is a common method of testing. This study examines assumptions of carbon dioxide evolution testing. Test substances used included: glucose, adipic acid, benzoic acid, and n-hexadecane. Chemical composition other than carbon content appears to influence minimally the percentages conversion to CO[sub 2]. However, that although CO[sub 2] evolution seemed proportional to the carbon content and concentration of the test substance, at least one-half of the evolved net CO[sub 2] did not come directly frommore » the test substance. Conversion to CO[sub 2] in the soil appeared to depend on carbon content only. In experiments of 1 month or longer, the net CO[sub 2] evolution in response to substrate may be above 100% of the added substrate carbon. Whether this applies to all substrate additions remains to be studied. The authors conclude that net CO[sub 2] and [sup 14]CO[sub 2] evolution measurements are useful as a first-tier tests for assessing biodegradability in soil. 11 refs., 6 figs.« less

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.

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.

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.

Evolution of cooperation driven by social-welfare-based migration

NASA Astrophysics Data System (ADS)

Li, Yan; Ye, Hang; Zhang, Hong

2016-03-01

Individuals' migration behavior may play a significant role in the evolution of cooperation. In reality, individuals' migration behavior may depend on their perceptions of social welfare. To study the relationship between social-welfare-based migration and the evolution of cooperation, we consider an evolutionary prisoner's dilemma game (PDG) in which an individual's migration depends on social welfare but not on the individual's own payoff. By introducing three important social welfare functions (SWFs) that are commonly studied in social science, we find that social-welfare-based migration can promote cooperation under a wide range of parameter values. In addition, these three SWFs have different effects on cooperation, especially through the different spatial patterns formed by migration. Because the relative efficiency of the three SWFs will change if the parameter values are changed, we cannot determine which SWF is optimal for supporting cooperation. We also show that memory capacity, which is needed to evaluate individual welfare, may affect cooperation levels in opposite directions under different SWFs. Our work should be helpful for understanding the evolution of human cooperation and bridging the chasm between studies of social preferences and studies of social cooperation.

New frontiers in the study of human cultural and genetic evolution.

PubMed

Ross, Cody T; Richerson, Peter J

2014-12-01

In this review, we discuss the dynamic linkages between culture and the genetic evolution of the human species. We begin by briefly describing the framework of gene-culture coevolutionary (or dual-inheritance) models for human evolutionary change. Until recently, the literature on gene-culture coevolution was composed primarily of mathematical models and formalized theory describing the complex dynamics underlying human behavior, adaptation, and technological evolution, but had little empirical support concerning genetics. The rapid progress in the fields of molecular genetics and genomics, however, is now providing the kinds of data needed to produce rich empirical support for gene-culture coevolutionary models. We briefly outline how theoretical and methodological progress in genome sciences has provided ways for the strength of selection on genes to be evaluated, and then outline how evidence of selection on several key genes can be directly linked to human cultural practices. We then describe some exciting new directions in the empirical study of gene-culture coevolution, and conclude with a discussion of the role of gene-culture evolutionary models in the future integration of medical, biological, and social sciences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Environmental influences on the evolution of body size in Ammonoids

NASA Astrophysics Data System (ADS)

Hines, S.; Khong, C.; Pelagio, M.; Seixas, G.; Payne, J.

2012-12-01

A major debate in evolutionary biology and paleobiology focuses on the relative importance of ecological interactions between species versus changes in the physical environment in governing large-scale evolutionary patterns. Body size is among the most important traits of any organism, and so identifying the factors that influence size evolution can shed light on both the causes and consequences of many major evolutionary trends. However, the extent to which body size evolution over time can be explained by changes in the physical versus ecological context remains unknown. In this study, we examined body size evolution in ammonoids, an extinct group of marine cephalopods. We collected a representative body size for each genus from illustrated specimens in the Treatise on Invertebrate Paleontology. We then examined relative statistical support for six models of size evolution: random walk, directional trend, stasis, and environmental control by oxygen availability, temperature, and global sea level. No model is unambiguously supported over all others. Unbiased random walk was the best supported model (34%) and environmental control by atmospheric pO2 was the second best supported model (22%). Stasis received the least support (<<1%). Because we find pO2 to be inversely correlated with ammonoid size, we suspect that the observed correlation does not reflect a direct causal relationship. Overall, our results suggest that no single, simple model can be used to characterize the evolution of ammonoid size over the entire history of this clade. We speculate that controls on ammonoid size evolution varied through geological time, both due to long-term shifts in the ecological structure of marine communities and short-term perturbations associated with major extinction events.

Dynamic evolution of light-induced orientation of dye-doped liquid crystals in liquid phase studied by time-resolved optically heterodyned optical Kerr effect technique.

PubMed

Yang, Pei; Liu, Liying; Xu, Lei

2008-02-28

Transient evolution of light-induced molecular reorientation both in 1-amino-anthraquinone (1AAQ) dye and azobenzene doped isotropic liquid crystals (LCs) were studied by time-resolved optically heterodyned optical Kerr effect method. The results give clear direct experimental proof that under short pulse (30 ps) excitation, LC molecules orientate toward the excitation light polarization direction in the 1AAQ/LC system. However, LC molecular orientation becomes orthogonal to the light polarization in azobenzene/LC system. Time-resolved excited-state absorption of 1AAQ and wavelength dependent excited-state absorption of azobenzene were also observed and their contributions to the early dynamics of the third order optical responses of the two systems were confirmed. A simplified two-level mean-field theory was derived to reveal the intensity dependence of orientation enhancement factor in azobenzene/LC system considering the photoisomerization process.

A DNS study of turbulent mixing of two passive scalars

NASA Astrophysics Data System (ADS)

Juneja, A.; Pope, S. B.

1996-08-01

We employ direct numerical simulations to study the mixing of two passive scalars in stationary, homogeneous, isotropic turbulence. The present work is a direct extension of that of Eswaran and Pope from one scalar to two scalars and the focus is on examining the evolution states of the scalar joint probability density function (jpdf) and the conditional expectation of the scalar diffusion to motivate better models for multi-scalar mixing. The initial scalar fields are chosen to conform closely to a ``triple-delta function'' jpdf corresponding to blobs of fluid in three distinct states. The effect of the initial length scales and diffusivity of the scalars on the evolution of the jpdf and the conditional diffusion is investigated in detail as the scalars decay from their prescribed initial state. Also examined is the issue of self-similarity of the scalar jpdf at large times and the rate of decay of the scalar variance and dissipation.

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops.

PubMed

Sherratt, Emma; Serb, Jeanne M; Adams, Dean C

2017-12-08

Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops. Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion. Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry between valves. Our observation that morphological integration of the valves making up the shell is consistently strong suggests tight developmental pathways are responsible for the concerted evolution of these structures while environmental pressures are driving whole shell shape. Finally, our study shows that directional asymmetry in shell shape among species is an important aspect of scallop macroevolution.

Natural selection on immune defense: A field experiment.

PubMed

Langeloh, Laura; Behrmann-Godel, Jasminca; Seppälä, Otto

2017-02-01

Predicting the evolution of phenotypic traits requires an understanding of natural selection on them. Despite its indispensability in the fight against parasites, selection on host immune defense has remained understudied. Theory predicts immune traits to be under stabilizing selection due to associated trade-offs with other fitness-related traits. Empirical studies, however, report mainly positive directional selection. This discrepancy could be caused by low phenotypic variation in the examined individuals and/or variation in host resource level that confounds trade-offs in empirical studies. In a field experiment where we maintained Lymnaea stagnalis snails individually in cages in a lake, we investigated phenotypic selection on two immune defense traits, phenoloxidase (PO)-like activity and antibacterial activity, in hemolymph. We used a diverse laboratory population and manipulated snail resource level by limiting their food supply. For six weeks, we followed immune activity, growth, and two fitness components, survival and fecundity of snails. We found that PO-like activity and growth were under stabilizing selection, while antibacterial activity was under positive directional selection. Selection on immune traits was mainly driven by variation in survival. The form of selection on immune defense apparently depends on the particular trait, possibly due to its importance for countering the present parasite community. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Phase-field modeling of the beta to omega phase transformation in Zr–Nb alloys

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

Yeddu, Hemantha Kumar; Lookman, Turab

A three-dimensional elastoplastic phase-field model is developed, using the Finite Element Method (FEM), for modeling the athermal beta to omega phase transformation in Zr–Nb alloys by including plastic deformation and strain hardening of the material. The microstructure evolution during athermal transformation as well as under different stress states, e.g. uni-axial tensile and compressive, bi-axial tensile and compressive, shear and tri-axial loadings, is studied. The effects of plasticity, stress states and the stress loading direction on the microstructure evolution as well as on the mechanical properties are studied. The input data corresponding to a Zr – 8 at.% Nb alloy aremore » acquired from experimental studies as well as by using the CALPHAD method. Our simulations show that the four different omega variants grow as ellipsoidal shaped particles. Our results show that due to stress relaxation, the athermal phase transformation occurs slightly more readily in the presence of plasticity compared to that in its absence. The evolution of omega phase is different under different stress states, which leads to the differences in the mechanical properties of the material. The variant selection mechanism, i.e. formation of different variants under different stress loading directions, is also nicely captured by our model.« less

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.

Constrained evolution of the sex comb in Drosophila simulans.

PubMed

Maraqa, M S; Griffin, R; Sharma, M D; Wilson, A J; Hunt, J; Hosken, D J; House, C M

2017-02-01

Male fitness is dependent on sexual traits that influence mate acquisition (precopulatory sexual selection) and paternity (post-copulatory sexual selection), and although many studies have documented the form of selection in one or the other of these arenas, fewer have done it for both. Nonetheless, it appears that the dominant form of sexual selection is directional, although theoretically, populations should converge on peaks in the fitness surface, where selection is stabilizing. Many factors, however, can prevent populations from reaching adaptive peaks. Genetic constraints can be important if they prevent the development of highest fitness phenotypes, as can the direction of selection if it reverses across episodes of selection. In this study, we examine the evidence that these processes influence the evolution of the multivariate sex comb morphology of male Drosophila simulans. To do this, we conduct a quantitative genetic study together with a multivariate selection analysis to infer how the genetic architecture and selection interact. We find abundant genetic variance and covariance in elements of the sex comb. However, there was little evidence for directional selection in either arena. Significant nonlinear selection was detected prior to copulation when males were mated to nonvirgin females, and post-copulation during sperm offence (again with males mated to nonvirgins). Thus, contrary to our predictions, the evolution of the D. simulans sex comb is limited neither by genetic constraints nor by antagonistic selection between pre- and post-copulatory arenas, but nonlinear selection on the multivariate phenotype may prevent sex combs from evolving to reach some fitness maximizing optima. © 2016 The Authors. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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.

The roles of tolerance in the evolution, maintenance and breakdown of mutualism

NASA Astrophysics Data System (ADS)

Edwards, David P.

2009-10-01

Tolerance strategies are cost-reduction mechanisms that enable organisms to recover some of the fitness lost to damage, but impose limited or no cost on antagonists. They are frequently invoked in studies of plant-herbivore and of host-parasite interactions, but the possible roles of tolerance in mutualism (interspecific cooperation) have yet to be thoroughly examined. This review identifies candidate roles for tolerance in the evolution, maintenance and breakdown of mutualism. Firstly, by reducing the cost of damage, tolerance provides a key pathway by which pre-mutualistic hosts can reduce the cost of association with their parasites, promoting cooperation. This holds for the evolution of ‘evolved dependency’ type mutualism, where a host requires an antagonist that does not direct any reward to their partner for some resource, and of ‘outright mutualism’, where participants directly trade benefits. Secondly, in outright mutualism, tolerance might maintain cooperation by reducing the cost of a persisting negative trait in a symbiotic partner. Finally, the evolution of tolerance might also provide a pathway out of mutualism because the host could evolve a cheaper alternative to continued cooperation with its mutualistic partner, permitting autonomy. A key consequence of tolerance is that it contrasts with partner choice mechanisms that impose large costs on cheats, and I highlight understanding any trade-off between tolerance and partner choice as an important research topic in the evolution of cooperation. I conclude by identifying tolerance as part of a more general phenomenon of co-adaptation in mutualism and parasitism that drives the evolution of the cost/benefit ratio from the interaction.

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.

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

Genetic correlations and sex-specific adaptation in changing environments.

PubMed

Connallon, Tim; Hall, Matthew D

2016-10-01

Females and males have conflicting evolutionary interests. Selection favors the evolution of different phenotypes within each sex, yet divergence between the sexes is constrained by the shared genetic basis of female and male traits. Current theory predicts that such "sexual antagonism" should be common: manifesting rapidly during the process of adaptation, and slow in its resolution. However, these predictions apply in temporally stable environments. Environmental change has been shown empirically to realign the direction of selection acting on shared traits and thereby alleviate signals of sexually antagonistic selection. Yet there remains no theory for how common sexual antagonism should be in changing environments. Here, we analyze models of sex-specific evolutionary divergence under directional and cyclic environmental change, and consider the impact of genetic correlations on long-run patterns of sex-specific adaptation. We find that environmental change often aligns directional selection between the sexes, even when they have divergent phenotypic optima. Nevertheless, some forms of environmental change generate persistent sexually antagonistic selection that is difficult to resolve. Our results reinforce recent empirical observations that changing environmental conditions alleviate conflict between males and females. They also generate new predictions regarding the scope for sexually antagonistic selection and its resolution in changing environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Evolution of brain region volumes during artificial selection for relative brain size.

PubMed

Kotrschal, Alexander; Zeng, Hong-Li; van der Bijl, Wouter; Öhman-Mägi, Caroline; Kotrschal, Kurt; Pelckmans, Kristiaan; Kolm, Niclas

2017-12-01

The vertebrate brain shows an extremely conserved layout across taxa. Still, the relative sizes of separate brain regions vary markedly between species. One interesting pattern is that larger brains seem associated with increased relative sizes only of certain brain regions, for instance telencephalon and cerebellum. Till now, the evolutionary association between separate brain regions and overall brain size is based on comparative evidence and remains experimentally untested. Here, we test the evolutionary response of brain regions to directional selection on brain size in guppies (Poecilia reticulata) selected for large and small relative brain size. In these animals, artificial selection led to a fast response in relative brain size, while body size remained unchanged. We use microcomputer tomography to investigate how the volumes of 11 main brain regions respond to selection for larger versus smaller brains. We found no differences in relative brain region volumes between large- and small-brained animals and only minor sex-specific variation. Also, selection did not change allometric scaling between brain and brain region sizes. Our results suggest that brain regions respond similarly to strong directional selection on relative brain size, which indicates that brain anatomy variation in contemporary species most likely stem from direct selection on key regions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The temporal distribution of directional gradients under selection for an optimum.

PubMed

Chevin, Luis-Miguel; Haller, Benjamin C

2014-12-01

Temporal variation in phenotypic selection is often attributed to environmental change causing movements of the adaptive surface relating traits to fitness, but this connection is rarely established empirically. Fluctuating phenotypic selection can be measured by the variance and autocorrelation of directional selection gradients through time. However, the dynamics of these gradients depend not only on environmental changes altering the fitness surface, but also on evolution of the phenotypic distribution. Therefore, it is unclear to what extent variability in selection gradients can inform us about the underlying drivers of their fluctuations. To investigate this question, we derive the temporal distribution of directional gradients under selection for a phenotypic optimum that is either constant or fluctuates randomly in various ways in a finite population. Our analytical results, combined with population- and individual-based simulations, show that although some characteristic patterns can be distinguished, very different types of change in the optimum (including a constant optimum) can generate similar temporal distributions of selection gradients, making it difficult to infer the processes underlying apparent fluctuating selection. Analyzing changes in phenotype distributions together with changes in selection gradients should prove more useful for inferring the mechanisms underlying estimated fluctuating selection. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Landform Erosion and Volatile Redistribution on Ganymede and Callisto

NASA Technical Reports Server (NTRS)

Moore, Jeffrey Morgan; Howard, Alan D.; McKinnon, William B.; Schenk, Paul M.; Wood, Stephen E.

2009-01-01

We have been modeling landscape evolution on the Galilean satellites driven by volatile transport. Our work directly addresses some of the most fundamental issues pertinent to deciphering icy Galilean satellite geologic histories by employing techniques currently at the forefront of terrestrial, martian, and icy satellite landscape evolution studies [e.g., 1-6], including modeling of surface and subsurface energy and volatile exchanges, and computer simulation of long-term landform evolution by a variety of processes. A quantitative understanding of the expression and rates of landform erosion, and of volatile redistribution on landforms, is especially essential in interpreting endogenic landforms that have, in many cases, been significantly modified by erosion [e.g., 7-9].

Language Interdependence between American Sign Language and English: A Review of Empirical Studies

ERIC Educational Resources Information Center

Rusher, Melissa Ausbrooks

2012-01-01

This study provides a contemporary definition of American Sign Language/English bilingual education (AEBE) and outlines an essential theoretical framework. Included is a history and evolution of the methodology. The author also summarizes the general findings of twenty-six (26) empirical studies conducted in the United States that directly or…

Combining archeomagnetic and volcanic data with historical geomagnetic observations to reconstruct global field evolution over the past 1000 years, including new paleomagnetic data from historical lava flows on Fogo, Cape Verde

NASA Astrophysics Data System (ADS)

Korte, M. C.; Senftleben, R.; Brown, M. C.; Finlay, C. C.; Feinberg, J. M.; Biggin, A. J.

2016-12-01

Geomagnetic field evolution of the recent past can be studied using different data sources: Jackson et al. (2000) combined historical observations with modern field measurements to derive a global geomagnetic field model (gufm1) spanning 1590 to 1990. Several published young archeo- and volcanic paleomagnetic data fall into this time interval. Here, we directly combine data from these different sources to derive a global field model covering the past 1000 years. We particularly focus on reliably recovering dipole moment evolution prior to the times of the first direct absolute intensity observations at around 1840. We first compared the different data types and their agreement with the gufm1 model to assess their compatibility and reliability. We used these results, in combination with statistical modelling tests, to obtain suitable uncertainty estimates as weighting factors for the data in the final model. In addition, we studied samples from seven lava flows from the island of Fogo, Cape Verde, erupted between 1664 and 1857. Oriented samples were available for two of them, providing declination and inclination results. Due to the complicated mineralogy of three of the flows, microwave paleointensity experiments using a modified version of the IZZI protocol were carried out on flows erupted in 1664, 1769, 1816 and 1847. The new directional results are compared with nearby historical data and the influence on, and agreement with, the new model are discussed.

A continued role for signaling functions in the early evolution of feathers.

PubMed

Ruxton, Graeme D; Persons Iv, W Scott; Currie, Philip J

2017-03-01

Persons and Currie (2015) argued against either flight, thermoregulation, or signaling as a functional benefit driving the earliest evolution of feathers; rather, they favored simple feathers having an initial tactile sensory function, which changed to a thermoregulatory function as density increased. Here, we explore the relative merits of early simple feathers that may have originated as tactile sensors progressing instead toward a signaling, rather than (or in addition to) a thermoregulatory function. We suggest that signaling could act in concert with a sensory function more naturally than could thermoregulation. As such, the dismissal of a possible signaling function and the presumption that an initial sensory function led directly to a thermoregulatory function (implicit in the title "bristles before down") are premature. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

PubMed Central

Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

2016-01-01

Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO. PMID:26961962

Using a Classical Gluon Cascade to study the Equilibration of a Gluon-Plasma

NASA Astrophysics Data System (ADS)

McConnell, Lucas

2015-10-01

Using a classical gluon cascade, we study the thermalisation of a gluon-plasma in a homogeneous box by considering the time evolution of the entropy, and in particular how the thermalisation time depends on the strong coupling αs. We then partition the volume into cells with a linearly increasing temperature gradient in one direction, and homogeneous/isotropic in the the other two directions. We allow the gluons to stream in one direction in order to study how they then evolve spatially. We examine cases with and without collisions. We study the entropy as well as the flow-velocity in the z-direction and find that the system initially has a flow which dissipates over time as the gluons become distributed homogeneously throughout the box.

Is a larger refuge always better? Dispersal and dose in pesticide resistance evolution.

PubMed

Takahashi, Daisuke; Yamanaka, Takehiko; Sudo, Masaaki; Andow, David A

2017-06-01

The evolution of resistance against pesticides is an important problem of modern agriculture. The high-dose/refuge strategy, which divides the landscape into treated and nontreated (refuge) patches, has proven effective at delaying resistance evolution. However, theoretical understanding is still incomplete, especially for combinations of limited dispersal and partially recessive resistance. We reformulate a two-patch model based on the Comins model and derive a simple quadratic approximation to analyze the effects of limited dispersal, refuge size, and dominance for high efficacy treatments on the rate of evolution. When a small but substantial number of heterozygotes can survive in the treated patch, a larger refuge always reduces the rate of resistance evolution. However, when dominance is small enough, the evolutionary dynamics in the refuge population, which is indirectly driven by migrants from the treated patch, mainly describes the resistance evolution in the landscape. In this case, for small refuges, increasing the refuge size will increase the rate of resistance evolution. Our analysis distils major driving forces from the model, and can provide a framework for understanding directional selection in source-sink environments. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Evolution of the magnetic field generated by the Kelvin-Helmholtz instability

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

Modestov, M.; Bychkov, V.; Brodin, G.

2014-07-15

The Kelvin-Helmholtz instability in an ionized plasma is studied with a focus on the magnetic field generation via the Biermann battery (baroclinic) mechanism. The problem is solved by using direct numerical simulations of two counter-directed flows in 2D geometry. The simulations demonstrate the formation of eddies and their further interaction and merging resulting in a large single vortex. In contrast to general belief, it is found that the instability generated magnetic field may exhibit significantly different structures from the vorticity field, despite the mathematically identical equations controlling the magnetic field and vorticity evolution. At later stages of the nonlinear instabilitymore » development, the magnetic field may keep growing even after the hydrodynamic vortex strength has reached its maximum and started decaying due to dissipation.« less

Uncovering the genetic signature of quantitative trait evolution with replicated time series data.

PubMed

Franssen, S U; Kofler, R; Schlötterer, C

2017-01-01

The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

Spatial distribution of structural defects in Cz-seeded directionally solidified silicon ingots: An etch pit study

NASA Astrophysics Data System (ADS)

Lantreibecq, A.; Legros, M.; Plassat, N.; Monchoux, J. P.; Pihan, E.

2018-02-01

The PV properties of wafers processed from Cz-seeded directionally solidified silicon ingots suffer from variable structural defects. In this study, we draw an overview on the types of structural defects encountered in the specific case of full 〈1 0 0〉 oriented growth. We found micro twins, background dislocations, and subgrains boundaries. We discuss the possible links between thermomechanical stresses and growth processes with spatial evolution of both background dislocation densities and subgrain boundaries length.

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.

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.

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.

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.

Genetics of Genome-Wide Recombination Rate Evolution in Mice from an Isolated Island.

PubMed

Wang, Richard J; Payseur, Bret A

2017-08-01

Recombination rate is a heritable quantitative trait that evolves despite the fundamentally conserved role that recombination plays in meiosis. Differences in recombination rate can alter the landscape of the genome and the genetic diversity of populations. Yet our understanding of the genetic basis of recombination rate evolution in nature remains limited. We used wild house mice ( Mus musculus domesticus ) from Gough Island (GI), which diverged recently from their mainland counterparts, to characterize the genetics of recombination rate evolution. We quantified genome-wide autosomal recombination rates by immunofluorescence cytology in spermatocytes from 240 F 2 males generated from intercrosses between GI-derived mice and the wild-derived inbred strain WSB/EiJ. We identified four quantitative trait loci (QTL) responsible for inter-F 2 variation in this trait, the strongest of which had effects that opposed the direction of the parental trait differences. Candidate genes and mutations for these QTL were identified by overlapping the detected intervals with whole-genome sequencing data and publicly available transcriptomic profiles from spermatocytes. Combined with existing studies, our findings suggest that genome-wide recombination rate divergence is not directional and its evolution within and between subspecies proceeds from distinct genetic loci. Copyright © 2017 by the Genetics Society of America.

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.

Complex Pattern Formation from Current-Driven Dynamics of Single-Layer Homoepitaxial Islands on Crystalline Conducting Substrates

NASA Astrophysics Data System (ADS)

Kumar, Ashish; Dasgupta, Dwaipayan; Maroudas, Dimitrios

2017-07-01

We report a systematic study of complex pattern formation resulting from the driven dynamics of single-layer homoepitaxial islands on surfaces of face-centered-cubic (fcc) crystalline conducting substrates under the action of an externally applied electric field. The analysis is based on an experimentally validated nonlinear model of mass transport via island edge atomic diffusion, which also accounts for edge diffusional anisotropy. We analyze the morphological stability and simulate the field-driven evolution of rounded islands for an electric field oriented along the fast edge diffusion direction. For larger-than-critical island sizes on {110 } and {100 } fcc substrates, we show that multiple necking instabilities generate complex island patterns, including not-simply-connected void-containing islands mediated by sequences of breakup and coalescence events and distributed symmetrically with respect to the electric field direction. We analyze the dependence of the formed patterns on the original island size and on the duration of application of the external field. Starting from a single large rounded island, we characterize the evolution of the number of daughter islands and their average size and uniformity. The evolution of the average island size follows a universal power-law scaling relation, and the evolution of the total edge length of the islands in the complex pattern follows Kolmogorov-Johnson-Mehl-Avrami kinetics. Our study makes a strong case for the use of electric fields, as precisely controlled macroscopic forcing, toward surface patterning involving complex nanoscale features.

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.

Direct benefits of choosing a high-fitness mate can offset the indirect costs associated with intralocus sexual conflict.

PubMed

Pischedda, Alison; Chippindale, Adam K

2017-06-01

Intralocus sexual conflict generates a cost to mate choice: high-fitness partners transmit genetic variation that confers lower fitness to offspring of the opposite sex. Our earlier work in the fruit fly, Drosophila melanogaster, revealed that these indirect genetic costs were sufficient to reverse potential "good genes" benefits of sexual selection. However, mate choice can also confer direct fitness benefits by inducing larger numbers of progeny. Here, we consider whether direct benefits through enhanced fertility could offset the costs associated with intralocus sexual conflict in D. melanogaster. Using hemiclonal analysis, we found that females mated to high-fitness males produced 11% more offspring compared to those mated to low-fitness males, and high-fitness females produced 34% more offspring than low-fitness females. These direct benefits more than offset the reduction in offspring fitness caused by intralocus sexual conflict, creating a net fitness benefit for each sex to pairing with a high-fitness partner. Our findings highlight the need to consider both direct and indirect effects when investigating the fitness impacts of mate choice. Direct fitness benefits may shelter sexually antagonistic alleles from selection, suggesting a novel mechanism for the maintenance of fitness variation. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

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.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

PubMed Central

McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

PubMed

McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.

Spatial heterogeneity and the evolution of sex in diploids.

PubMed

Agrawal, Aneil F

2009-07-01

Much of the theoretical work on the evolution of sex has focused on the effects of recombination. In diploids, segregation also occurs during sexual reproduction. Segregation breaks down some types of genetic associations that are not affected by recombination and thus influences the evolution of sex in ways that are not apparent from studying the evolution of recombination as a surrogate for sex. Here I examine the evolution of sex in diploids experiencing spatially heterogeneous selection. If divergent selection causes genetic differentiation, then migration can be a powerful force generating genetic associations that may not be favored by selection. An advantage to sex can arise from breaking down these associations. By examining modifiers of both sex and recombination, the model allows for a direct comparison of the forces acting on these related but different processes, illuminating the role of segregation. The model also includes inbreeding, which has been shown to be important for both segregation and recombination. I find that inbreeding affects the evolution of sex through segregation, not recombination. Several suggestions for empirical experiments are given.

Why the short face? Developmental disintegration of the neurocranium drives convergent evolution in neotropical electric fishes.

PubMed

Evans, Kory M; Waltz, Brandon; Tagliacollo, Victor; Chakrabarty, Prosanta; Albert, James S

2017-03-01

Convergent evolution is widely viewed as strong evidence for the influence of natural selection on the origin of phenotypic design. However, the emerging evo-devo synthesis has highlighted other processes that may bias and direct phenotypic evolution in the presence of environmental and genetic variation. Developmental biases on the production of phenotypic variation may channel the evolution of convergent forms by limiting the range of phenotypes produced during ontogeny. Here, we study the evolution and convergence of brachycephalic and dolichocephalic skull shapes among 133 species of Neotropical electric fishes (Gymnotiformes: Teleostei) and identify potential developmental biases on phenotypic evolution. We plot the ontogenetic trajectories of neurocranial phenotypes in 17 species and document developmental modularity between the face and braincase regions of the skull. We recover a significant relationship between developmental covariation and relative skull length and a significant relationship between developmental covariation and ontogenetic disparity. We demonstrate that modularity and integration bias the production of phenotypes along the brachycephalic and dolichocephalic skull axis and contribute to multiple, independent evolutionary transformations to highly brachycephalic and dolichocephalic skull morphologies.

Phenotypic convergence in bacterial adaptive evolution to ethanol stress.

PubMed

Horinouchi, Takaaki; Suzuki, Shingo; Hirasawa, Takashi; Ono, Naoaki; Yomo, Tetsuya; Shimizu, Hiroshi; Furusawa, Chikara

2015-09-03

Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. During adaptive evolution, phenotype and genotype dynamically changes; however, the relationship between these changes and associated constraints is yet to be fully elucidated. In this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and were similar among independently evolved ethanol tolerant populations, which indicate the existence of evolutionary constraints in the dynamics of adaptive evolution. Furthermore, the contribution of identified mutations in one of the tolerant strains was evaluated using site-directed mutagenesis. The result demonstrated that the introduction of all identified mutations cannot fully explain the observed tolerance in the tolerant strain. The results demonstrated that the convergence of adaptive phenotypic changes and diverse genotypic changes, which suggested that the phenotype-genotype mapping is complex. The integration of transcriptome and genome data provides a quantitative understanding of evolutionary constraints.

An Autonomous System for Experimental Evolution of Microbial Cultures: Test Results Using Ultraviolet-C Radiation and Escherichia Coli.

NASA Technical Reports Server (NTRS)

Ouandji, Cynthia; Wang, Jonathan; Arismendi, Dillon; Lee, Alonzo; Blaich, Justin; Gentry, Diana

2017-01-01

At its core, the field of microbial experimental evolution seeks to elucidate the natural laws governing the history of microbial life by understanding its underlying driving mechanisms. However, observing evolution in nature is complex, as environmental conditions are difficult to control. Laboratory-based experiments for observing population evolution provide more control, but manually culturing and studying multiple generations of microorganisms can be time consuming, labor intensive, and prone to inconsistency. We have constructed a prototype, closed system device that automates the process of directed evolution experiments in microorganisms. It is compatible with any liquid microbial culture, including polycultures and field samples, provides flow control and adjustable agitation, continuously monitors optical density (OD), and can dynamically control environmental pressures such as ultraviolet-C (UV-C) radiation and temperature. Here, the results of the prototype are compared to iterative exposure and survival assays conducted using a traditional hood, UV-C lamp, and shutter system.

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

PubMed

Turcotte, Martin M; Reznick, David N; Daniel Hare, J

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

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.

Evolution and dynamics of shear-layer structures in near-wall turbulence

NASA Technical Reports Server (NTRS)

Johansson, Arne V.; Alfredsson, P. H.; Kim, John

1991-01-01

Near-wall flow structures in turbulent shear flows are analyzed, with particular emphasis on the study of their space-time evolution and connection to turbulence production. The results are obtained from investigation of a database generated from direct numerical simulation of turbulent channel flow at a Reynolds number of 180 based on half-channel width and friction velocity. New light is shed on problems associated with conditional sampling techniques, together with methods to improve these techniques, for use both in physical and numerical experiments. The results clearly indicate that earlier conceptual models of the processes associated with near-wall turbulence production, based on flow visualization and probe measurements need to be modified. For instance, the development of asymmetry in the spanwise direction seems to be an important element in the evolution of near-wall structures in general, and for shear layers in particular. The inhibition of spanwise motion of the near-wall streaky pattern may be the primary reason for the ability of small longitudinal riblets to reduce turbulent skin friction below the value for a flat surface.

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

PubMed Central

van Hal, Sebastiaan J.; Steen, Jason A.; Espedido, Björn A.; Grimmond, Sean M.; Cooper, Matthew A.; Holden, Matthew T. G.; Bentley, Stephen D.; Gosbell, Iain B.; Jensen, Slade O.

2014-01-01

Objectives To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure. Methods The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed. Results Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure. Conclusions This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture ‘bias’ and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies. PMID:24047554

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

PubMed

van Hal, Sebastiaan J; Steen, Jason A; Espedido, Björn A; Grimmond, Sean M; Cooper, Matthew A; Holden, Matthew T G; Bentley, Stephen D; Gosbell, Iain B; Jensen, Slade O

2014-02-01

To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure. The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed. Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure. This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture 'bias' and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies.

Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs.

PubMed

Klaus, Sebastian; Mendoza, José C E; Liew, Jia Huan; Plath, Martin; Meier, Rudolf; Yeo, Darren C J

2013-04-23

This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations of Sundathelphusa freshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722-271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits-just like constructive traits-is most likely driven by strong directional selection.

Investigating yellow dung fly body size evolution in the field: Response to climate change?

PubMed

Blanckenhorn, Wolf U

2015-08-01

Uncovering genetic responses to selection in wild populations typically requires tracking individuals over generations and use of animal models. Our group monitored the body size of one Swiss Yellow Dung Fly (Scathophaga stercoraria; Diptera: Scathophagidae) field population over 15 years, including intermittent common-garden rearing in the laboratory to assess body size with minimized environmental and maximized genetic variation. Contrary to expectations based on repeated heritability and phenotypic selection assessments over the years (reported elsewhere), field body sizes declined by >10% and common-garden laboratory sizes by >5% from 1993 to 2009. Our results confirm the temperature-size rule (smaller when warmer) and, albeit entirely correlational, could be mediated by climate change, as over this period mean temperature at the site increased by 0.5°C, although alternative systematic environmental changes cannot be entirely excluded. Monitoring genetic responses to selection in wild invertebrate populations is thus possible, though indirect, and wild populations may evolve in directions not consistent with strongly positive directional selection favoring large body size. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

PubMed

Barrera-Redondo, Josué; Ramírez-Barahona, Santiago; Eguiarte, Luis E

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Adult Education: Evolution and Achievements in a Developing Field of Study.

ERIC Educational Resources Information Center

Peters, John M.; And Others

This volume is a companion to "Adult Education: Outlines of an Emerging Field of University Study" (more commonly known as "the black book"), a classic work published in 1964. It explores the developments, accomplishments, and changes in the field since 1964 and charts new directions for research, theory, and practice in the study of adult…

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Kolmogorov Flow in Three Dimensions

NASA Technical Reports Server (NTRS)

Shebalin, John V.; Woodruff, Stephen L.

1996-01-01

A numerical study of the long-time evolution of incompressible Navier-Stokes turbulence forced at a single long-wavelength Fourier mode, i.e., a Kolmogorov flow, has been completed. The boundary conditions are periodic in three dimensions and the forcing is effected by imposing a steady, two-dimensional, sinusoidal shear velocity which is directed along the x-direction and varies along the z-direction. A comparison with experimental data shows agreement with measured cross-correlations of the turbulent velocity components which lie in the mean-flow plane. A statistical analysis reveals that the shear-driven turbulence studied here has significant spectral anisotropy which increases with wave number.

Friction-induced nano-structural evolution of graphene as a lubrication additive

NASA Astrophysics Data System (ADS)

Zhao, Jun; Mao, Junyuan; Li, Yingru; He, Yongyong; Luo, Jianbin

2018-03-01

Graphene has attracted enormous attention in the field of lubrication based on its excellent physical and chemical properties. Although many studies have obtained thermally or chemically- exfoliated graphene and investigated their wide and important application, few studies have reported their physical nano-structural evolution under friction. In this study, we investigated the lubrication properties of graphene additives with different layer numbers and interlayer spacing by exfoliating. The additives with a higher degrees of exfoliation changed to ordering under friction, and had better lubrication properties, while that with a lower degrees exhibited obvious structural defects and high friction. Therefore, the original degrees of exfoliation plays a key role in the structural evolution of graphene and superior lubrication can be achieved through the physical nano-structure changing to ordering, even graphitization. Furthermore, the ordered tribofilm on the frictional interfaces was parallel to the sliding direction, meaning the highly exfoliated graphene indeed reaching slippage between its layers, which wasn't experimentally discovered in previous studies. This work provides a new understanding of the relationship between friction-induced nano-structural evolution and lubrication properties of graphene as a lubrication additive, and has great potential for the structural design of graphene as a lubrication additive.

The concurrent evolution of cooperation and the population structures that support it.

PubMed

Powers, Simon T; Penn, Alexandra S; Watson, Richard A

2011-06-01

The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Convergence of temperate and tropical stream fish assemblages

EPA Science Inventory

The hypothesis of convergence takes the deterministic view that community (or assemblage) structure can be predicted from the environment, and that the environment is expected to drive evolution in a predictable direction. Here we present results of a comparative study of freshwa...

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.

The evolution and distribution of life in the Precambrian eon-global perspective and the Indian record.

PubMed

Sharma, M; Shukla, Y

2009-11-01

The discovery of Precambrian microfossils in 1954 opened a new vista of investigations in the field of evolution of life. Although the Precambrian encompasses 87% of the earth's history, the pace of organismal evolution was quite slow. The life forms as categorised today in the three principal domains viz. the Bacteria, the Archaea and the Eucarya evolved during this period. In this paper, we review the advancements made in the Precambrian palaeontology and its contribution in understanding the evolution of life forms on earth. These studies have enriched the data base on the Precambrian life. Most of the direct evidence includes fossil prokaryotes, protists, advanced algal fossils, acritarchs, and the indirect evidence is represented by the stromatolites, trace fossils and geochemical fossils signatures. The Precambrian fossils are preserved in the form of compressions, impressions, and permineralized and biomineralized remains.

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 Nature, Number and Evolution of Hot-Spots in Ammonium Nitrate

NASA Astrophysics Data System (ADS)

Proud, W. G.; Kirby, I. J.; Field, J. E.

2004-07-01

Ammonium nitrate (AN) is a commonly used fertiliser and also one component of the most widely used explosive in the world AN: Fuel Oil mixtures. This study uses a combination of high-speed photography, UV/Visible spectroscopy and modelling. By using thin beds, <0.5 mm thick, with a porosity of 22%vol the number and evolution of hot-spots in ammonium nitrate are monitored directly under dynamic loading conditions. The critical conditions for ignition are defined in terms of energy localisation mechanisms, temperature rise and inter-communication between the hot-spots.

Evolution of community structure in the world trade web

NASA Astrophysics Data System (ADS)

Tzekina, I.; Danthi, K.; Rockmore, D. N.

2008-06-01

In this note we study the bilateral merchandise trade flows between 186 countries over the 1948 2005 period using data from the International Monetary Fund. We use the network visualization package Pajek to identify network structure and behavior across thresholds and over time. In particular, we focus on the evolution of trade “islands” in a world trade network in which countries are linked with directed edges weighted according to the fraction of total dollars sent from one country to another. We find mixed evidence for globalization.

What Pinnipeds Have to Say about Human Speech, Music, and the Evolution of Rhythm.

PubMed

Ravignani, Andrea; Fitch, W Tecumseh; Hanke, Frederike D; Heinrich, Tamara; Hurgitsch, Bettina; Kotz, Sonja A; Scharff, Constance; Stoeger, Angela S; de Boer, Bart

2016-01-01

Research on the evolution of human speech and music benefits from hypotheses and data generated in a number of disciplines. The purpose of this article is to illustrate the high relevance of pinniped research for the study of speech, musical rhythm, and their origins, bridging and complementing current research on primates and birds. We briefly discuss speech, vocal learning, and rhythm from an evolutionary and comparative perspective. We review the current state of the art on pinniped communication and behavior relevant to the evolution of human speech and music, showing interesting parallels to hypotheses on rhythmic behavior in early hominids. We suggest future research directions in terms of species to test and empirical data needed.

What Pinnipeds Have to Say about Human Speech, Music, and the Evolution of Rhythm

PubMed Central

Ravignani, Andrea; Fitch, W. Tecumseh; Hanke, Frederike D.; Heinrich, Tamara; Hurgitsch, Bettina; Kotz, Sonja A.; Scharff, Constance; Stoeger, Angela S.; de Boer, Bart

2016-01-01

Research on the evolution of human speech and music benefits from hypotheses and data generated in a number of disciplines. The purpose of this article is to illustrate the high relevance of pinniped research for the study of speech, musical rhythm, and their origins, bridging and complementing current research on primates and birds. We briefly discuss speech, vocal learning, and rhythm from an evolutionary and comparative perspective. We review the current state of the art on pinniped communication and behavior relevant to the evolution of human speech and music, showing interesting parallels to hypotheses on rhythmic behavior in early hominids. We suggest future research directions in terms of species to test and empirical data needed. PMID:27378843

Robotic instrumentation: Evolution and microsurgical applications

PubMed Central

Parekattil, Sijo J.; Moran, Michael E.

2010-01-01

This article presents a review of the history and evolution of robotic instrumentation and its applications in urology. A timeline for the evolution of robotic instrumentation is presented to better facilitate an understanding of our current-day applications. Some new directions including robotic microsurgical applications (robotic assisted denervation of the spermatic cord for chronic orchialgia and robotic assisted vasectomy reversal) are presented. There is a paucity of prospective comparative effectiveness studies for a number of robotic applications. However, right or wrong, human nature has always led to our infatuation with the concept of using tools to meet our needs. This chapter is a brief tribute to where we have come from and where we may be potentially heading in the field of robotic assisted urologic surgery. PMID:21116362

Fitness consequences of larval traits persist across the metamorphic boundary.

PubMed

Crean, Angela J; Monro, Keyne; Marshall, Dustin J

2011-11-01

Metamorphosis is thought to provide an adaptive decoupling between traits specialized for each life-history stage in species with complex life cycles. However, an increasing number of studies are finding that larval traits can carry-over to influence postmetamorphic performance, suggesting that these life-history stages may not be free to evolve independently of each other. We used a phenotypic selection framework to compare the relative and interactive effects of larval size, time to hatching, and time to settlement on postmetamorphic survival and growth in a marine invertebrate, Styela plicata. Time to hatching was the only larval trait found to be under directional selection, individuals that took more time to hatch into larvae survived better after metamorphosis but grew more slowly. Nonlinear selection was found to act on multivariate trait combinations, once again acting in opposite directions for selection acting via survival and growth. Individuals with above average values of larval traits were most likely to survive, but surviving individuals with intermediate larval traits grew to the largest size. These results demonstrate that larval traits can have multiple, complex fitness consequences that persist across the metamorphic boundary; and thus postmetamorphic selection pressures may constrain the evolution of larval traits. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

PubMed

Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

2013-11-01

Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

The Reel Deal In 3D: The Spatio-Temporal Evolution of YSO Jets

NASA Astrophysics Data System (ADS)

Frank, Adam

2014-10-01

Jets are a ubiquitous phenomena in astrophysics, though in most cases their central engines are unresolvable. Thus the structure of the jets often acts as a proxy for understanding the objects creating them. Jets are also of interest in their own right, serving as critical examples of rapidly evolving astrophysical magnetized plasma systems. And while millions of CPU hours {at least} have been spent simulating the kinds of astrophysical plasma dynamics that occur routinely in jets, we rarely have had the chance to study their real-time evolution. In this proposal we seek to use a unique multi-epoch HST dataset of protostellar jets to carry forward an innovative theoretical, numerical and laboratory-based study of magnetized outflows and the plasma processes which determine their evolution. Our work will make direct and detailed contact with these HST data sets and will articulate newly-observed features of jet dynamics that have not been possible to explore before. Using numerical simulations and laboratory plasma studies we seek to articulate the full 3-D nature of new behaviors seen in the HST data. Our collaboration includes the use of scaled laboratory plasma experiments with hypersonic magnetized radiative jets. The MHD experiments have explored how jets break up into clumps via kink-mode instabilities. Therefore such experiments are directly relevant to the initial conditions in our models.

The emphasis given to evolution in state science standards: A lever for change in evolution education?

NASA Astrophysics Data System (ADS)

Skoog, Gerald; Bilica, Kimberly

2002-07-01

This study analyzed the science frameworks of 49 states and the District of Colombia to determine the emphasis given to evolution in these documents at the middle and secondary levels. These concepts were species evolve over time, speciation, diversity of life, descent with modification from common ancestry, evidence of evolution, natural selection, pace and direction of evolution, and human evolution. Collectively, the 50 science frameworks emphasized evolution in a manner that suggests that if the public's support for standards-based curricula is a reality, the study of evolution will be emphasized in an unprecedented manner in the nation's schools in the near future. However, all concepts were not emphasized equally in these documents. For example, human evolution was included in only seven documents. The word evolution is absent from some standards. Despite these negatives, recent actions to improve existing standards or to adopt new standards that emphasize evolution have occurred. The metaphor lever of change is often used in the context of school reform. This metaphor suggests a simple system where one change can result in a desired outcome. However, in classrooms where curriculum decisions evolve constantly, multiple factors interact and reinforce one another in response to both internal and external contingencies that emerge. Educational change can not be reduced to a simple linear cause/effect situation. The change process involved is nonlinear where what goes in is not proportional to what comes out because of feedback loops and other factors that complicate results. This nonlinearity is reflected in the varied responses of teachers to specific contingencies. Yet, systems can be changed and nudged towards a structure where desired outcomes will emerge. Judicial rulings indicating that the teaching of evolution cannot be prohibited or equal time for creationism mandated, improved coverage of evolution in secondary school biology textbooks, the negative response of many leaders, scientists, organizations, and editorial writers to the 1999 decision of the Kansas State Board of Education to deemphasize and misrepresent evolution in the state's science standards, and the emphasis given to evolution in the standards reviewed for this study, all coalesce to provide needed support for administrators and teachers who are striving to create science curricula that emphasize evolution in a manner commensurate with its importance in understanding the natural world and our place within it.

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

Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses.

PubMed

Pievani, Telmo; Serrelli, Emanuele

2011-01-01

Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.

Predicting Position on Teaching Creationism (Instead of Evolution) in Public Schools

ERIC Educational Resources Information Center

Lac, Andrew; Hemovich, Vanessa; Himelfarb, Igor

2010-01-01

The federal government has repeatedly denied the introduction of creationism into public schools as it is a direct violation of the separation of church and state. Little is known about those who would opt to eliminate evolution in scientific curriculum altogether. The authors examined this more extreme anti-evolution perspective in a nationally…

A discrete mathematical model of the dynamic evolution of a transportation network

NASA Astrophysics Data System (ADS)

Malinetskii, G. G.; Stepantsov, M. E.

2009-09-01

A dynamic model of the evolution of a transportation network is proposed. The main feature of this model is that the evolution of the transportation network is not a process of centralized transportation optimization. Rather, its dynamic behavior is a result of the system self-organization that occurs in the course of the satisfaction of needs in goods transportation and the evolution of the infrastructure of the network nodes. Nonetheless, the possibility of soft control of the network evolution direction is taken into account.

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.

The macroevolution of size and complexity in insect male genitalia

PubMed Central

Rudoy, Andrey

2016-01-01

The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables. PMID:27114865

Non-Dissipative Structural Evolutions in Granular Materials

NASA Astrophysics Data System (ADS)

Pouragha, Mehdi; Wan, Richard

2017-06-01

The structure of the contact network in granular assemblies can evolve due to either dissipative mechanisms such as sliding at contact points, or non-dissipative mechanisms through the phenomenon of contact gain and loss. Being associated with negligible deformations, non-dissipative mechanisms is actually active even in the small strain range of 10-3, especially in the case of densely packed assemblies. Hence, from a constitutive modelling point of view, it is crucial to be able to estimate such non-dissipative evolutions since both elastic and plastic properties of granular assemblies highly depend on contact network characteristics. The current study proposes an analytical scheme that allows us to estimate the non-dissipative contact gain/loss regime in terms of directional changes in the average contact force. The probability distribution of contact forces is used to compute the number of lost contact for each direction. Similarly, the number of newly formed contacts is estimated by considering the probability distribution of the gap between neighbouring particles. Based on the directional contact gain/loss computed, the changes in coordination number and fabric anisotropy can be found which, together with statistical treatments of Love-Weber stress expression, form a complete system of equations describing the evolution of other controlling microvariables. Finally, the results of the calculations have been compared with DEM simulations which verify the accuracy of the proposed scheme.

Quantum gates by periodic driving

PubMed Central

Shi, Z. C.; Wang, W.; Yi, X. X.

2016-01-01

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions—it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation. PMID:26911900

Experimental Overview of Direct Photon Results in Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Novitzky, Norbert

2016-07-01

Direct photons are color blind probes and thus they provide unique opportunities to study the colored medium created in heavy ion collisions. There are many different sources of direct photons each probing different physics processes as the system evolves. In basic 2 → 2 processes the prompt photons from primary hard scatterings offer the most precise measurements of the outgoing parton energy in the opposite direction. In heavy ion collisions the created medium emits photons as thermal radiation, whose rate and anisotropies provide a unique prospective on the properties and evolution of the system. Recent results on direct photons from the LHC and RHIC experiments are briefly summarized in this paper.

Numerical Study on the Tensile Behavior of 3D Four Directional Cylindrical Braided Composite Shafts

NASA Astrophysics Data System (ADS)

Zhao, Guoqi; Wang, Jiayi; Hao, Wenfeng; Liu, Yinghua; Luo, Ying

2017-10-01

The tensile behavior of 3D four directional cylindrical braided composite shafts was analyzed with the numerical method. The unit cell models for the 3D four directional cylindrical braided composite shafts with various braiding angles were constructed with ABAQUS. Hashin's failure criterion was used to analyze the tensile strength and the damage evolution of the unit cells. The influence of the braiding angle on the tensile behavior of the 3D four directional cylindrical braided composite shafts was analyzed. The numerical results showed that the tensile strength along the braiding direction increased as the braiding angle decreased. These results should play an integral role in the design of braiding composites shafts.

The validity of multiphase DNS initialized on the basis of single--point statistics

NASA Astrophysics Data System (ADS)

Subramaniam, Shankar

1999-11-01

A study of the point--process statistical representation of a spray reveals that single--point statistical information contained in the droplet distribution function (ddf) is related to a sequence of single surrogate--droplet pdf's, which are in general different from the physical single--droplet pdf's. The results of this study have important consequences for the initialization and evolution of direct numerical simulations (DNS) of multiphase flows, which are usually initialized on the basis of single--point statistics such as the average number density in physical space. If multiphase DNS are initialized in this way, this implies that even the initial representation contains certain implicit assumptions concerning the complete ensemble of realizations, which are invalid for general multiphase flows. Also the evolution of a DNS initialized in this manner is shown to be valid only if an as yet unproven commutation hypothesis holds true. Therefore, it is questionable to what extent DNS that are initialized in this manner constitute a direct simulation of the physical droplets.

A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

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

Wu, Meiye

The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infectmore » and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.« less

On mechanical mechanism of damage evolution in articular cartilage.

PubMed

Men, Yu-Tao; Jiang, Yan-Long; Chen, Ling; Zhang, Chun-Qiu; Ye, Jin-Duo

2017-09-01

Superficial lesions of cartilage are the direct indication of osteoarthritis. To investigate the mechanical mechanism of cartilage with micro-defect under external loading, a new plain strain numerical model with micro-defect was proposed and damage evolution progression in cartilage over time has been simulated, the parameter were studied including load style, velocity of load and degree of damage. The new model consists of the hierarchical structure of cartilage and depth-dependent arched fibers. The numerical results have shown that not only damage of the cartilage altered the distribution of the stress but also matrix and fiber had distinct roles in affecting cartilage damage, and damage in either matrix or fiber could promote each other. It has been found that the superficial cracks in cartilage spread preferentially along the tangent direction of the fibers. It is the arched distribution form of fibers that affects the crack spread of cartilage, which has been verified by experiment. During the process of damage evolution, its extension direction and velocity varied constantly with the damage degree. The rolling load could cause larger stress and strain than sliding load. Strain values of the matrix initially increased and then decreased gradually with the increase of velocity, and velocity had a greater effect on matrix than fibers. Damage increased steadily before reaching 50%, sharply within 50 to 85%, and smoothly and slowly after 85%. The finding of the paper may help to understand the mechanical mechanism why the cracks in cartilage spread preferentially along the tangent direction of the fibers. Copyright © 2017 Elsevier B.V. All rights reserved.

Darwin's legacy II: why biology is not physics, or why it has taken a century to see the dependence of genes on the environment.

PubMed

Singh, Rama S

2015-01-01

Genes and environment make the organism. Darwin stood firm in his denial of any direct role of environment in the modification of heredity. His theory of evolution heralded two debates: one about the importance and adequacy of natural selection as the main mechanism of evolution, and the other about the role of genes versus environment in the modification of phenotype and evolution. Here, I provide an overview of the second debate and show that the reasons for the gene versus environment battle were twofold: first, there was confusion about the role of environment in modifying the inheritance of a trait versus the evolution of that trait, and second, there was misunderstanding about the meaning of environment and its interaction with genes in the production of phenotypes. It took nearly a century to see that environment does not directly affect the inheritance of a phenotype (i.e., its heredity), but it is nevertheless the primary mover of phenotypic evolution. Effects of genes and environment are not separate but interdependent. One cannot separate the effect of genes from that of environment, or nature from nurture. To answer the question posed in the title, it is partly because the 20th century has been a century of unending progress in genetics. But also because unlike physics, biology is not colorblind; progress in biology has often been delayed beyond the Kuhnian paradigm change due to built-in interest in negating the influence of environment. Those who are against evolution, of course, cannot be expected to understand the role of environment in evolution. Those for it, many biologists included, believing in the supremacy of genes empowers them by giving adaptation a solely gene-directed (self-driven) "teleological" interpretation.

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

[An increase in efficiency of adaptations and a weakening of organism protective reactions in the process of biological evolution].

PubMed

Ivanov, K P

2014-01-01

The main direction of evolution of living organisms is development of the central nervous system and sense organ, an increase of energy exchange development of homoiothermia, development of the more and more complex forms of behavior, an increase in energy expenditure in connection with an increase of the organism activity, and development of adaptation to the habitat. Such fundamental processes were subjected and have been subjected to numerous studies and discussions. However, in different animals there exist different species peculiarities of evolution of physiological functions, from which finally formed are fundamental evolutionary processes. We studied some of these specific processes by dividing them into two categories. The first category is "Increase of efficiency of adaptation" in development of biological evolution. By this term we mean development of amazing by perfection specific physiological mechanisms of adaptive character. The second category is "Weakening of protective organism reactions". By this we understand disturbance of protective mechanisms of the organism immune system, discoordination of movement of leukocytes along microvessels, the absence of efficient collateral circulation in brain and in heart, etc.

Temporal and spatial evolution characteristics of water environment quality in Heze

NASA Astrophysics Data System (ADS)

Gao, Qian; Zhao, Qiang; Li, Xiumei

2018-06-01

The evolution of water environment is relatively complicated. The study of its characteristics is helpful to grasp the general direction of spatial and temporal evolution of water environment in Heze city, and to carry out water resources development and water environment protection more rationally. The comprehensive pollution index method for calculation, and the observed data are handled by Excel. In order to facilitate the analysis of the basin, Arcgis is utilized to map the watershed map. In addition, for the spatial evolution, surfer12 is used to analyze the spatial evolution characteristics the spatial evolution, and to draw the pictures of spatial evolution of chemical oxygen demand and water quality evolution. The study shows that: (1) In Heze, the quality of water environment has been improved year by year from 2006 to 2013. In 2014, the water environment has deteriorated. The content of volatile phenol has increased greatly, and the evolution trend of COD is close to the trend of the comprehensive pollution index. (2) In terms of Spatial state of water environment, the water quality of Zhuzhao New River and Wanfu River is poor, and Dongyu River water quality is better. Zhuzhao New River and Wanfu River water qualityis often worse than grade V or V, and Dongyu River water quality is mostly maintained in the grade Ⅳ. Through the analysis on the spatial revolution characteristics of water quality and chemical oxygen demand(COD),as a result, water quality is poor in the northern region,and the water quality in the southern region is better in Heze. Although the water quality has changed in recent years, the overall pattern is relatively stable.

Intrasexual competition facilitates the evolution of alternative mating strategies in a colour polymorphic fish.

PubMed

Hurtado-Gonzales, Jorge L; Uy, J Albert C

2010-12-23

Intense competition for access to females can lead to males exploiting different components of sexual selection, and result in the evolution of alternative mating strategies (AMSs). Males of Poecilia parae, a colour polymorphic fish, exhibit five distinct phenotypes: drab-coloured (immaculata), striped (parae), structural-coloured (blue) and carotenoid-based red and yellow morphs. Previous work indicates that immaculata males employ a sneaker strategy, whereas the red and yellow morphs exploit female preferences for carotenoid-based colours. Mating strategies favouring the maintenance of the other morphs remain to be determined. Here, we report the role of agonistic male-male interactions in influencing female mating preferences and male mating success, and in facilitating the evolution of AMSs. Our study reveals variation in aggressiveness among P. parae morphs during indirect and direct interactions with sexually receptive females. Two morphs, parae and yellow, use aggression to enhance their mating success (i.e., number of copulations) by 1) directly monopolizing access to females, and 2) modifying female preferences after winning agonistic encounters. Conversely, we found that the success of the drab-coloured immaculata morph, which specializes in a sneak copulation strategy, relies in its ability to circumvent both male aggression and female choice when facing all but yellow males. Strong directional selection is expected to deplete genetic variation, yet many species show striking genetically-based polymorphisms. Most studies evoke frequency dependent selection to explain the persistence of such variation. Consistent with a growing body of evidence, our findings suggest that a complex form of balancing selection may alternatively explain the evolution and maintenance of AMSs in a colour polymorphic fish. In particular, this study demonstrates that intrasexual competition results in phenotypically distinct males exhibiting clear differences in their levels of aggression to exclude potential sexual rivals. By being dominant, the more aggressive males are able to circumvent female mating preferences for attractive males, whereas another male type incorporates subordinate behaviours that allow them to circumvent male aggression and female mating preferences. Together, these and previous results indicate that exploiting different aspects of social interactions may allow males to evolve distinct mating strategies and thus the long term maintenance of polymorphisms within populations.

Hormonally active phytochemicals and vertebrate evolution.

PubMed

Lambert, Max R; Edwards, Thea M

2017-06-01

Living plants produce a diversity of chemicals that share structural and functional properties with vertebrate hormones. Wildlife species interact with these chemicals either through consumption of plant materials or aquatic exposure. Accumulating evidence shows that exposure to these hormonally active phytochemicals (HAPs) often has consequences for behavior, physiology, and fecundity. These fitness effects suggest there is potential for an evolutionary response by vertebrates to HAPs. Here, we explore the toxicological HAP-vertebrate relationship in an evolutionary framework and discuss the potential for vertebrates to adapt to or even co-opt the effects of plant-derived chemicals that influence fitness. We lay out several hypotheses about HAPs and provide a path forward to test whether plant-derived chemicals influence vertebrate reproduction and evolution. Studies of phytochemicals with direct impacts on vertebrate reproduction provide an obvious and compelling system for studying evolutionary toxicology. Furthermore, an understanding of whether animal populations evolve in response to HAPs could provide insightful context for the study of rapid evolution and how animals cope with chemical agents in the environment.

Houston managed lanes case study : the evolution of the Houston HOV system

DOT National Transportation Integrated Search

2003-09-01

A nine-mile contraflow High Occupancy Vehicle (HOV) lane on the I-45 North Freeway in Houston, Texas was implemented as a demonstration project in 1979. This demonstration borrowed an off-peak direction traffic lane for use by buses and vanpools in t...

A Transmission Electron Microscope Investigation of Space Weathering Effects in Hayabusa Samples

NASA Technical Reports Server (NTRS)

Keller, Lindsay P.; Berger, Eve L.

2014-01-01

The Hayabusa mission to asteroid 25143 Itokawa successfully returned the first direct samples of the regolith from the surface of an asteroid. The Hayabusa samples thus present a special opportunity to directly investigate the evolution of asteroidal surfaces, from the development of the regolith to the study of the more complex effects of space weathering. Here we describe the mineralogy, microstructure and composition of three Hayabusa mission particles using transmission electron microscope (TEM) techniques

Peak broadening and peak shift pole figures investigations by STRESS-SPEC diffractometer at FRM II

NASA Astrophysics Data System (ADS)

Gan, W. M.; Randau, C.; Hofmann, M.; Brokmeier, H. G.; Mueller, M.; Schreyer, A.

2012-02-01

This paper studied for the first time peak intensity, peak position and FHWM pole figures with one time measurement at the neutron diffractometer STRESS-SPEC via in-situ tensile deformation on austenitic steel. Fibre distribution with its evolution from central tensile direction to normal direction of these three kinds of pole figures was obtained. Variation of peak position and FWHM can be correlated to the reorientation of the texture component.

Directional selection in temporally replicated studies is remarkably consistent.

PubMed

Morrissey, Michael B; Hadfield, Jarrod D

2012-02-01

Temporal variation in selection is a fundamental determinant of evolutionary outcomes. A recent paper presented a synthetic analysis of temporal variation in selection in natural populations. The authors concluded that there is substantial variation in the strength and direction of selection over time, but acknowledged that sampling error would result in estimates of selection that were more variable than the true values. We reanalyze their dataset using techniques that account for the necessary effect of sampling error to inflate apparent levels of variation and show that directional selection is remarkably constant over time, both in magnitude and direction. Thus we cannot claim that the available data support the existence of substantial temporal heterogeneity in selection. Nonetheless, we conject that temporal variation in selection could be important, but that there are good reasons why it may not appear in the available data. These new analyses highlight the importance of applying techniques that estimate parameters of the distribution of selection, rather than parameters of the distribution of estimated selection (which will reflect both sampling error and "real" variation in selection); indeed, despite availability of methods for the former, focus on the latter has been common in synthetic reviews of the aspects of selection in nature, and can lead to serious misinterpretations. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

In the Shadow of Intelligent Design: The Teaching of Evolution

ERIC Educational Resources Information Center

Cleaves, Anna; Toplis, Rob

2007-01-01

The theory of evolution by natural selection is contrasted in the media, and in some schools, with creationist ideas, in which the diversity of life on Earth is said to be the result of direct species-by-species creation, not of evolution. More recently, the Intelligent Design movement has claimed that "certain features of the universe and of…

Flow Modulation and Force Control of Flapping Wings

DTIC Science & Technology

2014-10-29

evolution of which reflect the wing morphology and kinematics. While the near-wake vortex system directly reflects the action of the wing on the...at 8 different stroke positions, which demonstrate the evolution of the vortex wake structure. The contour plot of Z vorticity at X-Y plane (Z...20 Figure 14. Smoke patterns showing the evolution of the flow structure in an

Directed evolution of cell size in Escherichia coli.

PubMed

Yoshida, Mari; Tsuru, Saburo; Hirata, Naoko; Seno, Shigeto; Matsuda, Hideo; Ying, Bei-Wen; Yomo, Tetsuya

2014-12-17

In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes

PubMed Central

Holzman, Roi; Collar, David C.; Price, Samantha A.; Hulsey, C. Darrin; Thomson, Robert C.; Wainwright, Peter C.

2012-01-01

Morphological diversification does not proceed evenly across the organism. Some body parts tend to evolve at higher rates than others, and these rate biases are often attributed to sexual and natural selection or to genetic constraints. We hypothesized that variation in the rates of morphological evolution among body parts could also be related to the performance consequences of the functional systems that make up the body. Specifically, we tested the widely held expectation that the rate of evolution for a trait is negatively correlated with the strength of biomechanical trade-offs to which it is exposed. We quantified the magnitude of trade-offs acting on the morphological components of three feeding-related functional systems in four radiations of teleost fishes. After accounting for differences in the rates of morphological evolution between radiations, we found that traits that contribute more to performance trade-offs tend to evolve more rapidly, contrary to the prediction. While ecological and genetic factors are known to have strong effects on rates of phenotypic evolution, this study highlights the role of the biomechanical architecture of functional systems in biasing the rates and direction of trait evolution. PMID:21993506

Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes.

PubMed

Holzman, Roi; Collar, David C; Price, Samantha A; Hulsey, C Darrin; Thomson, Robert C; Wainwright, Peter C

2012-04-07

Morphological diversification does not proceed evenly across the organism. Some body parts tend to evolve at higher rates than others, and these rate biases are often attributed to sexual and natural selection or to genetic constraints. We hypothesized that variation in the rates of morphological evolution among body parts could also be related to the performance consequences of the functional systems that make up the body. Specifically, we tested the widely held expectation that the rate of evolution for a trait is negatively correlated with the strength of biomechanical trade-offs to which it is exposed. We quantified the magnitude of trade-offs acting on the morphological components of three feeding-related functional systems in four radiations of teleost fishes. After accounting for differences in the rates of morphological evolution between radiations, we found that traits that contribute more to performance trade-offs tend to evolve more rapidly, contrary to the prediction. While ecological and genetic factors are known to have strong effects on rates of phenotypic evolution, this study highlights the role of the biomechanical architecture of functional systems in biasing the rates and direction of trait evolution.

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.

Directed evolution of GH43 ß-xylosidase XylBH43 thermal stability and L186 saturation

USDA-ARS?s Scientific Manuscript database

Directed evolution of ß-xylosidase XylBH43 using DNA family shuffling identified three mutations R45K, M69P, and L186Y that affect thermal stability parameter Kt0.5 by -1.8±0.1 º C, 1.7±0.3 º C, and 3.2±0.4 º C, respectively. In addition, a cluster of four mutations near hairpin loop-D83 improved K...

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.

Distinguishing between direct and indirect directional couplings in large oscillator networks: Partial or non-partial phase analyses?

NASA Astrophysics Data System (ADS)

Rings, Thorsten; Lehnertz, Klaus

2016-09-01

We investigate the relative merit of phase-based methods for inferring directional couplings in complex networks of weakly interacting dynamical systems from multivariate time-series data. We compare the evolution map approach and its partialized extension to each other with respect to their ability to correctly infer the network topology in the presence of indirect directional couplings for various simulated experimental situations using coupled model systems. In addition, we investigate whether the partialized approach allows for additional or complementary indications of directional interactions in evolving epileptic brain networks using intracranial electroencephalographic recordings from an epilepsy patient. For such networks, both direct and indirect directional couplings can be expected, given the brain's connection structure and effects that may arise from limitations inherent to the recording technique. Our findings indicate that particularly in larger networks (number of nodes ≫10 ), the partialized approach does not provide information about directional couplings extending the information gained with the evolution map approach.

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

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

Taheri, M; Teslich, N; Lu, J P

An in situ method for studying the role of laser energy on the microstructural evolution of polycrystalline Si is presented. By monitoring both laser energy and microstructural evolution simultaneously in the dynamic transmission electron microscope, information on grain size and defect concentration can be correlated directly with processing conditions. This proof of principle study provides fundamental scientific information on the crystallization process that has technological importance for the development of thin film transistors. In conclusion, we successfully developed a method for studying UV laser processing of Si films in situ on nanosecond time scales, with ultimate implications for TFT applicationmore » improvements. In addition to grain size distribution as a function of laser energy density, we found that grain size scaled with laser energy in general. We showed that nanosecond time resolution allowed us to see the nucleation and growth front during processing, which will help further the understanding of microstructural evolution of poly-Si films for electronic applications. Future studies, coupled with high resolution TEM, will be performed to study grain boundary migration, intergranular defects, and grain size distribution with respect to laser energy and adsorption depth.« less

The rule of declining adaptability in microbial evolution experiments

PubMed Central

Couce, Alejandro; Tenaillon, Olivier A.

2015-01-01

One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research. PMID:25815007

Direct Numerical Simulation of Fingering Instabilities in Coating Flows

NASA Astrophysics Data System (ADS)

Eres, Murat H.; Schwartz, Leonard W.

1998-11-01

We consider stability and finger formation in free surface flows. Gravity driven downhill drainage and temperature gradient driven climbing flows are two examples of such problems. The former situation occurs when a mound of viscous liquid on a vertical wall is allowed to flow. Constant surface shear stress due to temperature gradients (Marangoni stress) can initiate the latter problem. The evolution equations are derived using the lubrication approximation. We also include the effects of finite-contact angles in the evolution equations using a disjoining pressure model. Evolution equations for both problems are solved using an efficient alternating-direction-implicit method. For both problems a one-dimensional base state is established, that is steady in a moving reference frame. This base state is unstable to transverse perturbations. The transverse wavenumbers for the most rapidly growing modes are found through direct numerical solution of the nonlinear evolution equations, and are compared with published experimental results. For a range of finite equilibrium contact angles, the fingers can grow without limit leading to semi-finite steady fingers in a moving coordinate system. A computer generated movie of the nonlinear simulation results, for several sets of input parameters, will be shown.

Selection platforms for directed evolution in synthetic biology

PubMed Central

Tizei, Pedro A.G.; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B.

2016-01-01

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules–gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function–be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. PMID:27528765

Selection platforms for directed evolution in synthetic biology.

PubMed

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

Oligovalent Fab display on M13 phage improved by directed evolution.

PubMed

Huovinen, Tuomas; Sanmark, Hanna; Ylä-Pelto, Jani; Vehniäinen, Markus; Lamminmäki, Urpo

2010-03-01

Efficient display of antibody on filamentous phage M13 coat is crucial for successful biopanning selections. We applied a directed evolution strategy to improve the oligovalent display of a poorly behaving Fab fragment fused to phage gene-3 for minor coat protein (g3p). The Fab displaying clones were enriched from a randomly mutated Fab gene library with polyclonal anti-mouse IgG antibodies. Contribution of each mutation to the improved phenotype of one selected mutant was studied. It was found out that two point mutations had significant contribution to the display efficiency of Fab clones superinfected with hyperphage. The most dramatic effect was connected to a start codon mutation, from AUG to GUG, of the PelB signal sequence preceding the heavy chain. The clone carrying this mutation, FabM(GUG), displayed Fab 19-fold better and yielded twofold higher phage titers than the original Fab.

Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes.

PubMed

Li, Guangyue; Wang, Jian-Bo; Reetz, Manfred T

2018-04-01

Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

A level set approach for shock-induced α-γ phase transition of RDX

NASA Astrophysics Data System (ADS)

Josyula, Kartik; Rahul; De, Suvranu

2018-02-01

We present a thermodynamically consistent level sets approach based on regularization energy functional which can be directly incorporated into a Galerkin finite element framework to model interface motion. The regularization energy leads to a diffusive form of flux that is embedded within the level sets evolution equation which maintains the signed distance property of the level set function. The scheme is shown to compare well with the velocity extension method in capturing the interface position. The proposed level sets approach is employed to study the α-γphase transformation in RDX single crystal shocked along the (100) plane. Example problems in one and three dimensions are presented. We observe smooth evolution of the phase interface along the shock direction in both models. There is no diffusion of the interface during the zero level set evolution in the three dimensional model. The level sets approach is shown to capture the characteristics of the shock-induced α-γ phase transformation such as stress relaxation behind the phase interface and the finite time required for the phase transformation to complete. The regularization energy based level sets approach is efficient, robust, and easy to implement.

The Evolution of Networked Computing in the Teaching of Japanese as a Foreign Language.

ERIC Educational Resources Information Center

Harrison, Richard

1998-01-01

Reviews the evolution of Internet-based projects in Japanese computer-assisted language learning and suggests future directions in which the field may develop, based on emerging network technology and learning theory. (Author/VWL)

Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis

PubMed Central

Nannemann, David P; Birmingham, William R; Scism, Robert A; Bachmann, Brian O

2011-01-01

To address the synthesis of increasingly structurally diverse small-molecule drugs, methods for the generation of efficient and selective biological catalysts are becoming increasingly important. ‘Directed evolution’ is an umbrella term referring to a variety of methods for improving or altering the function of enzymes using a nature-inspired twofold strategy of mutagenesis followed by selection. This article provides an objective assessment of the effectiveness of directed evolution campaigns in generating enzymes with improved catalytic parameters for new substrates from the last decade, excluding studies that aimed to select for only improved physical properties and those that lack kinetic characterization. An analysis of the trends of methodologies and their success rates from 81 qualifying examples in the literature reveals the average fold improvement for kcat (or Vmax), Km and kcat/Km to be 366-, 12- and 2548-fold, respectively, whereas the median fold improvements are 5.4, 3 and 15.6. Further analysis by enzyme class, library-generation methodology and screening methodology explores relationships between successful campaigns and the methodologies employed. PMID:21644826

Femininity and Kin-Directed Altruism in Androphilic Men: A Test of an Evolutionary Developmental Model.

PubMed

VanderLaan, Doug P; Petterson, Lanna J; Vasey, Paul L

2016-04-01

Androphilia refers to sexual attraction and arousal toward males whereas gynephilia refers to sexual attraction and arousal toward females. This study tested the adaptive feminine phenotype model of the evolution of male androphilia via kin selection, which posits that the development of an evolved disposition toward elevated kin-directed altruism among androphilic males is contingent on the behavioral expression of femininity. Gynephilic men, androphilic women, and androphilic men (N = 387) completed measures of childhood and adulthood gender expression and concern for kin's well-being. Adulthood femininity correlated positively with uncle/aunt-like tendencies among androphilic men and women. Although androphilic women reported greater willingness to invest in nieces and nephews than gynephilic and androphilic men, mediation analyses indicated that adult femininity completely mediated these group differences. In addition, changes in the expression of femininity between childhood and adulthood were associated with parallel changes in concern for the well-being of kin among androphilic men. Thus, these findings suggest that femininity is key to the expression of kin-directed altruism among androphilic males and may have been important in the evolution of male androphilia.

Size variation, growth strategies, and the evolution of modularity in the mammalian skull.

PubMed

Porto, Arthur; Shirai, Leila Teruko; de Oliveira, Felipe Bandoni; Marroig, Gabriel

2013-11-01

Allometry is a major determinant of within-population patterns of association among traits and, therefore, a major component of morphological integration studies. Even so, the influence of size variation over evolutionary change has been largely unappreciated. Here, we explore the interplay between allometric size variation, modularity, and life-history strategies in the skull from representatives of 35 mammalian families. We start by removing size variation from within-species data and analyzing its influence on integration magnitudes, modularity patterns, and responses to selection. We also carry out a simulation in which we artificially alter the influence of size variation in within-taxa matrices. Finally, we explore the relationship between size variation and different growth strategies. We demonstrate that a large portion of the evolution of modularity in the mammalian skull is associated to the evolution of growth strategies. Lineages with highly altricial neonates have adult variation patterns dominated by size variation, leading to high correlations among traits regardless of any underlying modular process and impacting directly their potential to respond to selection. Greater influence of size variation is associated to larger intermodule correlations, less individualized modules, and less flexible responses to natural selection. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Consumer-resource interactions and the evolution of migration.

PubMed

Drown, Devin M; Dybdahl, Mark F; Gomulkiewicz, Richard

2013-11-01

Theoretical studies have demonstrated that selection will favor increased migration when fitnesses vary both temporally and spatially, but it is far from clear how pervasive those theoretical conditions are in nature. Although consumer-resource interactions are omnipresent in nature and can generate spatial and temporal variation, it is unknown even in theory whether these dynamics favor the evolution of migration. We develop a mathematical model to address whether and how migration evolves when variability in fitness is determined at least in part by consumer-resource coevolutionary interactions. Our analyses show that such interactions can drive the evolution of migration in the resource, consumer, or both species and thus supplies a general explanation for the pervasiveness of migration. Over short time scales, we show the direction of change in migration rate is determined primarily by the state of local adaptation of the species involved: rates increase when a species is locally maladapted and decrease when locally adapted. Our results reveal that long-term evolutionary trends in migration rates can differ dramatically depending on the strength or weakness of interspecific interactions and suggest an explanation for the evolutionary divergence of migration rates among interacting species. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Optimality models in the age of experimental evolution and genomics.

PubMed

Bull, J J; Wang, I-N

2010-09-01

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well-researched organism allows dissection of the evolutionary process to identify causes of model failure--whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation--an especially useful augmentation to well-researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.

Continuous directed evolution of aminoacyl-tRNA synthetases

PubMed Central

Bryson, David I.; Fan, Chenguang; Guo, Li-Tao; Miller, Corwin; Söll, Dieter; Liu, David R.

2017-01-01

Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of non-canonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp. pyrrolysyl-tRNA synthetase (PylRS) improved its enzymatic efficiency (kcat/KMtRNA) 45-fold compared to the parent enzyme. Transplantation of the evolved mutations into other PylRS-derived synthetases improved yields of proteins containing non-canonical residues up to 9.7-fold. Simultaneous positive and negative selection PACE over 48 h greatly improved the selectivity of a promiscuous Methanocaldococcus jannaschii tyrosyl-tRNA synthetase variant for site-specific incorporation of p-iodo-L-phenylalanine. These findings offer new AARSs that increase the utility of orthogonal translation systems and establish the capability of PACE to efficiently evolve orthogonal AARSs with high activity and amino acid specificity. PMID:29035361

A molecular description of the evolution of resistance

NASA Technical Reports Server (NTRS)

Ordoukhanian, P.; Joyce, G. F.

1999-01-01

BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.

Mapping the Geometric Evolution of Protein Folding Motor.

PubMed

Jerath, Gaurav; Hazam, Prakash Kishore; Shekhar, Shashi; Ramakrishnan, Vibin

2016-01-01

Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ1 and χ2, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.

Mechanical responses, texture evolution, and yield loci of extruded AZ31 magnesium alloy under various loading conditions: Experiment and modeling

NASA Astrophysics Data System (ADS)

Kabirian, Farhoud

Mechanical responses and texture evolution of extruded AZ31 Mg are measured under uniaxial (tension-compression) and multiaxial (free-end torsion) loadings. Compression loading is carried out in three different directions at temperature and strain rate ranges of 77-423 K and 10-4 -3000 s -1, respectively. Texture evolution at different intermediate strains reveals that crystal reorientation is exhausted at smaller strains with increase in strain rate while increase in temperature retards twinning. In addition to the well-known tension-compression yield asymmetry, a strong anisotropy in strain hardening response is observed. Strain hardening during the compression experiment is intensified with decreasing and increasing temperature and strain rate, respectively. This complex behavior is explained through understanding the roles of deformation mechanisms using the Visco-Plastic Self Consistent (VPSC) model. In order to calibrate the VPSC model's constants as accurate as possible, a vast number of mechanical responses including stress-strain curves in tension, compression in three directions, and free-end torsion, texture evolution at different strains, lateral strains of compression samples, twin volume fraction, and axial strain during the torsion experiment. Modeling results show that depending on the number of measurements used for calibration, roles of different mechanisms in plastic deformation change significantly. In addition, a precise definition of yield is established for the extruded AZ31magnesium alloy after it is subjected to different loading conditions (uniaxial to multiaxial) at four different plastic strains. The yield response is measured in ?-? space. Several yield criteria are studied to predict yield response of extruded AZ31. This study proposes an asymmetrical fourth-order polynomial yield function. Material constants in this model can be directly calculated using mechanical measurements. Convexity of the proposed model is discussed, and domains of constants where convexity holds are determined. Effects of grain refinement induced by Equal Channel Angular Pressing, ECAP, on mechanical responses and texture evolution are investigated. Yield strength in compression increases after ECAP, however, strain-hardening rate drops with number of ECAP passes while failure strain increases. Texture measurements reveal the higher propensity to twinning in the extruded material compared with ECAPed magnesium. Calculated Schmid factor maps are utilized to connect the observed mechanical responses to the texture.

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.

A Comparative Study of Foreign Direct Investment Flow Using Diffusion Models

NASA Astrophysics Data System (ADS)

Li, Yiming; Chiang, Yi-Hui; Yu, Shao-Ming; Chiang, Su-Yun; Hung, C.-H.

2007-12-01

In this work, we apply an improvement dynamic model of the foreign direct investment (FDI) flow to analyze the evolution of FDI flow. In comparison with the fundamental growth model of FDI, the simulation result is further accurate if the asymmetric growth pattern and heterogeneity of the potential adopters are considered. According to the result, the internal influence dominates the growth of FDI flow from Taiwan to China during 2001-2006, taking the electronics industry for example.

Direct observation of morphological evolution of a catalyst during carbon nanotube forest growth: new insights into growth and growth termination

NASA Astrophysics Data System (ADS)

Jeong, Seojeong; Lee, Jaegeun; Kim, Hwan-Chul; Hwang, Jun Yeon; Ku, Bon-Cheol; Zakharov, Dmitri N.; Maruyama, Benji; Stach, Eric A.; Kim, Seung Min

2016-01-01

In this study, we develop a new methodology for transmission electron microscopy (TEM) analysis that enables us to directly investigate the interface between carbon nanotube (CNT) arrays and the catalyst and support layers for CNT forest growth without any damage induced by a post-growth TEM sample preparation. Using this methodology, we perform in situ and ex situ TEM investigations on the evolution of the morphology of the catalyst particles and observe the catalyst particles to climb up through CNT arrays during CNT forest growth. We speculate that the lifted catalysts significantly affect the growth and growth termination of CNT forests along with Ostwald ripening and sub-surface diffusion. Thus, we propose a modified growth termination model which better explains various phenomena related to the growth and growth termination of CNT forests.In this study, we develop a new methodology for transmission electron microscopy (TEM) analysis that enables us to directly investigate the interface between carbon nanotube (CNT) arrays and the catalyst and support layers for CNT forest growth without any damage induced by a post-growth TEM sample preparation. Using this methodology, we perform in situ and ex situ TEM investigations on the evolution of the morphology of the catalyst particles and observe the catalyst particles to climb up through CNT arrays during CNT forest growth. We speculate that the lifted catalysts significantly affect the growth and growth termination of CNT forests along with Ostwald ripening and sub-surface diffusion. Thus, we propose a modified growth termination model which better explains various phenomena related to the growth and growth termination of CNT forests. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05547d

Hamilton's rule and the causes of social evolution

PubMed Central

Bourke, Andrew F. G.

2014-01-01

Hamilton's rule is a central theorem of inclusive fitness (kin selection) theory and predicts that social behaviour evolves under specific combinations of relatedness, benefit and cost. This review provides evidence for Hamilton's rule by presenting novel syntheses of results from two kinds of study in diverse taxa, including cooperatively breeding birds and mammals and eusocial insects. These are, first, studies that empirically parametrize Hamilton's rule in natural populations and, second, comparative phylogenetic analyses of the genetic, life-history and ecological correlates of sociality. Studies parametrizing Hamilton's rule are not rare and demonstrate quantitatively that (i) altruism (net loss of direct fitness) occurs even when sociality is facultative, (ii) in most cases, altruism is under positive selection via indirect fitness benefits that exceed direct fitness costs and (iii) social behaviour commonly generates indirect benefits by enhancing the productivity or survivorship of kin. Comparative phylogenetic analyses show that cooperative breeding and eusociality are promoted by (i) high relatedness and monogamy and, potentially, by (ii) life-history factors facilitating family structure and high benefits of helping and (iii) ecological factors generating low costs of social behaviour. Overall, the focal studies strongly confirm the predictions of Hamilton's rule regarding conditions for social evolution and their causes. PMID:24686934

Hamilton's rule and the causes of social evolution.

PubMed

Bourke, Andrew F G

2014-05-19

Hamilton's rule is a central theorem of inclusive fitness (kin selection) theory and predicts that social behaviour evolves under specific combinations of relatedness, benefit and cost. This review provides evidence for Hamilton's rule by presenting novel syntheses of results from two kinds of study in diverse taxa, including cooperatively breeding birds and mammals and eusocial insects. These are, first, studies that empirically parametrize Hamilton's rule in natural populations and, second, comparative phylogenetic analyses of the genetic, life-history and ecological correlates of sociality. Studies parametrizing Hamilton's rule are not rare and demonstrate quantitatively that (i) altruism (net loss of direct fitness) occurs even when sociality is facultative, (ii) in most cases, altruism is under positive selection via indirect fitness benefits that exceed direct fitness costs and (iii) social behaviour commonly generates indirect benefits by enhancing the productivity or survivorship of kin. Comparative phylogenetic analyses show that cooperative breeding and eusociality are promoted by (i) high relatedness and monogamy and, potentially, by (ii) life-history factors facilitating family structure and high benefits of helping and (iii) ecological factors generating low costs of social behaviour. Overall, the focal studies strongly confirm the predictions of Hamilton's rule regarding conditions for social evolution and their causes.

Evolution of sprint speed in African savannah herbivores in relation to predation.

PubMed

Bro-Jørgensen, Jakob

2013-11-01

Predator-prey arms races are widely speculated to underlie fast speed in terrestrial mammals. However, due to lack of empirical testing, both the specificity of any evolutionary coupling between particular predator and prey species, and the relevance of alternative food-based hypotheses of speed evolution, remain obscure. Here I examine the ecological links between the sprint speed of African savannah herbivores, their vulnerability to predators, and their diet. I show that sprint speed is strongly predicted by the vulnerability of prey to their main predators; however, the direction of the link depends on the hunting style of the predator. Speed increases with vulnerability to pursuit predators, whereas vulnerability to ambush predators is associated with particularly slow speed. These findings suggest that differential vulnerability to specific predators can indeed drive interspecific variation in speed within prey communities, but that predator hunting style influences the intensity and consistency with which selection on speed is coupled between particular species. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

The Local Structure of Globalization. The Network Dynamics of Foreign Direct Investments in the International Electricity Industry

NASA Astrophysics Data System (ADS)

Koskinen, Johan; Lomi, Alessandro

2013-05-01

We study the evolution of the network of foreign direct investment (FDI) in the international electricity industry during the period 1994-2003. We assume that the ties in the network of investment relations between countries are created and deleted in continuous time, according to a conditional Gibbs distribution. This assumption allows us to take simultaneously into account the aggregate predictions of the well-established gravity model of international trade as well as local dependencies between network ties connecting the countries in our sample. According to the modified version of the gravity model that we specify, the probability of observing an investment tie between two countries depends on the mass of the economies involved, their physical distance, and the tendency of the network to self-organize into local configurations of network ties. While the limiting distribution of the data generating process is an exponential random graph model, we do not assume the system to be in equilibrium. We find evidence of the effects of the standard gravity model of international trade on evolution of the global FDI network. However, we also provide evidence of significant dyadic and extra-dyadic dependencies between investment ties that are typically ignored in available research. We show that local dependencies between national electricity industries are sufficient for explaining global properties of the network of foreign direct investments. We also show, however, that network dependencies vary significantly over time giving rise to a time-heterogeneous localized process of network evolution.

Direct estimate of the spontaneous germ line mutation rate in African green monkeys.

PubMed

Pfeifer, Susanne P

2017-12-01

Here, I provide the first direct estimate of the spontaneous mutation rate in an Old World monkey, using a seven individual, three-generation pedigree of African green monkeys. Eight de novo mutations were identified within ∼1.5 Gbp of accessible genome, corresponding to an estimated point mutation rate of 0.94 × 10 -8 per site per generation, suggesting an effective population size of ∼12000 for the species. This estimation represents a significant improvement in our knowledge of the population genetics of the African green monkey, one of the most important nonhuman primate models in biomedical research. Furthermore, by comparing mutation rates in Old World monkeys with the only other direct estimates in primates to date-humans and chimpanzees-it is possible to uniquely address how mutation rates have evolved over longer time scales. While the estimated spontaneous mutation rate for African green monkeys is slightly lower than the rate of 1.2 × 10 -8 per base pair per generation reported in chimpanzees, it is similar to the lower range of rates of 0.96 × 10 -8 -1.28 × 10 -8 per base pair per generation recently estimated from whole genome pedigrees in humans. This result suggests a long-term constraint on mutation rate that is quite different from similar evidence pertaining to recombination rate evolution in primates. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

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.

Establishment and application of a modified membrane-blot assay for Rhizomucor miehei lipases aimed at improving their methanol tolerance and thermostability.

PubMed

He, Dong; Luo, Wen; Wang, Zhiyuan; Lv, Pengmei; Yuan, Zhenhong; Huang, Shaowei; Xv, Jingliang

2017-07-01

Directed evolution has been proved an effective way to improve the stability of proteins, but high throughput screening assays for directed evolution with simultaneous improvement of two or more properties are still rare. In this study, we aimed to establish a membrane-blot assay for use in the high-throughput screening of Rhizomucor miehei lipases (RMLs). With the assistance of the membrane-blot screening assay, a mutant E47K named G10 that showed improved thermal stability was detected in the first round of error-prone PCR. Using G10 as the parent, two variants G10-11 and G10-20 that showed improved thermal stability and methanol tolerance without loss of activity compared to the wild type RML were obtained. The T 50 60 -value of G10-11 and G10-20 increased by 12°C and 6.5°C, respectively. After incubation for 1h, the remaining residual activity of G10-11 and G10-20 was 63.45% and 74.33%, respectively, in 50% methanol, and 15.98% and 30.22%, respectively, in 80% methanol. Thus, we successfully developed a membrane-blot assay that could be used for the high-throughput screening of RMLs with improved thermostability and methanol tolerance. Based on our findings, we believe that our newly developed membrane-blot assay will have potential applications in directed evolution in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution in response to direct and indirect ecological effects in pitcher plant inquiline communities.

PubMed

terHorst, Casey P

2010-12-01

Ecologists have long recognized the importance of indirect ecological effects on species abundances, coexistence, and diversity. However, the evolutionary consequences of indirect interactions are rarely considered. Here I conduct selection experiments and examine the evolutionary response of Colpoda sp., a ciliated protozoan, to other members of the inquiline community of purple pitcher plants (Sarracenia purpurea). I measured the evolution of six traits in response to (1) predation by mosquito larvae, (2) competition from other ciliated protozoans, and (3) simultaneous predation and competition. The latter treatment incorporated both direct effects and indirect effects due to interactions between predators and competitors. Population growth rate and cell size evolved in response to direct effects of predators and competitors. However, trait values in the multispecies treatment were similar to those in the monoculture treatment, indicating that direct effects were offset by strong indirect effects on the evolution of traits. For most of the traits measured, indirect effects were opposed to, and often stronger than, direct effects. These indirect effects occurred as a result of behavioral changes of the predator in the presence of competitors and as a result of reduced densities of competitors in the presence of predators. Incorporating indirect effects provides a more realistic description of how species evolve in complex natural communities.

Large Scale Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1997-01-01

Jet noise is a major concern in the design of commercial aircraft. Studies by various researchers suggest that aerodynamic noise is a major contributor to jet noise. Some of these studies indicate that most of the aerodynamic jet noise due to turbulent mixing occurs when there is a rapid variation in turbulent structure, i.e. rapidly growing or decaying vortices. The objective of this research was to simulate a compressible round jet to study the non-linear evolution of vortices and the resulting acoustic radiations. In particular, to understand the effect of turbulence structure on the noise. An ideal technique to study this problem is Direct Numerical Simulations(DNS), because it provides precise control on the initial and boundary conditions that lead to the turbulent structures studied. It also provides complete 3-dimensional time dependent data. Since the dynamics of a temporally evolving jet are not greatly different from those, of a spatially evolving jet, a temporal jet problem was solved, using periodicity ill the direction of the jet axis. This enables the application of Fourier spectral methods in the streamwise direction. Physically this means that turbulent structures in the jet are repeated in successive downstream cells instead of being gradually modified downstream into a jet plume. The DNS jet simulation helps us understand the various turbulent scales and mechanisms of turbulence generation in the evolution of a compressible round jet. These accurate flow solutions will be used in future research to estimate near-field acoustic radiation by computing the total outward flux across a surface and determine how it is related to the evolution of the turbulent solutions. Furthermore, these simulations allow us to investigate the sensitivity of acoustic radiations to inlet/boundary conditions, with possible application to active noise suppression. In addition, the data generated can be used to compute various turbulence quantities such as mean velocities, turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved Direct Numerical Simulation (DNS) of a turbulent jet flow is produced.

Digital Direct-to-Consumer Advertising: A Perfect Storm of Rapid Evolution and Stagnant Regulation

PubMed Central

Mackey, Tim K.

2016-01-01

The adoption and use of digital forms of direct-to-consumer advertising (also known as "eDTCA") is on the rise. At the same time, the universe of eDTCA is expanding, as technology on Internet-based platforms continues to evolve, from static websites, to social media, and nearly ubiquitous use of mobile devices. However, little is known about how this unique form of pharmaceutical marketing impacts consumer behavior, public health, and overall healthcare utilization. The study by Kim analyzing US Food and Drug Administration (FDA) notices of violations (NOVs) and warning letters regarding online promotional activities takes us in the right direction, but study results raise as many questions as it does answers. Chief among these are unanswered concerns about the unique regulatory challenges posed by the "disruptive" qualities of eDTCA, and whether regulators have sufficient resources and oversight powers to proactively address potential violations. Further, the globalization of eDTCA via borderless Internet-based technologies raises larger concerns about the potential global impact of this form of health marketing unique to only the United States and New Zealand. Collectively, these challenges make it unlikely that regulatory science will be able to keep apace with the continued rapid evolution of eDTCA unless more creative policy solutions are explored. PMID:27239871

Enzymes useful for chiral compound synthesis: structural biology, directed evolution, and protein engineering for industrial use.

PubMed

Kataoka, Michihiko; Miyakawa, Takuya; Shimizu, Sakayu; Tanokura, Masaru

2016-07-01

Biocatalysts (enzymes) have many advantages as catalysts for the production of useful compounds as compared to chemical catalysts. The stereoselectivity of the enzymes is one advantage, and thus the stereoselective production of chiral compounds using enzymes is a promising approach. Importantly, industrial application of the enzymes for chiral compound production requires the discovery of a novel useful enzyme or enzyme function; furthermore, improving the enzyme properties through protein engineering and directed evolution approaches is significant. In this review, the significance of several enzymes showing stereoselectivity (quinuclidinone reductase, aminoalcohol dehydrogenase, old yellow enzyme, and threonine aldolase) in chiral compound production is described, and the improvement of these enzymes using protein engineering and directed evolution approaches for further usability is discussed. Currently, enzymes are widely used as catalysts for the production of chiral compounds; however, for further use of enzymes in chiral compound production, improvement of enzymes should be more essential, as well as discovery of novel enzymes and enzyme functions.

Ultra-high-throughput screening method for the directed evolution of glucose oxidase.

PubMed

Ostafe, Raluca; Prodanovic, Radivoje; Nazor, Jovana; Fischer, Rainer

2014-03-20

Glucose oxidase (GOx) is used in many industrial processes that could benefit from improved versions of the enzyme. Some improvements like higher activity under physiological conditions and thermal stability could be useful for GOx applications in biosensors and biofuel cells. Directed evolution is one of the currently available methods to engineer improved GOx variants. Here, we describe an ultra-high-throughput screening system for sorting the best enzyme variants generated by directed evolution that incorporates several methodological refinements: flow cytometry, in vitro compartmentalization, yeast surface display, fluorescent labeling of the expressed enzyme, delivery of glucose substrate to the reaction mixture through the oil phase, and covalent labeling of the cells with fluorescein-tyramide. The method enables quantitative screening of gene libraries to identify clones with improved activity and it also allows cells to be selected based not only on the overall activity but also on the specific activity of the enzyme. Copyright © 2014 Elsevier Ltd. All rights reserved.

Niche construction, sources of selection and trait coevolution.

PubMed

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

2017-10-06

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

Effect of differential speed rolling on the texture evolution of Mg-4Zn-1Gd alloy

NASA Astrophysics Data System (ADS)

Shim, Myeong-Shik; Suh, Byeong-Chan; Kim, Jae H.; Kim, Nack J.

2015-05-01

The microstructural and texture evolution during differential speed rolling process of Mg 4Zn-1Gd (wt%) alloy have been investigated by means of electron backscatter diffraction observation and texture analysis. The angular distribution of basal poles are inclined about 10° from the normal direction towards the rolling direction and the maximum intensities of basal poles are decreased, compared to the conventional rolling process. Such an inclination of angular distribution of basal poles can be induced by the operation of shear stress along the rolling direction, as much as one quarter of tensile stress along the RD and one quarter of compressive stress along the ND. When the reduction ratios in differential speed rolling increase, there is no difference in texture evolution although there is a significant change in activated twinning systems. In addition, the engineering stresses after differential speed rolling are also similar to that after conventional rolling process, while ductility and stretch formability in the former are worse than those in the latter.

The Minimum-Mass Surface Density of the Solar Nebula using the Disk Evolution Equation

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2005-01-01

The Hayashi minimum-mass power law representation of the pre-solar nebula (Hayashi 1981, Prog. Theo. Phys.70,35) is revisited using analytic solutions of the disk evolution equation. A new cumulative-planetary-mass-model (an integrated form of the surface density) is shown to predict a smoother surface density compared with methods based on direct estimates of surface density from planetary data. First, a best-fit transcendental function is applied directly to the cumulative planetary mass data with the surface density obtained by direct differentiation. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the planetary data. The latter model indicates a decay rate of r -1/2 in the inner disk followed by a rapid decay which results in a sharper outer boundary than predicted by the minimum mass model. The model is shown to be a good approximation to the finite-size early Solar Nebula and by extension to extra solar protoplanetary disks.

Evidence for strong intralocus sexual conflict in the Indian meal moth, Plodia interpunctella.

PubMed

Lewis, Zenobia; Wedell, Nina; Hunt, John

2011-07-01

Males and females share a genome and express many shared phenotypic traits, which are often selected in opposite directions. This generates intralocus sexual conflict that may constrain trait evolution by preventing the sexes from reaching their optimal phenotype. Furthermore, if present across multiple loci, intralocus sexual conflict can result in a gender load that may diminish the benefits of sexual selection and help maintain genetic variation for fitness. Despite the importance of intralocus sexual conflict, surprisingly few empirical studies conclusively demonstrate its operation. We show that the pattern of multivariate selection acting on three sexually dimorphic life-history traits (development time, body size, and longevity) in the Indian meal moth, Plodia interpunctella, is opposing for the sexes. Moreover, we combined our estimates of selection with the additive genetic variance-covariance matrix (G) to predict the evolutionary response of the life-history traits in the sexes and showed that the angle between the vector of responses and the vector of sexually antagonistic selection was almost orthogonal at 84.70°. Thus, G biases the predicted response of life-history traits in the sexes away from the direction of sexually antagonistic selection, confirming the presence of strong intralocus sexual conflict in this species. Despite this, sexual dimorphism has evolved in all of the life-history traits examined suggesting that mechanism(s) have evolved to resolve this conflict and allow the sexes to reach their life-history optima. We argue that intralocus sexual conflict is likely to play an important role in the evolution of divergent life-history strategies between the sexes in this species. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

The Seasonal Evolution of Sea Ice Floe Size Distribution

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. “The Seasonal Evolution of Sea Ice Floe Size Distribution... seasonally in the southern Beaufort and Chukchi Seas region. OBJECTIVES The objective of this work was to determine the seasonal evolution of the...summer melt season using (4). The technique allows for the direct observation of lateral melt and the 3 calculation of changes in floe perimeter, and

Rapid directed evolution of stabilized proteins with cellular high-throughput encapsulation solubilization and screening (CHESS).

PubMed

Yong, K J; Scott, D J

2015-03-01

Directed evolution is a powerful method for engineering proteins towards user-defined goals and has been used to generate novel proteins for industrial processes, biological research and drug discovery. Typical directed evolution techniques include cellular display, phage display, ribosome display and water-in-oil compartmentalization, all of which physically link individual members of diverse gene libraries to their translated proteins. This allows the screening or selection for a desired protein function and subsequent isolation of the encoding gene from diverse populations. For biotechnological and industrial applications there is a need to engineer proteins that are functional under conditions that are not compatible with these techniques, such as high temperatures and harsh detergents. Cellular High-throughput Encapsulation Solubilization and Screening (CHESS), is a directed evolution method originally developed to engineer detergent-stable G proteins-coupled receptors (GPCRs) for structural biology. With CHESS, library-transformed bacterial cells are encapsulated in detergent-resistant polymers to form capsules, which serve to contain mutant genes and their encoded proteins upon detergent mediated solubilization of cell membranes. Populations of capsules can be screened like single cells to enable rapid isolation of genes encoding detergent-stable protein mutants. To demonstrate the general applicability of CHESS to other proteins, we have characterized the stability and permeability of CHESS microcapsules and employed CHESS to generate thermostable, sodium dodecyl sulfate (SDS) resistant green fluorescent protein (GFP) mutants, the first soluble proteins to be engineered using CHESS. © 2014 Wiley Periodicals, Inc.

Directionality theory and the evolution of body size.

PubMed

Demetrius, L

2000-12-07

Directionality theory, a dynamic theory of evolution that integrates population genetics with demography, is based on the concept of evolutionary entropy, a measure of the variability in the age of reproducing individuals in a population. The main tenets of the theory are three principles relating the response to the ecological constraints a population experiences, with trends in entropy as the population evolves under mutation and natural selection. (i) Stationary size or fluctuations around a stationary size (bounded growth): a unidirectional increase in entropy; (ii) prolonged episodes of exponential growth (unbounded growth), large population size: a unidirectional decrease in entropy; and (iii) prolonged episodes of exponential growth (unbounded growth), small population size: random, non-directional change in entropy. We invoke these principles, together with an allometric relationship between entropy, and the morphometric variable body size, to provide evolutionary explanations of three empirical patterns pertaining to trends in body size, namely (i) Cope's rule, the tendency towards size increase within phyletic lineages; (ii) the island rule, which pertains to changes in body size that occur as species migrate from mainland populations to colonize island habitats; and (iii) Bergmann's rule, the tendency towards size increase with increasing latitude. The observation that these ecotypic patterns can be explained in terms of the directionality principles for entropy underscores the significance of evolutionary entropy as a unifying concept in forging a link between micro-evolution, the dynamics of gene frequency change, and macro-evolution, dynamic changes in morphometric variables.

Publications of the exobiology program for 1989: A special bibliography

NASA Technical Reports Server (NTRS)

1991-01-01

A listing of 1989 publications resulting from research supported by the Exobiology Program is presented. Research supported by the Exobiology Program is explored in the following areas: (1) cosmic evolution of biogenic compounds; (2) prebiotic evolution; (3) early evolution of life; (4) and evolution of advanced life. Pre-mission and pre-project activities supporting these areas are supported in the areas of solar system exploration and search for extraterrestrial intelligence. The planetary protection subject area is included here because of its direct relevance to the Exobiology Program.

Generation and evolution of anisotropic turbulence and related energy transfer in drifting proton-alpha plasmas

NASA Astrophysics Data System (ADS)

Maneva, Y. G.; Poedts, S.

2018-05-01

The power spectra of magnetic field fluctuations in the solar wind typically follow a power-law dependence with respect to the observed frequencies and wave-numbers. The background magnetic field often influences the plasma properties, setting a preferential direction for plasma heating and acceleration. At the same time the evolution of the solar-wind turbulence at the ion and electron scales is influenced by the plasma properties through local micro-instabilities and wave-particle interactions. The solar-wind-plasma temperature and the solar-wind turbulence at sub- and sup-ion scales simultaneously show anisotropic features, with different components and fluctuation power in parallel with and perpendicular to the orientation of the background magnetic field. The ratio between the power of the magnetic field fluctuations in parallel and perpendicular direction at the ion scales may vary with the heliospheric distance and depends on various parameters, including the local wave properties and nonthermal plasma features, such as temperature anisotropies and relative drift speeds. In this work we have performed two-and-a-half-dimensional hybrid simulations to study the generation and evolution of anisotropic turbulence in a drifting multi-ion species plasma. We investigate the evolution of the turbulent spectral slopes along and across the background magnetic field for the cases of initially isotropic and anisotropic turbulence. Finally, we show the effect of the various turbulent spectra for the local ion heating in the solar wind.

Molecular analysis of ancient caries

PubMed Central

Simón, Marc; Montiel, Rafael; Smerling, Andrea; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A.; Jiménez-Marín, Andrea R.; Malgosa, Assumpció

2014-01-01

An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains. PMID:25056622

Persistent directional selection on body size and a resolution to the paradox of stasis.

PubMed

Rollinson, Njal; Rowe, Locke

2015-09-01

Directional selection on size is common but often fails to result in microevolution in the wild. Similarly, macroevolutionary rates in size are low relative to the observed strength of selection in nature. We show that many estimates of selection on size have been measured on juveniles, not adults. Further, parents influence juvenile size by adjusting investment per offspring. In light of these observations, we help resolve this paradox by suggesting that the observed upward selection on size is balanced by selection against investment per offspring, resulting in little or no net selection gradient on size. We find that trade-offs between fecundity and juvenile size are common, consistent with the notion of selection against investment per offspring. We also find that median directional selection on size is positive for juveniles but no net directional selection exists for adult size. This is expected because parent-offspring conflict exists over size, and juvenile size is more strongly affected by investment per offspring than adult size. These findings provide qualitative support for the hypothesis that upward selection on size is balanced by selection against investment per offspring, where parent-offspring conflict over size is embodied in the opposing signs of the two selection gradients. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Direct Band Gap Gallium Antimony Phosphide (GaSbxP1−x) Alloys

PubMed Central

Russell, H. B.; Andriotis, A. N.; Menon, M.; Jasinski, J. B.; Martinez-Garcia, A.; Sunkara, M. K.

2016-01-01

Here, we report direct band gap transition for Gallium Phosphide (GaP) when alloyed with just 1–2 at% antimony (Sb) utilizing both density functional theory based computations and experiments. First principles density functional theory calculations of GaSbxP1−x alloys in a 216 atom supercell configuration indicate that an indirect to direct band gap transition occurs at x = 0.0092 or higher Sb incorporation into GaSbxP1−x. Furthermore, these calculations indicate band edge straddling of the hydrogen evolution and oxygen evolution reactions for compositions ranging from x = 0.0092 Sb up to at least x = 0.065 Sb making it a candidate for use in a Schottky type photoelectrochemical water splitting device. GaSbxP1−x nanowires were synthesized by reactive transport utilizing a microwave plasma discharge with average compositions ranging from x = 0.06 to x = 0.12 Sb and direct band gaps between 2.21 eV and 1.33 eV. Photoelectrochemical experiments show that the material is photoactive with p-type conductivity. This study brings attention to a relatively uninvestigated, tunable band gap semiconductor system with tremendous potential in many fields. PMID:26860470

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

PubMed

Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H

2016-04-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Protein interactions and ligand binding: from protein subfamilies to functional specificity.

PubMed

Rausell, Antonio; Juan, David; Pazos, Florencio; Valencia, Alfonso

2010-02-02

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.

The dynamic evolution of social ties and user-generated content: a case study on a Douban group

NASA Astrophysics Data System (ADS)

Shan, Siqing; Ren, Jie; Li, Cangyan

2017-11-01

As platforms based on user-generated content (UGC), social media platforms emphasise the social ties between users and user participation, which promote the communication and propagation of ideas and help to build and maintain relationships. However, many researchers have studied only predefined social networks, such as academic social networks. We believe that there are certain characteristics associated with the network's UGC worth evaluating. We conducted research in communities in which content attracts discussion and new members and examined the evolution patterns of social and content networks in a topic-oriented Douban group. Datasets of user and content information in communities of interest were collected through web crawler software. Networks based on social and content ties were constructed and analysed. We chose scale, density, centrality, average path length and cluster coefficient as measures for exploring the evolution and correlation of both types of networks. These findings are valuable for social media marketing and helpful in directing and controlling public opinion.

Big cats as a model system for the study of the evolution of intelligence.

PubMed

Borrego, Natalia

2017-08-01

Currently, carnivores, and felids in particular, are vastly underrepresented in cognitive literature, despite being an ideal model system for tests of social and ecological intelligence hypotheses. Within Felidae, big cats (Panthera) are uniquely suited to studies investigating the evolutionary links between social, ecological, and cognitive complexity. Intelligence likely did not evolve in a unitary way but instead evolved as the result of mutually reinforcing feedback loops within the physical and social environments. The domain-specific social intelligence hypothesis proposes that social complexity drives only the evolution of cognitive abilities adapted only to social domains. The domain-general hypothesis proposes that the unique demands of social life serve as a bootstrap for the evolution of superior general cognition. Big cats are one of the few systems in which we can directly address conflicting predictions of the domain-general and domain-specific hypothesis by comparing cognition among closely related species that face roughly equivalent ecological complexity but vary considerably in social complexity. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of inviscid Kelvin-Helmholtz instability from a piecewise linear shear layer

NASA Astrophysics Data System (ADS)

Guha, Anirban; Rahmani, Mona; Lawrence, Gregory

2012-11-01

Here we study the evolution of 2D, inviscid Kelvin-Helmholtz instability (KH) ensuing from a piecewise linear shear layer. Although KH pertaining to smooth shear layers (eg. Hyperbolic tangent profile) has been thorough investigated in the past, very little is known about KH resulting from sharp shear layers. Pozrikidis and Higdon (1985) have shown that piecewise shear layer evolves into elliptical vortex patches. This non-linear state is dramatically different from the well known spiral-billow structure of KH. In fact, there is a little acknowledgement that elliptical vortex patches can represent non-linear KH. In this work, we show how such patches evolve through the interaction of vorticity waves. Our work is based on two types of computational methods (i) Contour Dynamics: a boundary-element method which tracks the evolution of the contour of a vortex patch using Lagrangian marker points, and (ii) Direct Numerical Simulation (DNS): an Eulerian pseudo-spectral method heavily used in studying hydrodynamic instability and turbulence.

The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons

PubMed Central

Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison P.; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E. G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H.; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W. H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H.

2016-01-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before the teleost genome duplication (TGD). The slowly evolving gar genome conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and miRNA genes). Numerous conserved non-coding elements (CNEs, often cis-regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles of such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses revealed that the sum of expression domains and levels from duplicated teleost genes often approximate patterns and levels of gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes, and the function of human regulatory sequences. PMID:26950095

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

Correlated evolution of beak morphology and song in the neotropical woodcreeper radiation.

PubMed

Derryberry, Elizabeth Perrault; Seddon, Nathalie; Claramunt, Santiago; Tobias, Joseph Andrew; Baker, Adam; Aleixo, Alexandre; Brumfield, Robb Thomas

2012-09-01

Mating signals may diversify as a byproduct of morphological adaptation to different foraging niches, potentially driving speciation. Although many studies have focused on the direct influence of ecological and sexual selection on signal divergence, the role of indirect mechanisms remains poorly understood. Using phenotypic and molecular datasets, we explored the interplay between morphological and vocal evolution in an avian radiation characterized by dramatic beak variation, the Neotropical woodcreepers (Dendrocolaptinae). We found evidence of a trade-off between the rate of repetition of song syllables and frequency bandwidth: slow paced songs had either narrow or wide frequency bandwidths, and bandwidth decreased as song pace increased. This bounded phenotypic space for song structure supports the hypothesis that passerine birds face a motor constraint during song production. Diversification of acoustic characters within this bounded space was correlated with diversification of beak morphology. In particular, species with larger beaks produced slower songs with narrower frequency bandwidths, suggesting that ecological selection on beak morphology influences the diversification of woodcreeper songs. Because songs in turn mediate mate choice and species recognition in birds, these results indicate a broader role for ecology in avian diversification. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Feed-backs among inbreeding, inbreeding depression in sperm traits, and sperm competition can drive evolution of costly polyandry.

PubMed

Bocedi, Greta; Reid, Jane M

2017-12-01

Ongoing ambitions are to understand the evolution of costly polyandry and its consequences for species ecology and evolution. Emerging patterns could stem from feed-back dynamics between the evolving mating system and its genetic environment, defined by interactions among kin including inbreeding. However, such feed-backs are rarely considered in nonselfing systems. We use a genetically explicit model to demonstrate a mechanism by which inbreeding depression can select for polyandry to mitigate the negative consequences of mating with inbred males, rather than to avoid inbreeding, and to elucidate underlying feed-backs. Specifically, given inbreeding depression in sperm traits, costly polyandry evolved to ensure female fertility, without requiring explicit inbreeding avoidance. Resulting sperm competition caused evolution of sperm traits and further mitigated the negative effect of inbreeding depression on female fertility. The evolving mating system fed back to decrease population-wide homozygosity, and hence inbreeding. However, the net overall decrease was small due to compound effects on the variances in sex-specific reproductive success and paternity skew. Purging of deleterious mutations did not eliminate inbreeding depression in sperm traits or hence selection for polyandry. Overall, our model illustrates that polyandry evolution, both directly and through sperm competition, might facilitate evolutionary rescue for populations experiencing sudden increases in inbreeding. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The evolution of reproductive diversity in Afrobatrachia: A phylogenetic comparative analysis of an extensive radiation of African frogs.

PubMed

Portik, Daniel M; Blackburn, David C

2016-09-01

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift toward using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Evolution of genitalia: theories, evidence, and new directions.

PubMed

Eberhard, William G

2010-01-01

Many hypotheses have been proposed to explain why male intromittent genitalia consistently tend to diverge more rapidly than other body traits of the same individuals in a wide range of animal taxa. Currently the two most popular involve sexual selection: sexually antagonistic coevolution (SAC) and cryptic female choice (CFC). A review of the most extensive attempts to discriminate between these two hypotheses indicates that SAC is not likely to have played a major role in explaining this pattern of genital evolution. Promising lines for future, more direct tests of CFC include experimental modification of male genital form and female sensory abilities, analysis of possible male-female dialogues during copulation, and direct observations of genital behavior.

A model of directional selection applied to the evolution of drug resistance in HIV-1.

PubMed

Seoighe, Cathal; Ketwaroo, Farahnaz; Pillay, Visva; Scheffler, Konrad; Wood, Natasha; Duffet, Rodger; Zvelebil, Marketa; Martinson, Neil; McIntyre, James; Morris, Lynn; Hide, Winston

2007-04-01

Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the neutral rate. Rapid evolution at sites that confer resistance to drugs can be used to help elucidate the mechanisms of evolution of drug resistance and to discover or corroborate novel resistance mutations. We have implemented standard maximum likelihood methods that are used to detect diversifying selection and adapted them for use with serially sampled reverse transcriptase (RT) coding sequences isolated from a group of 300 HIV-1 subtype C-infected women before and after single-dose nevirapine (sdNVP) to prevent mother-to-child transmission. We have also extended the standard models of codon evolution for application to the detection of directional selection. Through simulation, we show that the directional selection model can provide a substantial improvement in sensitivity over models of diversifying selection. Five of the sites within the RT gene that are known to harbor mutations that confer resistance to nevirapine (NVP) strongly supported the directional selection model. There was no evidence that other mutations that are known to confer NVP resistance were selected in this cohort. The directional selection model, applied to serially sampled sequences, also had more power than the diversifying selection model to detect selection resulting from factors other than drug resistance. Because inference of selection from serial samples is unlikely to be adversely affected by recombination, the methods we describe may have general applicability to the analysis of positive selection affecting recombining coding sequences when serially sampled data are available.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa.

PubMed

O'Hara, Niamh B; Rest, Joshua S; Franks, Steven J

2016-01-01

Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering postdrought, which was previously shown to be adaptive. Here, we report the novel finding that postdrought descendant plants were also more susceptible to disease, indicating a rapid evolutionary shift to increased susceptibility. This was accompanied by an evolutionary shift to increased specific leaf area (thinner leaves) following drought. We found that flowering time and disease susceptibility displayed plastic responses to experimental drought treatments, but that this plasticity did not match the direction of evolution, indicating that plastic and evolutionary responses to changes in climate can be opposed. The observed evolutionary shift to increased disease susceptibility accompanying adaptation to drought provides evidence that even if populations can rapidly adapt in response to climate change, evolution in other traits may have ecological effects that could make species more vulnerable. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Electromagnetic effects as a new source of information on the space-time evolution of heavy ion collisions

NASA Astrophysics Data System (ADS)

Davis, Nikolaos; Rybicki, Andrzej; Szczurek, Antoni

2017-12-01

We review our studies of spectator-induced electromagnetic (EM) effects on charged pion emission in ultrarelativistic heavy ion collisions. These effects are found to consist in the electromagnetic charge splitting of pion directed flow as well as very large distortions in spectra and ratios of produced charged particles. As it emerges from our analysis, they offer sensitivity to the actual distance, dE, between the pion formation zone at freeze-out and the spectator matter. As a result, this offers a new possibility of studying the space-time evolution of dense and hot matter created in the course of the collision. Having established that dE traces the longitudinal evolution of the system and therefore rapidly decreases as a function of pion rapidity, we investigate the latter finding in view of pion feed-over from intermediate resonance production. As a result, we obtain a first estimate of the pion decoupling time from EM effects which we compare to existing HBT data. We conclude that spectator-induced EM interactions can serve as a new tool for studying the space-time characteristics and longitudinal evolution of the system. We discuss the future perspectives for this activity on the basis of existing and future data from the NA61/SHINE experiment.

Environmental Security: Evolution of a New Concept in Security Studies

DTIC Science & Technology

1999-04-01

vi ENVIRONMENTAL IMPACT OF POPULATION...1970�s. Environmental security and its direct impact on national and international security has not gone unnoticed by our nation�s leaders. Former...understanding of the �where and under what circumstances� environmental degradation, scarcity, and conflict occur and how they will impact U.S. environmental

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…

Negotiating Competing Progressive Era Reform Impulses at Teachers College, 1889-1927

ERIC Educational Resources Information Center

Murrow, Sonia; McCarthy, Mary Rose

2017-01-01

This case study situates the evolution of Teachers College as a negotiation between two strands of Progressive Era social reform--one that emphasized direct service and one that emphasized the development of education as a profession. While in the early years of Teachers College efforts at professionalizing education were privileged, the…

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

PubMed Central

Murrell, Ben; de Oliveira, Tulio; Seebregts, Chris; Kosakovsky Pond, Sergei L.; Scheffler, Konrad

2012-01-01

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance. PMID:22589711

Modeling HIV-1 drug resistance as episodic directional selection.

PubMed

Murrell, Ben; de Oliveira, Tulio; Seebregts, Chris; Kosakovsky Pond, Sergei L; Scheffler, Konrad

2012-01-01

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance.

How Can Evolution Learn?

PubMed

Watson, Richard A; Szathmáry, Eörs

2016-02-01

The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the 'uninformed' process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles - the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Engineering 7β-Hydroxysteroid Dehydrogenase for Enhanced Ursodeoxycholic Acid Production by Multiobjective Directed Evolution.

PubMed

Zheng, Ming-Min; Chen, Ke-Cai; Wang, Ru-Feng; Li, Hao; Li, Chun-Xiu; Xu, Jian-He

2017-02-15

Ursodeoxycholic acid (UDCA) is the main active ingredient of natural bear bile powder with multiple pharmacological functions. 7β-Hydroxysteroid dehydrogenase (HSDH) is a key biocatalyst for the synthesis of UDCA. However, all the 7β-HSDHs reported commonly suffer from poor activity and thermostability, resulting in limited productivity of UDCA. In this study, a multiobjective directed evolution (MODE) strategy was proposed and applied to improve the activity, thermostability, and pH optimum of a 7β-HSDH. The best variant (V 3-1 ) showed a specific activity 5.5-fold higher than and a half-life 3-fold longer than those of the wild type. In addition, the pH optimum of the variant was shifted to a weakly alkaline value. In the cascade reaction, the productivity of UDCA with V 3-1 increased to 942 g L -1 day -1 , in contrast to 141 g L -1 day -1 with the wild type. Therefore, this study provides a useful strategy for improving the catalytic efficiency of a key enzyme that significantly facilitated the bioproduction of UDCA.

Modelling of anisotropic growth in biological tissues. A new approach and computational aspects.

PubMed

Menzel, A

2005-03-01

In this contribution, we develop a theoretical and computational framework for anisotropic growth phenomena. As a key idea of the proposed phenomenological approach, a fibre or rather structural tensor is introduced, which allows the description of transversely isotropic material behaviour. Based on this additional argument, anisotropic growth is modelled via appropriate evolution equations for the fibre while volumetric remodelling is realised by an evolution of the referential density. Both the strength of the fibre as well as the density follow Wolff-type laws. We however elaborate on two different approaches for the evolution of the fibre direction, namely an alignment with respect to strain or with respect to stress. One of the main benefits of the developed framework is therefore the opportunity to address the evolutions of the fibre strength and the fibre direction separately. It is then straightforward to set up appropriate integration algorithms such that the developed framework fits nicely into common, finite element schemes. Finally, several numerical examples underline the applicability of the proposed formulation.

Observation of direct evolution from antiferromagnetism to superconductivity in C u1 -xL ixFeAs (0 ≤x ≤1.0 )

NASA Astrophysics Data System (ADS)

Li, Kunkun; Yuan, Duanduan; Guo, Jiangang; Chen, Xiaolong

2018-04-01

We report the structure, antiferromagnetism, and superconductivity in C u1 -xL ixFeAs (0 ≤x ≤1.0 ) samples. A direct evolution from antiferromagnetism to superconductivity is observed as increasing doping level of Li. A phase diagram is constructed to show this evolution, which features no coexistence region between superconductivity and antiferromagnetism. This behavior shows that antiferromagnetic CuFeAs can be regarded as a parent compound to the observed superconductivity by equivalent doping, which is different from the cases with other FeAs-based superconductors. Structural analyses and first-principles calculations indicate that the anion height of F e2A s2 tetrahedral layer plays a crucial role on the physical properties. Moreover, the simple Fermi surface nesting picture adopted to explain the evolution from spin-density wave to superconductor in other FeAs-based superconductors might be not applicable to C u1 -xL ixFeAs .

A particle astrophysics magnet facility: ASTROMAG

NASA Technical Reports Server (NTRS)

Ormes, Jonathan F. (Editor); Israel, Martin H. (Editor); Mewaldt, Richard A. (Editor); Wiedenbeck, Mark E. (Editor)

1988-01-01

The primary scientific objectives of ASTROMAG are to: examine cosmological models by searching for antimatter and dark matter candidates; study the origin and evolution of matter in the galaxy by direct sampling of galactic matter; and study the origin and acceleration of the relativistic particle plasma in the galaxy and its effects on the dynamics and evolution of the galaxy. These general scientific objectives will be met by ASTROMAG with particle detection instruments designed to make the following observations: search, for anti-nuclei of helium and heavier element; measure the spectra of anti-protons and positrons; measure the isotopic composition of cosmic ray nuclei at energies of several GeV/amu; and measure the energy spectra of cosmic ray nuclei to very high energies.

Pursuing Darwin’s curious parallel: Prospects for a science of cultural evolution

PubMed Central

2017-01-01

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities. PMID:28739929

Pursuing Darwin's curious parallel: Prospects for a science of cultural evolution.

PubMed

Mesoudi, Alex

2017-07-24

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities.

Evolution of haploid-diploid life cycles when haploid and diploid fitnesses are not equal.

PubMed

Scott, Michael F; Rescan, Marie

2017-02-01

Many organisms spend a significant portion of their life cycle as haploids and as diploids (a haploid-diploid life cycle). However, the evolutionary processes that could maintain this sort of life cycle are unclear. Most previous models of ploidy evolution have assumed that the fitness effects of new mutations are equal in haploids and homozygous diploids, however, this equivalency is not supported by empirical data. With different mutational effects, the overall (intrinsic) fitness of a haploid would not be equal to that of a diploid after a series of substitution events. Intrinsic fitness differences between haploids and diploids can also arise directly, for example because diploids tend to have larger cell sizes than haploids. Here, we incorporate intrinsic fitness differences into genetic models for the evolution of time spent in the haploid versus diploid phases, in which ploidy affects whether new mutations are masked. Life-cycle evolution can be affected by intrinsic fitness differences between phases, the masking of mutations, or a combination of both. We find parameter ranges where these two selective forces act and show that the balance between them can favor convergence on a haploid-diploid life cycle, which is not observed in the absence of intrinsic fitness differences. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Transverse momentum dependent evolution: Matching semi-inclusive deep inelastic scattering processes to Drell-Yan and W/Z boson production

NASA Astrophysics Data System (ADS)

Sun, Peng; Yuan, Feng

2013-12-01

We examine the QCD evolution for the transverse momentum dependent observables in hard processes of semi-inclusive hadron production in deep inelastic scattering and Drell-Yan lepton pair production in pp collisions, including the spin-average cross sections and Sivers single transverse spin asymmetries. We show that the evolution equations derived by a direct integral of the Collins-Soper-Sterman evolution kernel from low to high Q can describe well the transverse momentum distributions of the unpolarized cross sections in the Q2 range from 2 to 100GeV2. In addition, the matching is established between our evolution and the Collins-Soper-Sterman resummation with b* prescription and Konychev-Nodalsky parametrization of the nonperturbative form factors, which are formulated to describe the Drell-Yan lepton pair and W/Z boson production in hadronic collisions. With these results, we present the predictions for the Sivers single transverse spin asymmetries in Drell-Yan lepton pair production and W± boson production in polarized pp and π-p collisions for several proposed experiments. We emphasize that these experiments will not only provide crucial test of the sign change of the Sivers asymmetry but also provide important opportunities to study the QCD evolution effects.

Digital Direct-to-Consumer Advertising: A Perfect Storm of Rapid Evolution and Stagnant Regulation Comment on "Trouble Spots in Online Direct-to-Consumer Prescription Drug Promotion: A Content Analysis of FDA Warning Letters".

PubMed

Mackey, Tim K

2016-02-03

The adoption and use of digital forms of direct-to-consumer advertising (also known as "eDTCA") is on the rise. At the same time, the universe of eDTCA is expanding, as technology on Internet-based platforms continues to evolve, from static websites, to social media, and nearly ubiquitous use of mobile devices. However, little is known about how this unique form of pharmaceutical marketing impacts consumer behavior, public health, and overall healthcare utilization. The study by Kim analyzing US Food and Drug Administration (FDA) notices of violations (NOVs) and warning letters regarding online promotional activities takes us in the right direction, but study results raise as many questions as it does answers. Chief among these are unanswered concerns about the unique regulatory challenges posed by the "disruptive" qualities of eDTCA, and whether regulators have sufficient resources and oversight powers to proactively address potential violations. Further, the globalization of eDTCA via borderless Internet-based technologies raises larger concerns about the potential global impact of this form of health marketing unique to only the United States and New Zealand. Collectively, these challenges make it unlikely that regulatory science will be able to keep apace with the continued rapid evolution of eDTCA unless more creative policy solutions are explored. © 2016 by Kerman University of Medical Sciences.

Rapid evolution in insect pests: the importance of space and time in population genomics studies.

PubMed

Pélissié, Benjamin; Crossley, Michael S; Cohen, Zachary Paul; Schoville, Sean D

2018-04-01

Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems. Copyright © 2018 Elsevier Inc. All rights reserved.

Evidence of directional and stabilizing selection in contemporary humans.

PubMed

Sanjak, Jaleal S; Sidorenko, Julia; Robinson, Matthew R; Thornton, Kevin R; Visscher, Peter M

2018-01-02

Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species.

Angiosperm ovules: diversity, development, evolution

PubMed Central

Endress, Peter K.

2011-01-01

Background Ovules as developmental precursors of seeds are organs of central importance in angiosperm flowers and can be traced back in evolution to the earliest seed plants. Angiosperm ovules are diverse in their position in the ovary, nucellus thickness, number and thickness of integuments, degree and direction of curvature, and histological differentiations. There is a large body of literature on this diversity, and various views on its evolution have been proposed over the course of time. Most recently evo–devo studies have been concentrated on molecular developmental genetics in ovules of model plants. Scope The present review provides a synthetic treatment of several aspects of the sporophytic part of ovule diversity, development and evolution, based on extensive research on the vast original literature and on experience from my own comparative studies in a broad range of angiosperm clades. Conclusions In angiosperms the presence of an outer integument appears to be instrumental for ovule curvature, as indicated from studies on ovule diversity through the major clades of angiosperms, molecular developmental genetics in model species, abnormal ovules in a broad range of angiosperms, and comparison with gymnosperms with curved ovules. Lobation of integuments is not an atavism indicating evolution from telomes, but simply a morphogenetic constraint from the necessity of closure of the micropyle. Ovule shape is partly dependent on locule architecture, which is especially indicated by the occurrence of orthotropous ovules. Some ovule features are even more conservative than earlier assumed and thus of special interest in angiosperm macrosystematics. PMID:21606056

On the thermodynamics of multilevel evolution.

PubMed

Tessera, Marc; Hoelzer, Guy A

2013-09-01

Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term "evolution" employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Oscillatory ductile compaction dynamics in a cylinder

NASA Astrophysics Data System (ADS)

Uri, Lina; Dysthe, Dag Kristian; Feder, Jens

2006-09-01

Ductile compaction is common in many natural systems, but the temporal evolution of such systems is rarely studied. We observe surprising oscillations in the weight measured at the bottom of a self-compacting ensemble of ductile grains. The oscillations develop during the first ten hours of the experiment, and usually persist through the length of an experiment (one week). The weight oscillations are connected to the grain-wall contacts, and are directly correlated with the observed strain evolution and the dynamics of grain-wall contacts during the compaction. Here, we present the experimental results and characteristic time constants of the system, and discuss possible reasons for the measured weight oscillations.

Oscillatory ductile compaction dynamics in a cylinder.

PubMed

Uri, Lina; Dysthe, Dag Kristian; Feder, Jens

2006-09-01

Ductile compaction is common in many natural systems, but the temporal evolution of such systems is rarely studied. We observe surprising oscillations in the weight measured at the bottom of a self-compacting ensemble of ductile grains. The oscillations develop during the first ten hours of the experiment, and usually persist through the length of an experiment (one week). The weight oscillations are connected to the grain-wall contacts, and are directly correlated with the observed strain evolution and the dynamics of grain-wall contacts during the compaction. Here, we present the experimental results and characteristic time constants of the system, and discuss possible reasons for the measured weight oscillations.

Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates.

PubMed

Kozmikova, Iryna; Kozmik, Zbynek

2015-12-01

Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the origin of vertebrates and molecular mechanisms underlying vertebrate evolution. The evolution of developmental control mechanisms during invertebrate-to-vertebrate transition involved not only gene duplication events, but also specific changes in spatial and temporal expression of many genes. To get insight into the spatiotemporal regulation of gene expression during invertebrate-to-vertebrate transition, functional studies of amphioxus gene regulatory elements are highly warranted. Here, we review transgenic studies performed in amphioxus and vertebrates using promoters and enhancers derived from the genome of Branchiostoma floridae. We describe the current methods of transgenesis in amphioxus, provide evidence of Tol2 transposon-generated transgenic embryos of Branchiostoma lanceolatum and discuss possible future directions. We envision that comparative transgenic analysis of gene regulatory sequences in the context of amphioxus and vertebrate embryos will likely provide an important mechanistic insight into the evolution of vertebrate body plan. Copyright © 2015 Elsevier B.V. All rights reserved.

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

NASA Technical Reports Server (NTRS)

Lahav, Noam

1993-01-01

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

Chemical evolution and the origin of life: cumulative keyword subject index 1970-1986

NASA Technical Reports Server (NTRS)

Roy, A. C.; Powers, J. V.; Rummel, J. D. (Principal Investigator)

1990-01-01

This cumulative subject index encompasses the subject indexes of the bibliographies on Chemical Evolution and the Origin of Life that were first published in 1970 and have continued through publication of the 1986 bibliography supplement. Early bibliographies focused on experimental and theoretical material dealing directly with the concepts of chemical evolution and the origin of life, excluding the broader areas of exobiology, biological evolution, and geochemistry. In recent years, these broader subject areas have also been incorporated as they appear in literature searches relating to chemical evolution and the origin of life, although direct attempts have not been made to compile all of the citations in these broad areas. The keyword subject indexes have also undergone an analogous change in scope. Compilers of earlier bibliographies used the most specific term available in producing the subject index. Compilers of recent bibliographies have used a number of broad terms relating to the overall subject content of each citation and specific terms where appropriate. The subject indexes of these 17 bibliographies have, in general, been cumulatively compiled exactly as they originally appeared. However, some changes have been made in an attempt to correct errors, combine terms, and provide more meaningful terms.

Structuring evolution: biochemical networks and metabolic diversification in birds.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2016-08-25

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

76 FR 11940 - Airworthiness Directives; Turbomeca Model Arriel 1E2, 1S, and 1S1 Turboshaft Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... discrepancies led to a ``one-off'' abnormal evolution of gas generator (NG) rating during engine starting. In... evolution of gas generator (NG) rating during engine starting. In one of these cases, this resulted in an...

Animal Foraging and the Evolution of Goal-Directed Cognition

ERIC Educational Resources Information Center

Hills, Thomas T.

2006-01-01

Foraging-and feeding-related behaviors across eumetazoans share similar molecular mechanisms, suggesting the early evolution of an optimal foraging behavior called area-restricted search (ARS), involving mechanisms of dopamine and glutamate in the modulation of behavioral focus. Similar mechanisms in the vertebrate basal ganglia control motor…

Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea?

PubMed

Nielsen, Claus

2013-08-16

Two theories for the origin of animal life cycles with planktotrophic larvae are now discussed seriously: The terminal addition theory proposes a holopelagic, planktotrophic gastraea as the ancestor of the eumetazoans with addition of benthic adult stages and retention of the planktotrophic stages as larvae, i.e. the ancestral life cycles were indirect. The intercalation theory now proposes a benthic, deposit-feeding gastraea as the bilaterian ancestor with a direct development, and with planktotrophic larvae evolving independently in numerous lineages through specializations of juveniles. Information from the fossil record, from mapping of developmental types onto known phylogenies, from occurrence of apical organs, and from genetics gives no direct information about the ancestral eumetazoan life cycle; however, there are plenty of examples of evolution from an indirect development to direct development, and no unequivocal example of evolution in the opposite direction. Analyses of scenarios for the two types of evolution are highly informative. The evolution of the indirect spiralian life cycle with a trochophora larva from a planktotrophic gastraea is explained by the trochophora theory as a continuous series of ancestors, where each evolutionary step had an adaptational advantage. The loss of ciliated larvae in the ecdysozoans is associated with the loss of outer ciliated epithelia. A scenario for the intercalation theory shows the origin of the planktotrophic larvae of the spiralians through a series of specializations of the general ciliation of the juvenile. The early steps associated with the enhancement of swimming seem probable, but the following steps which should lead to the complicated downstream-collecting ciliary system are without any advantage, or even seem disadvantageous, until the whole structure is functional. None of the theories account for the origin of the ancestral deuterostome (ambulacrarian) life cycle. All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value.

Crossflow-Vortex Breakdown on Swept Wings: Correlation of Nonlinear Physics

NASA Technical Reports Server (NTRS)

Joslin, R. D.; Streett, C. L.

1994-01-01

The spatial evolution of cross flow-vortex packets in a laminar boundary layer on a swept wing are computed by the direct numerical simulation of the incompressible Navier- Stokes equations. A wall-normal velocity distribution of steady suction and blowing at the wing surface is used to generate a strip of equally spaced and periodic disturbances along the span. Three simulations are conducted to study the effect of initial amplitude on the disturbance evolution, to determine the role of traveling cross ow modes in transition, and to devise a correlation function to guide theories of transition prediction. In each simulation, the vortex packets first enter a chordwise region of linear independent growth, then, the individual packets coalesce downstream and interact with adjacent packets, and, finally, the vortex packets nonlinearly interact to generate inflectional velocity profiles. As the initial amplitude of the disturbance is increased, the length of the evolution to breakdown decreases. For this pressure gradient, stationary modes dominate the disturbance evolution. A two-coeffcient function was devised to correlate the simulation results. The coefficients, combined with a single simulation result, provide sufficient information to generate the evolution pattern for disturbances of any initial amplitude.

Global analysis of genes involved in freshwater adaptation in threespine sticklebacks (Gasterosteus aculeatus).

PubMed

DeFaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Goto, Akira; Merilä, Juha

2011-06-01

Examples of parallel evolution of phenotypic traits have been repeatedly demonstrated in threespine sticklebacks (Gasterosteus aculeatus) across their global distribution. Using these as a model, we performed a targeted genome scan--focusing on physiologically important genes potentially related to freshwater adaptation--to identify genetic signatures of parallel physiological evolution on a global scale. To this end, 50 microsatellite loci, including 26 loci within or close to (<6 kb) physiologically important genes, were screened in paired marine and freshwater populations from six locations across the Northern Hemisphere. Signatures of directional selection were detected in 24 loci, including 17 physiologically important genes, in at least one location. Although no loci showed consistent signatures of selection in all divergent population pairs, several outliers were common in multiple locations. In particular, seven physiologically important genes, as well as reference ectodysplasin gene (EDA), showed signatures of selection in three or more locations. Hence, although these results give some evidence for consistent parallel molecular evolution in response to freshwater colonization, they suggest that different evolutionary pathways may underlie physiological adaptation to freshwater habitats within the global distribution of the threespine stickleback. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Specialization of the DNA-Cleaving Activity of a Group I Ribozyme Through In Vitro Evolution

NASA Technical Reports Server (NTRS)

Tsang, Joyce; Joyce, Gerald F.

1996-01-01

In an earlier study, an in vitro evolution procedure was applied to a large population of variants of the Tetrahymena group 1 ribozyme to obtain individuals with a 10(exp 5)-fold improved ability to cleave a target single-stranded DNA substrate under simulated physiological conditions. The evolved ribozymes also showed a twofold improvement, compared to the wild-type, in their ability to cleave a single-stranded RNA substrate. Here, we report continuation of the in vitro evolution process using a new selection strategy to achieve both enhanced DNA and diminished RNA-cleavage activity. Our strategy combines a positive selection for DNA cleavage with a negative selection against RNA binding. After 36 "generations" of in vitro evolution, the evolved population showed an approx. 100-fold increase in the ratio of DNA to RNA-cleavage activity. Site-directed mutagenesis experiment confirmed the selective advantage of two covarying mutations within the catalytic core of ribozyme that are largely responsible for this modified behavior. The population of ribozymes has now undergone a total of 63 successive generations of evolution, resulting in an average 28 mutations relative to the wild-type that are responsible for the altered phenotype.

Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection.

PubMed

Wise, Michael J; Rausher, Mark D

2013-06-01

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

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.

Perioperative goal-directed haemodynamic therapy based on flow parameters: a concept in evolution.

PubMed

Meng, L; Heerdt, P M

2016-12-01

Haemodynamic management incorporating direct or surrogate stroke volume monitoring has experienced a rapid evolution, because of emergence of the "goal-directed therapy" concept and technological developments aimed at providing a parameter leading to the goal. Nonetheless, consensus on both definitions of the ideal "goal" and strategies for achieving it remain elusive. For this review, we first consider basic physiological and patient monitoring factors relevant to the concept of "fluid responsiveness", and then focus upon randomized controlled trials and meta-analyses involving goal-directed haemodynamic therapy based on various flow parameters. Finally, we discuss the current status of noninvasive methods for monitoring fluid responsiveness. © The Author 2016. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Plasma-Assisted Growth of Silicon Nanowires by Sn Catalyst: Step-by-Step Observation

NASA Astrophysics Data System (ADS)

Tang, Jian; Maurice, Jean-Luc; Chen, Wanghua; Misra, Soumyadeep; Foldyna, Martin; Johnson, Erik V.; Roca i Cabarrocas, Pere

2016-10-01

A comprehensive study of the silicon nanowire growth process has been carried out. Silicon nanowires were grown by plasma-assisted-vapor-solid method using tin as a catalyst. We have focused on the evolution of the silicon nanowire density, morphology, and crystallinity. For the first time, the initial growth stage, which determines the nanowire (NW) density and growth direction, has been observed step by step. We provide direct evidence of the merging of Sn catalyst droplets and the formation of Si nanowires during the first 10 s of growth. We found that the density of Sn droplets decreases from 9000 Sn droplets/μm2 to 2000 droplets/μm2 after just 10 s of growth. Moreover, the long and straight nanowire density decreases from 170/μm2 after 2 min of growth to less than 10/μm2 after 90 min. This strong reduction in nanowire density is accompanied by an evolution of their morphology from cylindrical to conical, then to bend conical, and finally, to a bend inverted conical shape. Moreover, the changes in the crystalline structure of nanowires are from (i) monocrystalline to (ii) monocrystalline core/defective crystalline shell and then to (iii) monocrystalline core/defective crystalline shell/amorphous shell. The evolutions of NW properties have been explained in detail.

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.

Direct observation of pitting corrosion evolutions on carbon steel surfaces at the nano-to-micro- scales.

PubMed

Guo, Peng; La Plante, Erika Callagon; Wang, Bu; Chen, Xin; Balonis, Magdalena; Bauchy, Mathieu; Sant, Gaurav

2018-05-22

The Cl - -induced corrosion of metals and alloys is of relevance to a wide range of engineered materials, structures, and systems. Because of the challenges in studying pitting corrosion in a quantitative and statistically significant manner, its kinetics remain poorly understood. Herein, by direct, nano- to micro-scale observations using vertical scanning interferometry (VSI), we examine the temporal evolution of pitting corrosion on AISI 1045 carbon steel over large surface areas in Cl - -free, and Cl - -enriched solutions. Special focus is paid to examine the nucleation and growth of pits, and the associated formation of roughened regions on steel surfaces. By statistical analysis of hundreds of individual pits, three stages of pitting corrosion, namely, induction, propagation, and saturation, are quantitatively distinguished. By quantifying the kinetics of these processes, we contextualize our current understanding of electrochemical corrosion within a framework that considers spatial dynamics and morphology evolutions. In the presence of Cl - ions, corrosion is highly accelerated due to multiple autocatalytic factors including destabilization of protective surface oxide films and preservation of aggressive microenvironments within the pits, both of which promote continued pit nucleation and growth. These findings offer new insights into predicting and modeling steel corrosion processes in mid-pH aqueous environments.

Polishing the craft of genetic diversity creation in directed evolution.

PubMed

Tee, Kang Lan; Wong, Tuck Seng

2013-12-01

Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field. © 2013. Published by Elsevier Inc. All rights reserved.

Is floral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae).

PubMed

Tripp, Erin A; Manos, Paul S

2008-07-01

Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the large genus Ruellia. Phylogenetic analyses, morphological ordinations, ancestral state reconstructions, and a character mapping simulation were conducted to reveal key patterns in the direction and lability of floral characters associated with pollination. We found significant floral morphological differences among species that were generally associated with different groups of floral visitors. Floral evolution has been highly labile and also directional. Some specialized systems such as hawkmoth or bat pollination are likely evolutionary dead-ends. In contrast, specialized pollination by hummingbirds is clearly not a dead-end. We found evidence for multiple reverse transitions from presumed ancestral hummingbird pollination to more derived bee or insect pollination. These repeated origins of insect pollination from hummingbird-pollinated ancestors have not evolved without historical baggage. Flowers of insect-pollinated species derived from hummingbird-pollinated ancestors are morphologically more similar to hummingbird flowers than they are to other more distantly related insect-pollinated flowers. Finally, some pollinator switches were concomitant with changes in floral morphology that are associated with those pollinators. These observations are consistent with the hypothesis that some transitions have been adaptive in the evolution of Ruellia.

Sibling cooperation in earwig families provides insights into the early evolution of social life.

PubMed

Falk, Joachim; Wong, Janine W Y; Kölliker, Mathias; Meunier, Joël

2014-04-01

The evolutionary transition from solitary to social life is driven by direct and indirect fitness benefits of social interactions. Understanding the conditions promoting the early evolution of social life therefore requires identification of these benefits in nonderived social systems, such as animal families where offspring are mobile and able to disperse and will survive independently. Family life is well known to provide benefits to offspring through parental care, but research on sibling interactions generally focused on fitness costs to offspring due to competitive behaviors. Here we show experimentally that sibling interactions also reflect cooperative behaviors in the form of food sharing in nonderived families of the European earwig, Forficula auricularia. Food ingested by individual offspring was transferred to their siblings through mouth-to-anus contacts and active allo-coprophagy. These transfers occurred in both the presence and the absence of the tending mothers, even though the direct contact with the mothers limited sibling food sharing. Neither food deprivation or relatedness influenced the total amount of transferred food, but relatedness affected frass release and the behavioral mechanisms mediating food sharing. Related offspring obtained food predominately through allo-coprophagy, whereas unrelated offspring obtained food through mouth-to-anus contacts. Overall, this study emphasizes that sibling cooperation may be a key process promoting the early evolution of social life.

Publications of the Exobiology Program for 1988: A special bibliography

NASA Technical Reports Server (NTRS)

1990-01-01

The 1988 publications resulting from research pursued under the auspices of NASA's Exobiology Program are listed. The Exobiology Program is an integrated program designed to investigate those processes that may have been responsible for or related to the origin, evolution, and distribution of life in the universe. Research supported by this program is in the areas of cosmic evolution of biogenic compounds, prebiotic evolution, early evolution of life, and evolution of advanced life. Pre-mission and pre-project activities supporting these areas are included in the areas of solar system exploration and the search for extraterrestrial intelligence. A planetary protection subject area is also included because of its direct relevance to the Exobiology program.

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.

Distribution and evolution of genes responsible for biosynthesis of mycotoxins in Fusarium

USDA-ARS?s Scientific Manuscript database

Fusarium secondary metabolites (SMs) include some of the mycotoxins of greatest concern to food and feed safety. In fungi, genes directly involved in synthesis of the same SM are typically located adjacent to one another in gene clusters. To better understand the distribution and evolution of mycoto...

Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site.

PubMed

Prado, R A; Barbosa, J A; Ohmiya, Y; Viviani, V R

2011-07-01

The structural origin and evolution of bioluminescent activity of beetle luciferases from AMP/CoA ligases remains a mystery. Previously we cloned the luciferase-like enzyme from Zophobas morio mealworm, a reasonable protoluciferase model that could shine light on this mystery. Kinetic characterization and studies with D- and L-luciferin and their adenylates showed that stereoselectivity constitutes a critical feature for the origin of luciferase activity in AMP/CoA ligases. Comparison of the primary structures and modeling studies of this protoluciferase and the three main families of beetle luciferases showed that the carboxylic acid substrate binding site of this enzyme is smaller and more hydrophobic than the luciferin binding site of beetle luciferases, showing several substitutions of otherwise conserved residues. Thus, here we performed a site-directed mutagenesis survey of the carboxylic binding site motifs of the protoluciferase by replacing their residues by the respective conserved ones found in beetle luciferases in order to identify the structural determinants of luciferase/oxygenase activity. Although most of the substitutions had negative impact on the luminescence activity of the protoluciferase, only the substitution I327T improved the luminescence activity, resulting in a broad and 15 nm blue-shifted luminescence spectrum. Such substitution indicates the importance of the loop motif 322YGMSEI327 (341YGLTETT347 in Photinus pyralis luciferase) for luciferase activity, and indicates a possible route for the evolution of bioluminescence function of beetle luciferases.

Experimental evaluation of rigor mortis. VII. Effect of ante- and post-mortem electrocution on the evolution of rigor mortis.

PubMed

Krompecher, T; Bergerioux, C

1988-01-01

The influence of electrocution on the evolution of rigor mortis was studied on rats. Our experiments showed that: (1) Electrocution hastens the onset of rigor mortis. After an electrocution of 90 s, a complete rigor develops already 1 h post-mortem (p.m.) compared to 5 h p.m. for the controls. (2) Electrocution hastens the passing of rigor mortis. After an electrocution of 90 s, the first significant decrease occurs at 3 h p.m. (8 h p.m. in the controls). (3) These modifications in rigor mortis evolution are less pronounced in the limbs not directly touched by the electric current. (4) In case of post-mortem electrocution, the changes are slightly less pronounced, the resistance is higher and the absorbed energy is lower as compared with the ante-mortem electrocution cases. The results are completed by two practical observations on human electrocution cases.

Helical vortices: Quasiequilibrium states and their time evolution

NASA Astrophysics Data System (ADS)

Selçuk, Can; Delbende, Ivan; Rossi, Maurice

2017-08-01

The time evolution of a viscous helical vortex is investigated by direct numerical simulations of the Navier-Stokes equations where helical symmetry is enforced. Using conservation laws in the framework of helical symmetry, we elaborate an initial condition consisting in a finite core vortex, the time evolution of which leads to a generic quasiequilibrium state independent of the initial core size. Numerical results at different helical pitch values provide an accurate characterization in time for such helical states, for which specific techniques have been introduced: helix radius, angular velocity, stream function-velocity-vorticity relationships, and core properties (size, self-similarity, and ellipticity). Viscosity is shown to be at the origin of a small helical velocity component, which we relate to the helical vorticity component. Finally, changes in time of the flow topology are studied using the helical stream function and three-dimensional Lagrangian orbits.

US long distance fiber optic networks: Technology, evolution and advanced concepts. Volume 3: Advanced networks and economics

NASA Technical Reports Server (NTRS)

1986-01-01

This study projects until 2000 the evolution of long distance fiber optic networks in the U.S. Volume 1 is the executive Summary. Volume 2 focuses on fiber optic components and systems that are directly related to the operation of long-haul networks. Optimistic, pessimistic and most likely scenarios of technology development are presented. The activities of national and regional companies implementing fiber long haul networks are also highlighted, along with an analysis of the market and regulatory forces affecting network evolution. Volume 3 presents advanced fiber optic network concept definitions. Inter-LATA traffic is quantified and forms the basis for the construction of 11-, 15-, 17-, and 23-node networks. Using the technology projections from Volume 2, a financial model identifies cost drivers and determines circuit mile costs between any two LATAs. A comparison of fiber optics with alternative transmission concludes the report.

US long distance fiber optic networks: Technology, evolution and advanced concepts. Volume 2: Fiber optic technology and long distance networks

NASA Astrophysics Data System (ADS)

1986-10-01

The study projects until 2000 the evolution of long distance fiber optic networks in the U.S. Volume 1 is the Executive Summary. Volume 2 focuses on fiber optic components and systems that are directly related to the operation of long-haul networks. Optimistic, pessimistic and most likely scenarios of technology development are presented. The activities of national and regional companies implementing fiber long haul networks are also highlighted, along with an analysis of the market and regulatory forces affecting network evolution. Volume 3 presents advanced fiber optic network concept definitions. Inter-LATA traffic is quantified and forms the basis for the construction of 11-, 15-, 17-, and 23-node networks. Using the technology projections from Volume 2, a financial model identifies cost drivers and determines circuit mile costs between any two LATAs. A comparison of fiber optics with alternative transmission concludes the report.

US long distance fiber optic networks: Technology, evolution and advanced concepts. Volume 3: Advanced networks and economics

NASA Astrophysics Data System (ADS)

1986-10-01

This study projects until 2000 the evolution of long distance fiber optic networks in the U.S. Volume 1 is the executive Summary. Volume 2 focuses on fiber optic components and systems that are directly related to the operation of long-haul networks. Optimistic, pessimistic and most likely scenarios of technology development are presented. The activities of national and regional companies implementing fiber long haul networks are also highlighted, along with an analysis of the market and regulatory forces affecting network evolution. Volume 3 presents advanced fiber optic network concept definitions. Inter-LATA traffic is quantified and forms the basis for the construction of 11-, 15-, 17-, and 23-node networks. Using the technology projections from Volume 2, a financial model identifies cost drivers and determines circuit mile costs between any two LATAs. A comparison of fiber optics with alternative transmission concludes the report.

Seeking Synthesis: The Integrative Problem in Understanding Language and Its Evolution.

PubMed

Dale, Rick; Kello, Christopher T; Schoenemann, P Thomas

2016-04-01

We discuss two problems for a general scientific understanding of language, sequences and synergies: how language is an intricately sequenced behavior and how language is manifested as a multidimensionally structured behavior. Though both are central in our understanding, we observe that the former tends to be studied more than the latter. We consider very general conditions that hold in human brain evolution and its computational implications, and identify multimodal and multiscale organization as two key characteristics of emerging cognitive function in our species. This suggests that human brains, and cognitive function specifically, became more adept at integrating diverse information sources and operating at multiple levels for linguistic performance. We argue that framing language evolution, learning, and use in terms of synergies suggests new research questions, and it may be a fruitful direction for new developments in theory and modeling of language as an integrated system. Copyright © 2016 Cognitive Science Society, Inc.

Lagrangian model for the evolution of turbulent magnetic and passive scalar fields

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

Hater, T.; Grauer, R.; Homann, H.

2011-01-15

In this Brief Report we present an extension of the recent fluid deformation (RFD) closure introduced by Chevillard and Meneveau [L. Chevillard and C. Meneveau, Phys. Rev. Lett. 97, 174501 (2006)] which was developed for modeling the time evolution of Lagrangian fluctuations in incompressible Navier-Stokes turbulence. We apply the RFD closure to study the evolution of magnetic and passive scalar fluctuations. This comparison is especially interesting since the stretching term for the magnetic field and for the gradient of the passive scalar are similar but differ by a sign such that the effect of stretching and compression by the turbulentmore » velocity field is reversed. Probability density functions (PDFs) of magnetic fluctuations and fluctuations of the gradient of the passive scalar obtained from the RFD closure are compared against PDFs obtained from direct numerical simulations.« less

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

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

US long distance fiber optic networks: Technology, evolution and advanced concepts. Volume 2: Fiber optic technology and long distance networks

NASA Technical Reports Server (NTRS)

1986-01-01

The study projects until 2000 the evolution of long distance fiber optic networks in the U.S. Volume 1 is the Executive Summary. Volume 2 focuses on fiber optic components and systems that are directly related to the operation of long-haul networks. Optimistic, pessimistic and most likely scenarios of technology development are presented. The activities of national and regional companies implementing fiber long haul networks are also highlighted, along with an analysis of the market and regulatory forces affecting network evolution. Volume 3 presents advanced fiber optic network concept definitions. Inter-LATA traffic is quantified and forms the basis for the construction of 11-, 15-, 17-, and 23-node networks. Using the technology projections from Volume 2, a financial model identifies cost drivers and determines circuit mile costs between any two LATAs. A comparison of fiber optics with alternative transmission concludes the report.

Exoplanet Meteorology: Characterizing the Atmospheres of Directly Imaged Sub-Stellar Objects

NASA Astrophysics Data System (ADS)

Rajan, Abhijith; Gemini Planet Imager, Extrasolar Planets and Systems Imaging Group

2018-01-01

I study the structure, composition and dynamic evolution of directly imaged exoplanet and brown dwarf atmospheres, using spectrophotometric data collected from a range of ground and space based instrumentation. As part of my dissertation, I led studies exploring the atmospheres of brown dwarfs to search for weather variations, and characterized the near and mid infrared SEDs of imaged exoplanets to estimate their fundamental parameters. To understand the evolution of weather on brown dwarfs we conducted a multi-epoch study monitoring of 4 ultracool, T5 - Y0, brown dwarfs in the J-band to search for photometric variability. These cool brown dwarfs are predicted to have salt and sulfide clouds condensing in their upper atmosphere. The study found that cool brown dwarfs, fit with higher opacity clouds, were more likely to be variable. Through data taken with the Hubble Space Telescope and Gemini telescope we characterized the atmospheres of directly imaged exoplanets. For HR 8799, in near IR wavelengths unobservable from the ground, we constrained the presence of clouds in the outer planets. As a member of the Gemini Planet Imager Exoplanet Survey team, I analyzed archival HST data and examined the near-infrared colors of HD 106906b as seen with GPI, concluding that the companion shows weak evidence of a circumplanetary dust disk or cloud. Finally, by combining data spanning 1 - 5 um for the low mass Jupiter-like exoplanet, 51 Eri b, we found a cool effective temperature best fit by a patchy cloud atmosphere. This makes the planet an excellent candidate for future variability studies with the James Webb Space Telescope.

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.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Major regulatory factors in the evolution of development: the roles of goosecoid and Msx in the evolution of the direct-developing sea urchin Heliocidaris erythrogramma.

PubMed

Wilson, Keen A; Andrews, Mary E; Rudolf Turner, F; Raff, Rudolf A

2005-01-01

The transcription factors Gsc and Msx are expressed in the oral ectoderm of the indirect-developing sea urchin Heliocidaris tuberculata. Their patterns of expression are highly modified in the direct developer Heliocidaris erythrogramma, which lacks an oral ectoderm. We here test the hypothesis that they are large effect genes responsible for the loss of the oral ectoderm module in the direct-developing larva of H. erythrogramma as well as for the restoration of an overt oral ectoderm in H.e. xH.t. hybrids. We undertook misexpression/overexpression and knockdown assays in the two species and in hybrids by mRNA injection. The results indicate that dramatic changes of function of these transcription factors has occurred. One of these genes, Gsc, has the ability when misexpressed to partially restore oral ectoderm in H. erythrogramma. On the other hand, Msx has lost any oral function and instead has a role in mesoderm proliferation and patterning. In addition, we found that the H. tuberculataGsc is up regulated in H.e. xH.t. hybrids, showing a preferential use of the indirect developing parental gene in the development of the hybrid. We suggest that Gsc qualifies as a gene of large evolutionary effect and is partially responsible for the evolution of direct development of H. erythrogramma. We discuss these results in light of modularity and genetic networks in development, as well as in their implications for the rapid evolution of large morphological changes in development.

Phase and Texture Evolution in Chemically Derived PZT Thin Films on Pt Substrates

DTIC Science & Technology

2014-09-01

function of heating rate. The FWHM of the Ill PZT texture components is sim 2978 Journal of the American Ceramic Society Mhin et al. Vol. 97, No. 9...Z39.18 ABSTRACT Phase and Texture Evolution in Chemically Derived PZT Thin Films on Pt Substrates Report Title The crystallization of lead zirconate...phase influencing texture evolution. The results suggest that PZT nucleates directly on Pt, which explains the observation of a more highly oriented

Thermoadaptation-Directed Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426

PubMed Central

Kobayashi, Jyumpei; Wada, Keisuke; Furukawa, Megumi; Doi, Katsumi

2014-01-01

Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes. PMID:25326311

Thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from Geobacillus kaustophilus HTA426.

PubMed

Suzuki, Hirokazu; Kobayashi, Jyumpei; Wada, Keisuke; Furukawa, Megumi; Doi, Katsumi

2015-01-01

Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Directed evolution of P-glycoprotein cysteines reveals site-specific, non-conservative substitutions that preserve multidrug resistance.

PubMed

Swartz, Douglas J; Mok, Leo; Botta, Sri K; Singh, Anukriti; Altenberg, Guillermo A; Urbatsch, Ina L

2014-06-25

Pgp (P-glycoprotein) is a prototype ABC (ATP-binding-cassette) transporter involved in multidrug resistance of cancer. We used directed evolution to replace six cytoplasmic Cys (cysteine) residues in Pgp with all 20 standard amino acids and selected for active mutants. From a pool of 75000 transformants for each block of three Cys, we identified multiple mutants that preserved drug resistance and yeast mating activity. The most frequent substitutions were glycine and serine for Cys427 (24 and 20%, respectively) and Cys1070 (37 and 25%) of the Walker A motifs in the NBDs (nucleotide-binding domains), Cys1223 in NBD2 (25 and 8%) and Cys638 in the linker region (24 and 16%), whereas close-by Cys669 tolerated glycine (16%) and alanine (14%), but not serine (absent). Cys1121 in NBD2 showed a clear preference for positively charged arginine (38%) suggesting a salt bridge with Glu269 in the ICL2 (intracellular loop 2) may stabilize domain interactions. In contrast, three Cys residues in transmembrane α-helices could be successfully replaced by alanine. The resulting CL (Cys-less) Pgp was fully active in yeast cells, and purified proteins displayed drug-stimulated ATPase activities indistinguishable from WT (wild-type) Pgp. Overall, directed evolution identified site-specific, non-conservative Cys substitutions that allowed building of a robust CL Pgp, an invaluable new tool for future functional and structural studies, and that may guide the construction of other CL proteins where alanine and serine have proven unsuccessful.

Environment-dependent variation in selection on life history across small spatial scales.

PubMed

Lange, Rolanda; Monro, Keyne; J Marshall, Dustin

2016-10-01

Variation in life-history traits is ubiquitous, even though genetic variation is thought to be depleted by selection. One potential mechanism for the maintenance of trait variation is spatially variable selection. We explored spatial variation in selection in the field for a colonial marine invertebrate that shows phenotypic differences across a depth gradient of only 3 m. Our analysis included life-history traits relating to module size, colony growth, and phenology. Directional selection on colony growth varied in strength across depths, while module size was under directional selection at one depth but not the other. Differences in selection may explain some of the observed phenotypic differentiation among depths for one trait but not another: instead, selection should actually erode the differences observed for this trait. Our results suggest selection is not acting alone to maintain trait variation within and across environments in this system. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Structural Evolution of Q-Carbon and Nanodiamonds

NASA Astrophysics Data System (ADS)

Gupta, Siddharth; Bhaumik, Anagh; Sachan, Ritesh; Narayan, Jagdish

2018-04-01

This article provides insights pertaining to the first-order phase transformation involved in the growth of densely packed Q-carbon and nanodiamonds by nanosecond laser melting and quenching of diamond-like carbon (DLC) thin films. DLC films with different sp 3 content were melted rapidly in a controlled way in super-undercooled state and quenched, leading to formation of distinct nanostructures, i.e., nanodiamonds, Q-carbon, and Q-carbon nanocomposites. This analysis provides direct evidence of the dependence of the super-undercooling on the structural evolution of Q-carbon. Finite element heat flow calculations showed that the super-undercooling varies monotonically with the sp 3 content. The phenomenon of solid-liquid interfacial instability during directional solidification from the melt state is studied in detail. The resulting lateral segregation leads to formation of cellular filamentary Q-carbon nanostructures. The dependence of the cell size and wavelength at the onset of instability on the sp 3 content of DLC thin films was modeled based on perturbation theory.

Delayed collapses of Bose-Einstein condensates in relation to anti-de Sitter gravity.

PubMed

Biasi, Anxo F; Mas, Javier; Paredes, Angel

2017-03-01

We numerically investigate spherically symmetric collapses in the Gross-Pitaevskii equation with attractive nonlinearity in a harmonic potential. Even below threshold for direct collapse, the wave function bounces off from the origin and may eventually become singular after a number of oscillations in the trapping potential. This is reminiscent of the evolution of Einstein gravity sourced by a scalar field in anti de Sitter space where collapse corresponds to black-hole formation. We carefully examine the long time evolution of the wave function for continuous families of initial states in order to sharpen out this qualitative coincidence which may bring new insights in both directions. On the one hand, we comment on possible implications for the so-called Bosenova collapses in cold atom Bose-Einstein condensates. On the other hand, Gross-Pitaevskii provides a toy model to study the relevance of either the resonance conditions or the nonlinearity for the problem of anti de Sitter instability.

Observation of Compressible Plasma Mix in Cylindrically Convergent Implosions

NASA Astrophysics Data System (ADS)

Barnes, Cris W.; Batha, Steven H.; Lanier, Nicholas E.; Magelssen, Glenn R.; Tubbs, David L.; Dunne, A. M.; Rothman, Steven R.; Youngs, David L.

2000-10-01

An understanding of hydrodynamic mix in convergent geometry will be of key importance in the development of a robust ignition/burn capability on NIF, LMJ and future pulsed power machines. We have made use of the OMEGA laser facility at the University of Rochester to investigate directly the mix evolution in a convergent geometry, compressible plasma regime. The experiments comprise a plastic cylindrical shell imploded by direct laser irradiation. The cylindrical shell surrounds a lower density plastic foam which provides sufficient back pressure to allow the implosion to stagnate at a sufficiently high radius to permit quantitative radiographic diagnosis of the interface evolution near turnaround. The susceptibility to mix of the shell-foam interface is varied by choosing different density material for the inner shell surface (thus varying the Atwood number). This allows the study of shock-induced Richtmyer-Meshkov growth during the coasting phase, and Rayleigh-Taylor growth during the stagnation phase. The experimental results will be described along with calculational predictions using various radiation hydrodynamics codes and turbulent mix models.

Autonomy and Sensor Webs: The Evolution of Mission Operations

NASA Technical Reports Server (NTRS)

Sherwood, Rob

2008-01-01

Demonstration of these sensor web capabilities will enable fast responding science campaigns that combine spaceborne, airborne, and ground assets. Sensor webs will also require new operations paradigms. These sensor webs will be operated directly by scientists using science goals to control their instruments. We will explore these new operations architectures through a study of existing sensor web prototypes.

Poultry vaccination directed evolution of H9N2 low pathogenicity avian influenza viruses in Korea

USDA-ARS?s Scientific Manuscript database

Significant economic losses in the poultry industries have resulted from H9N2 low pathogenic avian influenza virus infections across North Africa, the Middle East and Asia. The present study investigated the evolutionary dynamics of H9N2 viruses circulating in Korea from 1996 to 2012. Our analysis o...

Microstructural Rearrangements and their Rheological Implications in a Model Thixotropic Elastoviscoplastic Fluid

NASA Astrophysics Data System (ADS)

Jamali, Safa; McKinley, Gareth H.; Armstrong, Robert C.

2017-01-01

We identify the sequence of microstructural changes that characterize the evolution of an attractive particulate gel under flow and discuss their implications on macroscopic rheology. Dissipative particle dynamics is used to monitor shear-driven evolution of a fabric tensor constructed from the ensemble spatial configuration of individual attractive constituents within the gel. By decomposing this tensor into isotropic and nonisotropic components we show that the average coordination number correlates directly with the flow curve of the shear stress versus shear rate, consistent with theoretical predictions for attractive systems. We show that the evolution in nonisotropic local particle rearrangements are primarily responsible for stress overshoots (strain-hardening) at the inception of steady shear flow and also lead, at larger times and longer scales, to microstructural localization phenomena such as shear banding flow-induced structure formation in the vorticity direction.

Multiphysics of bone remodeling: A 2D mesoscale activation simulation.

PubMed

Spingarn, C; Wagner, D; Rémond, Y; George, D

2017-01-01

In this work, we present an evolutive trabecular model for bone remodeling based on a boundary detection algorithm accounting for both biology and applied mechanical forces, known to be an important factor in bone evolution. A finite element (FE) numerical model using the Abaqus/Standard® software was used with a UMAT subroutine to solve the governing coupled mechanical-biological non-linear differential equations of the bone evolution model. The simulations present cell activation on a simplified trabeculae configuration organization with trabecular thickness of 200µm. For this activation process, the results confirm that the trabeculae are mainly oriented in the active direction of the principal mechanical stresses and according to the principal applied mechanical load directions. The trabeculae surface activation is clearly identified and can provide understanding of the different bone cell activations in more complex geometries and load conditions.

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.

Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface.

PubMed

Limsakul, Praopim; Peng, Qin; Wu, Yiqian; Allen, Molly E; Liang, Jing; Remacle, Albert G; Lopez, Tyler; Ge, Xin; Kay, Brian K; Zhao, Huimin; Strongin, Alex Y; Yang, Xiang-Lei; Lu, Shaoying; Wang, Yingxiao

2018-04-19

Monitoring enzymatic activities at the cell surface is challenging due to the poor efficiency of transport and membrane integration of fluorescence resonance energy transfer (FRET)-based biosensors. Therefore, we developed a hybrid biosensor with separate donor and acceptor that assemble in situ. The directed evolution and sequence-function analysis technologies were integrated to engineer a monobody variant (PEbody) that binds to R-phycoerythrin (R-PE) dye. PEbody was used for visualizing the dynamic formation/separation of intercellular junctions. We further fused PEbody with the enhanced CFP and an enzyme-specific peptide at the extracellular surface to create a hybrid FRET biosensor upon R-PE capture for monitoring membrane-type-1 matrix metalloproteinase (MT1-MMP) activities. This biosensor revealed asymmetric distribution of MT1-MMP activities, which were high and low at loose and stable cell-cell contacts, respectively. Therefore, directed evolution and rational design are promising tools to engineer molecular binders and hybrid FRET biosensors for monitoring molecular regulations at the surface of living cells. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evolution of meiotic recombination genes in maize and teosinte.

PubMed

Sidhu, Gaganpreet K; Warzecha, Tomasz; Pawlowski, Wojciech P

2017-01-25

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

PubMed Central

2013-01-01

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome. PMID:24267946

Numerical study on tilting salt finger in a laminar shear flow

NASA Astrophysics Data System (ADS)

Zhang, Xianfei; Wang, Ling-ling; Lin, Cheng; Zhu, Hai; Zeng, Cheng

2018-02-01

Salt fingers as a mixing mechanism in the ocean have been investigated for several decades, together with a key issue being focused on their convective evolution and flux ratio variation. However, related studies on tilting fingers in the ocean produced by shear flow have been ignored by previous researchers. In this paper, a 2-D numerical model is presented to study the evolution of the double-diffusion salt finger in a two-layer thermohaline system with laminar shear flow. The model is divided into a steady-state solver and double-diffusion convection system, aimed to reveal the effect of shear flow on salt fingers and analyze the mechanism behind the shear and fingers. Several cases are conducted for Re = 0 ˜ 900 to study the evolution of salt fingers in a laminar shear flow and the variation of salt flux with Re. The results show that salt fingers exist and tilt in the presence of laminar shear flow. The mass transport in the vertical direction is weakened as the Reynolds number increases. An asymmetric structure of the salt finger is discovered and accounts for the morphological tilt and salt flux reduction.

The MAGO experiment for dust environment monitoring on the Martian surface

NASA Astrophysics Data System (ADS)

Palumbo, P.; Battaglia, R.; Brucato, J. R.; Colangeli, L.; della Corte, V.; Esposito, F.; Ferrini, G.; Mazzotta Epifani, E.; Mennella, V.; Palomba, E.; Panizza, A.; Rotundi, A.

2004-01-01

Among the main directions identified for future Martian exploration, the study of the properties of dust dispersed in the atmosphere, its cycle and the impact on climate are considered of primary relevance. Dust storms, dust devils and the dust ``cycle'' have been identified and studied by past remote and in situ experiments, but little quantitative information is available on these processes, so far. The airborne dust contributes to the determination of the dynamic and thermodynamic evolution of the atmosphere, including the large-scale circulation processes and its impact on the climate of Mars. Moreover, aeolian erosion, redistribution of dust on the surface and weathering processes are mostly known only qualitatively. In order to improve our knowledge of the airborne dust evolution and other atmospheric processes, it is mandatory to measure the amount, mass-size distribution and dynamical properties of solid particles in the Martian atmosphere as a function of time. In this context, there is clearly a need for the implementation of experiments dedicated to study directly atmospheric dust. The Martian atmospheric grain observer (MAGO) experiment is aimed at providing direct quantitative measurements of mass and size distributions of dust particles, a goal that has never been fully achieved so far. The instrument design combines three types of sensors to monitor in situ the dust mass flux (micro balance system, MBS) and single grain properties (grain detection system, GDS+impact sensor, IS). Technical solutions and science capabilities are discussed in this paper.

Laboratory insights into the chemical and kinetic evolution of several organic molecules under simulated Mars surface UV radiation conditions

NASA Astrophysics Data System (ADS)

Poch, O.; Kaci, S.; Stalport, F.; Szopa, C.; Coll, P.

2014-11-01

The search for organic carbon at the surface of Mars, as clues of past habitability or remnants of life, is a major science goal of Mars' exploration. Understanding the chemical evolution of organic molecules under current martian environmental conditions is essential to support the analyses performed in situ. What molecule can be preserved? What is the timescale of organic evolution at the surface? This paper presents the results of laboratory investigations dedicated to monitor the evolution of organic molecules when submitted to simulated Mars surface ultraviolet radiation (190-400 nm), mean temperature (218 ± 2 K) and pressure (6 ± 1 mbar) conditions. Experiments are done with the MOMIE simulation setup (for Mars Organic Molecules Irradiation and Evolution) allowing both a qualitative and quantitative characterization of the evolution the tested molecules undergo (Poch, O. et al. [2013]. Planet. Space Sci. 85, 188-197). The chemical structures of the solid products and the kinetic parameters of the photoreaction (photolysis rate, half-life and quantum efficiency of photodecomposition) are determined for glycine, urea, adenine and chrysene. Mellitic trianhydride is also studied in order to complete a previous study done with mellitic acid (Stalport, F., Coll, P., Szopa, C., Raulin, F. [2009]. Astrobiology 9, 543-549), by studying the evolution of mellitic trianhydride. The results show that solid layers of the studied molecules have half-lives of 10-103 h at the surface of Mars, when exposed directly to martian UV radiation. However, organic layers having aromatic moieties and reactive chemical groups, as adenine and mellitic acid, lead to the formation of photoresistant solid residues, probably of macromolecular nature, which could exhibit a longer photostability. Such solid organic layers are found in micrometeorites or could have been formed endogenously on Mars. Finally, the quantum efficiencies of photodecomposition at wavelengths from 200 to 250 nm, determined for each of the studied molecules, range from 10-2 to 10-6 molecule photon-1 and apply for isolated molecules exposed at the surface of Mars. These kinetic parameters provide essential inputs for numerical modeling of the evolution of Mars' current reservoir of organic molecules. Organic molecules adsorbed on martian minerals may have different kinetic parameters and lead to different endproducts. The present study paves the way for the interpretation of more complex simulation experiments where organics will be mixed with martian mineral analogs.

Direct Observation of Lattice Aluminum Environments in Li Ion Cathodes LiNi1-y-zCoyAlzO2 and Al-Doped LiNixMnyCozO2 via (27)Al MAS NMR Spectroscopy.

PubMed

Dogan, Fulya; Vaughey, John T; Iddir, Hakim; Key, Baris

2016-07-06

Direct observations of local lattice aluminum environments have been a major challenge for aluminum-bearing Li ion battery materials, such as LiNi1-y-zCoyAlzO2 (NCA) and aluminum-doped LiNixMnyCozO2 (NMC). (27)Al magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy is the only structural probe currently available that can qualitatively and quantitatively characterize lattice and nonlattice (i.e., surface, coatings, segregation, secondary phase etc.) aluminum coordination and provide information that helps discern its effect in the lattice. In the present study, we use NMR to gain new insights into transition metal (TM)-O-Al coordination and evolution of lattice aluminum sites upon cycling. With the aid of first-principles DFT calculations, we show direct evidence of lattice Al sites, nonpreferential Ni/Co-O-Al ordering in NCA, and the lack of bulk lattice aluminum in aluminum-"doped" NMC. Aluminum coordination of the paramagnetic (lattice) and diamagnetic (nonlattice) nature is investigated for Al-doped NMC and NCA. For the latter, the evolution of the lattice site(s) upon cycling is also studied. A clear reordering of lattice aluminum environments due to nickel migration is observed in NCA upon extended cycling.

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.

Carbon in the Universe

NASA Technical Reports Server (NTRS)

Allamandola, Louis J.

2013-01-01

Over the past few decades, NASA missions have revealed that we live in a Universe that is not a hydrogen-dominated, physicist's paradise, but in a molecular Universe with complex molecules directly interwoven into its fabric. These missions have shown that molecules are an abundant and important component of astronomical objects at all stages of their evolution and that they play a key role in many processes that dominate the structure and evolution of galaxies. Closer to home in our galaxy, the Milky Way, they have revealed a unique and complex organic inventory of regions of star and planet formation that may well represent some of the prebiotic roots to life. Astrobiology emerges from the great interest in understanding astrochemical evolution from simple to complex molecules, especially those with biogenic potential and the roles they may play as primordial seeds in the origin of life on habitable worlds. The first part of this talk will highlight how infrared spectroscopic studies of interstellar space, combined with dedicated laboratory simulations, have revealed the widespread presence of complex organics across deep space. The remainder of the presentation will focus on the evolution of these materials and astrobiology.

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).

Protobiological informatoin, bidirectional recognition and reverse translation

NASA Technical Reports Server (NTRS)

Fox, S. W.; Nakashima, T.; Przybylski, A.; Vaughan, G.

1986-01-01

Emergence of protobiological information has been suggested by experiments in which heated mixtures of alpha-amino acids order themselves into a self limited array of thermal proteins. The polymers display selective catalytic, hormonal, and other activities. Interactions of varied cationic thermal proteins with polynucleotides indicate selective recognition in both directions. Reverse translation is partly a missing link in the molecular evolution flowsheet. The self ordering of amino acids serves conceptually as a deterministic evolutionary precursor of the modern coding mechanism. The possibility for the evolution of information at an early nontemplated protein stage is supported by findings of electrical signals from proteinoid microspheres prepared with no DNA/RNA in their history. The deposition of thermal copolyamino acids on lipid membranes in the Mueller-Rudin apparatus has here been found to produce electrical behavior like that evoked by bacterial EIM polypeptide. A new procedure is to make a film of membrane on the electrode; the results provide maximal repeatability. The principle of nonrandom biomacromolecular specificity identified by these studies in molecular evolution have been extrapolated to principles of evolution of advanced organisms.

Parallel evolution of sexual isolation in sticklebacks.

PubMed

Boughman, Janette Wenrick; Rundle, Howard D; Schluter, Dolph

2005-02-01

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

An Analysis on a Negotiation Model Based on Multiagent Systems with Symbiotic Learning and Evolution

NASA Astrophysics Data System (ADS)

Hossain, Md. Tofazzal

This study explores an evolutionary analysis on a negotiation model based on Masbiole (Multiagent Systems with Symbiotic Learning and Evolution) which has been proposed as a new methodology of Multiagent Systems (MAS) based on symbiosis in the ecosystem. In Masbiole, agents evolve in consideration of not only their own benefits and losses, but also the benefits and losses of opponent agents. To aid effective application of Masbiole, we develop a competitive negotiation model where rigorous and advanced intelligent decision-making mechanisms are required for agents to achieve solutions. A Negotiation Protocol is devised aiming at developing a set of rules for agents' behavior during evolution. Simulations use a newly developed evolutionary computing technique, called Genetic Network Programming (GNP) which has the directed graph-type gene structure that can develop and design the required intelligent mechanisms for agents. In a typical scenario, competitive negotiation solutions are reached by concessions that are usually predetermined in the conventional MAS. In this model, however, not only concession is determined automatically by symbiotic evolution (making the system intelligent, automated, and efficient) but the solution also achieves Pareto optimal automatically.

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

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.

The rock components and structures of Archean greenstone belts: An overview

NASA Technical Reports Server (NTRS)

Lowe, D. R.; Byerly, G. R.

1986-01-01

Knowledge of the character and evolution of the Earth's early crust is derived from the studies of the rocks and structures in Archean greenstone belts. Ability to resolve the petrologic, sedimentological and structural histories of greenstone belts, however, hinges first on an ability to apply the concepts and procedures of classical stratigraphy. Unfortunately, early Precambrian greenstone terrains present particular problems to stratigraphic analysis. Many current controversies of greenstone belt petrogenesis, sedimentology, tectonics and evolution arise more from an inability to develop a clear stratigraphic picture of the belts than from ambiguities in interpretation. Four particular stratigraphic problems that afflict studies of Archean greenstone belts are considered: determination of facing directions, correlation of lithologic units, identification of primary lithologies and discrimination of stratigraphic versus structural contacts.

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.

Foundational errors in the Neutral and Nearly-Neutral theories of evolution in relation to the Synthetic Theory: is a new evolutionary paradigm necessary?

PubMed

Valenzuela, Carlos Y

2013-01-01

The Neutral Theory of Evolution (NTE) proposes mutation and random genetic drift as the most important evolutionary factors. The most conspicuous feature of evolution is the genomic stability during paleontological eras and lack of variation among taxa; 98% or more of nucleotide sites are monomorphic within a species. NTE explains this homology by random fixation of neutral bases and negative selection (purifying selection) that does not contribute either to evolution or polymorphisms. Purifying selection is insufficient to account for this evolutionary feature and the Nearly-Neutral Theory of Evolution (N-NTE) included negative selection with coefficients as low as mutation rate. These NTE and N-NTE propositions are thermodynamically (tendency to random distributions, second law), biotically (recurrent mutation), logically and mathematically (resilient equilibria instead of fixation by drift) untenable. Recurrent forward and backward mutation and random fluctuations of base frequencies alone in a site make life organization and fixations impossible. Drift is not a directional evolutionary factor, but a directional tendency of matter-energy processes (second law) which threatens the biotic organization. Drift cannot drive evolution. In a site, the mutation rates among bases and selection coefficients determine the resilient equilibrium frequency of bases that genetic drift cannot change. The expected neutral random interaction among nucleotides is zero; however, huge interactions and periodicities were found between bases of dinucleotides separated by 1, 2... and more than 1,000 sites. Every base is co-adapted with the whole genome. Neutralists found that neutral evolution is independent of population size (N); thus neutral evolution should be independent of drift, because drift effect is dependent upon N. Also, chromosome size and shape as well as protein size are far from random.

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal

PubMed Central

Ackerly, David

2009-01-01

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to ≈300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification. PMID:19843698

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal.

PubMed

Ackerly, David

2009-11-17

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to approximately 300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification.

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.

Large Scale Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1997-01-01

Jet noise is a major concern in the design of commercial aircraft. Studies by various researchers suggest that aerodynamic noise is a major contributor to jet noise. Some of these studies indicate that most of the aerodynamic jet noise due to turbulent mixing occurs when there is a rapid variation in turbulent structure, i.e. rapidly growing or decaying vortices. The objective of this research was to simulate a compressible round jet to study the non-linear evolution of vortices and the resulting acoustic radiations. In particular, to understand the effect of turbulence structure on the noise. An ideal technique to study this problem is Direct Numerical Simulations (DNS), because it provides precise control on the initial and boundary conditions that lead to the turbulent structures studied. It also provides complete 3-dimensional time dependent data. Since the dynamics of a temporally evolving jet are not greatly different from those of a spatially evolving jet, a temporal jet problem was solved, using periodicity in the direction of the jet axis. This enables the application of Fourier spectral methods in the streamwise direction. Physically this means that turbulent structures in the jet are repeated in successive downstream cells instead of being gradually modified downstream into a jet plume. The DNS jet simulation helps us understand the various turbulent scales and mechanisms of turbulence generation in the evolution of a compressible round jet. These accurate flow solutions will be used in future research to estimate near-field acoustic radiation by computing the total outward flux across a surface and determine how it is related to the evolution of the turbulent solutions. Furthermore, these simulations allow us to investigate the sensitivity of acoustic radiations to inlet/boundary conditions, with possible appli(,a- tion to active noise suppression. In addition, the data generated can be used to compute, various turbulence quantities such as mean velocities, turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved DNS of a turbulent jet flow is produced.

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.

Cancellation exponent and multifractal structure in two-dimensional magnetohydrodynamics: direct numerical simulations and Lagrangian averaged modeling.

PubMed

Graham, Jonathan Pietarila; Mininni, Pablo D; Pouquet, Annick

2005-10-01

We present direct numerical simulations and Lagrangian averaged (also known as alpha model) simulations of forced and free decaying magnetohydrodynamic turbulence in two dimensions. The statistics of sign cancellations of the current at small scales is studied using both the cancellation exponent and the fractal dimension of the structures. The alpha model is found to have the same scaling behavior between positive and negative contributions as the direct numerical simulations. The alpha model is also able to reproduce the time evolution of these quantities in free decaying turbulence. At large Reynolds numbers, an independence of the cancellation exponent with the Reynolds numbers is observed.

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.

Variation in DNA methylation is not consistently reflected by CpG depletion or sociality in Hymenoptera

USDA-ARS?s Scientific Manuscript database

Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of social behavior is associated with enhanced gene regulatory potential, which may in...

Exploring Hydrogen Evolution and the Overpotential

ERIC Educational Resources Information Center

Lyon, Yana A.; Roberts, Adrienne A.; McMillin, David R.

2015-01-01

The laboratory experiment described provides insight into the energetics of hydrogen evolution at an electrode as well as the intrinsic barrier that typically impedes reaction. In the course of the exercise, students find that Sn(s) is thermodynamically capable of combining with protons to form hydrogen, but that the direct reaction occurs at a…

Evolution of the Anatomical Theatre in Padova

ERIC Educational Resources Information Center

Macchi, Veronica; Porzionato, Andrea; Stecco, Carla; Caro, Raffaele

2014-01-01

The anatomical theatre played a pivotal role in the evolution of medical education, allowing students to directly observe and participate in the process of dissection. Due to the increase of training programs in clinical anatomy, the Institute of Human Anatomy at the University of Padova has renovated its dissecting room. The main guidelines in…

The evolution of eyes and visually guided behaviour

PubMed Central

Nilsson, Dan-Eric

2009-01-01

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes. PMID:19720648

The role of sexual preferences in intrasexual female competition

PubMed Central

2012-01-01

Background While search costs have long been understood to affect the evolution of female preference, other costs associated with mating have been the focus of much less attention. Here I consider a novel mate choice cost: female-female intrasexual competition, that is, when females compete with each other for mates. This competition results in cost to female fecundity, such as a reduction in fertility due to decreased direct benefits, sperm limitation, or time and resources spent competing for a mate. I asked if female-female competition affects the evolution of preferences, and further, if the presence of multiple, different, preferences in a population can reduce competitive costs. Results Using population genetic models of preference and trait evolution, I found that intrasexual competition leads to direct selection against female preferences, and restricts the parameter space under which preference may evolve. I also examined how multiple, different, preferences affected preference evolution with female intrasexual competition. Conclusions Multiple preferences primarily serve to increase competitive costs and decrease the range of parameters under which preferences may evolve. PMID:23148567

A cortical circuit for voluntary laryngeal control: Implications for the evolution language.

PubMed

Hickok, Gregory

2017-02-01

The development of voluntary laryngeal control has been argued to be a key innovation in the evolution of language. Part of the evidence for this hypothesis comes from neuroscience. For example, comparative research has shown that humans have direct cortical innervation of motor neurons controlling the larynx, whereas nonhuman primates do not. Research on cortical motor control circuits has shown that the frontal lobe cortical motor system does not work alone; it is dependent on sensory feedback control circuits. Thus, the human brain must have evolved not only the required efferent motor pathway but also the cortical circuit for controlling those efferent signals. To fill this gap, I propose a link between the evolution of laryngeal control and neuroscience research on the human dorsal auditory-motor speech stream. Specifically, I argue that the dorsal stream Spt (Sylvian parietal-temporal) circuit evolved in step with the direct cortico-laryngeal control pathway and together represented a key advance in the evolution of speech. I suggest that a cortical laryngeal control circuit may play an important role in language by providing a prosodic frame for speech planning.

Selection on parental performance opposes selection for larger body mass in a wild population of blue tits.

PubMed

Thomson, Caroline E; Bayer, Florian; Crouch, Nicholas; Farrell, Samantha; Heap, Elizabeth; Mittell, Elizabeth; Zurita-Cassinello, Mar; Hadfield, Jarrod D

2017-03-01

There is abundant evidence in many taxa for positive directional selection on body size, and yet little evidence for microevolutionary change. In many species, variation in body size is partly determined by the actions of parents, so a proposed explanation for stasis is the presence of a negative genetic correlation between direct and parental effects. Consequently, selecting genes for increased body size would result in a correlated decline in parental effects, reducing body size in the following generation. We show that these arguments implicitly assume that parental care is cost free, and that including a cost alters the predicted genetic architectures needed to explain stasis. Using a large cross-fostered population of blue tits, we estimate direct selection on parental effects for body mass, and show it is negative. Negative selection is consistent with a cost to parental care, mainly acting through a reduction in current fecundity rather than survival. Under these conditions, evolutionary stasis is possible for moderately negative genetic correlations between direct and parental effects. This is in contrast to the implausibly extreme correlations needed when care is assumed to be cost-free. Thus, we highlight the importance of accounting correctly for complete selection acting on traits across generations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The characteristic black hole mass resulting from direct collapse in the early Universe

NASA Astrophysics Data System (ADS)

Latif, M. A.; Schleicher, D. R. G.; Schmidt, W.; Niemeyer, J. C.

2013-12-01

Black holes of a billion solar masses are observed in the infant Universe a few hundred million years after the big bang. The direct collapse of protogalactic gas clouds in primordial haloes with Tvir ≥ 104 K provides the most promising way to assemble massive black holes. In this study, we aim to determine the characteristic mass scale of seed black holes and the time evolution of the accretion rates resulting from the direct collapse model. We explore the formation of supermassive black holes via cosmological large eddy simulations (LES) by employing sink particles and following their evolution for 20 000 yr after the formation of the first sink. As the resulting protostars were shown to have cool atmospheres in the presence of strong accretion, we assume here that UV feedback is negligible during this calculation. We confirm this result in a comparison run without sinks. Our findings show that black hole seeds with characteristic mass of 105 M⊙ are formed in the presence of strong Lyman-Werner flux which leads to an isothermal collapse. The characteristic mass is about two times higher in LES compared to the implicit large eddy simulations. The accretion rates increase with time and reach a maximum value of 10 M⊙ yr-1 after 104 yr. Our results show that the direct collapse model is clearly feasible as it provides the expected mass of the seed black holes.

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.

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.

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

PubMed Central

Szitenberg, Amir; Cha, Soyeon; Opperman, Charles H.; Bird, David M.; Blaxter, Mark L.; Lunt, David H.

2016-01-01

Abstract Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes. PMID:27566762

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.

Fruit evolution and diversification in campanulid angiosperms.

PubMed

Beaulieu, Jeremy M; Donoghue, Michael J

2013-11-01

With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long-standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. Although these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Evolution of streamer groups in nonthermal plasma

NASA Astrophysics Data System (ADS)

Okubo, M.

2015-12-01

Nonthermal plasmas (NTPs) induced by atmospheric nanosecond pulsed corona discharge have been studied for controlling pollution from combustors, such as boilers, incinerators, and diesel engines. In high-speed short-width high-voltage pulsed corona discharge-induced plasmas, primary streamer evolution is followed by secondary streamer evolution. Though this phenomenon is known experimentally, the details of the structures of the streamers and their evolution mechanisms have not been fully clarified. In this letter, we perform quasi two-dimensional numerical analysis of nonequilibrium NTP induced by a nanosecond positive pulsed corona discharge. The continuum fluid equations for two-temperature nonequilibrium NTP are used as governing equations. In this study, 197 gas phase reactions for 25 chemical species and 21 surface reactions on the inner glass wall surface are considered in an air plasma under atmospheric pressure. The simulated behavior of the streamer groups agrees with experimental observations. Soon after the voltage increases on the reactor, primary streamers are formed, which may transit the complete gap, disappearing near the peak voltage. Next, second streamers appear, disappearing at the end of the applied voltage pulse. The streamer wavelength and the distance between the streamers in the axial direction are determined. Moreover, ozone generation is shown to be more significant in the secondary streamer. This simulation will allow better predictions for nanosecond positive pulsed plasma systems.

Inferring the Limit Behavior of Some Elementary Cellular Automata

NASA Astrophysics Data System (ADS)

Ruivo, Eurico L. P.; de Oliveira, Pedro P. B.

Cellular automata locally define dynamical systems, discrete in space, time and in the state variables, capable of displaying arbitrarily complex global emergent behavior. One core question in the study of cellular automata refers to their limit behavior, that is, to the global dynamical features in an infinite time evolution. Previous works have shown that for finite time evolutions, the dynamics of one-dimensional cellular automata can be described by regular languages and, therefore, by finite automata. Such studies have shown the existence of growth patterns in the evolution of such finite automata for some elementary cellular automata rules and also inferred the limit behavior of such rules based upon the growth patterns; however, the results on the limit behavior were obtained manually, by direct inspection of the structures that arise during the time evolution. Here we present the formalization of an automatic method to compute such structures. Based on this, the rules of the elementary cellular automata space were classified according to the existence of a growth pattern in their finite automata. Also, we present a method to infer the limit graph of some elementary cellular automata rules, derived from the analysis of the regular expressions that describe their behavior in finite time. Finally, we analyze some attractors of two rules for which we could not compute the whole limit set.

Dynamical evolution of young binaries and multiple systems

NASA Astrophysics Data System (ADS)

Reipurth, B.

Most stars, and perhaps all, are born in small multiple systems whose components interact, leading to chaotic dynamic behavior. Some components are ejected, either into distant orbits or into outright escapes, while the remaining components form temporary and eventually permanent binary systems. More than half of all such breakups of multiple systems occur during the protostellar phase, leading to the occasional ejection of protostars outside their nascent cloud cores. Such orphaned protostars are observed as wide companions to embedded protostars, and thus allow the direct study of protostellar objects. Dynamic interactions during early stellar evolution explain the shape and enormous width of the separation distribution function of binaries, from close spectroscopic binaries to the widest binaries.

[The cavernosometry].

PubMed

Mantovani, F; Mastromarino, G; Fenice, O; Canclini, L; Patelli, E; Colombo, F; Vecchio, D; Austoni, E

1994-09-01

The recent clinical and experimental research innovations in Andrology make possible the following classification of impotence: "Failure to initiate" "Failure to store" "Failure to fill" The last aspect, including veno-occlusive dysfunction, is continuously reevaluated by andrologic studies. The main diagnostic procedure of this complex problem, in constant evolution, is represented by cavernometry. Recently, but with full success, we are utilizing direct radioisotopic penogram in video sexy stimulation: in preselection function but probably in future with substitutive function of the more invasive and traditional cavernometry. In spite of this methodologic progress the findings of cavernometry are in continuous discussion as in tumultuous evolution, in anatomo-physiological environment, is the intracavernous district that, for many aspects, necessity of ulterior histochemical, pharmacodynamic and neurophysiological acknowledgements.

Boltzmann, Darwin and Directionality theory

NASA Astrophysics Data System (ADS)

Demetrius, Lloyd A.

2013-09-01

Boltzmann’s statistical thermodynamics is a mathematical theory which relates the macroscopic properties of aggregates of interacting molecules with the laws of their interaction. The theory is based on the concept thermodynamic entropy, a statistical measure of the extent to which energy is spread throughout macroscopic matter. Macroscopic evolution of material aggregates is quantitatively explained in terms of the principle: Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision. Darwin’s theory of evolution is a qualitative theory of the origin of species and the adaptation of populations to their environment. A central concept in the theory is fitness, a qualitative measure of the capacity of an organism to contribute to the ancestry of future generations. Macroscopic evolution of populations of living organisms can be qualitatively explained in terms of a neo-Darwinian principle: Fitness increases as the composition of the population changes under variation and natural selection. Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. This report reviews the analytical and empirical support for directionality theory, and invokes the microevolutionary dynamics of variation and selection to delineate the principles which govern macroevolutionary dynamics of speciation and extinction. We also elucidate the relation between thermodynamic entropy, which pertains to the extent of energy spreading and sharing within inanimate matter, and evolutionary entropy, which refers to the rate of energy appropriation from the environment and allocation within living systems. We show that the entropic principle of thermodynamics is the limit as R→0, M→∞, (where R denote the resource production rate, and M denote population size) of the entropic principle of evolution. We exploit this relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. Life history variation and the evolution of senescence The evolutionary dynamics of speciation and extinction Evolutionary trends in body size. The origin of sporadic forms of cancer and neurological diseases, and the evolution of cooperation are important recent applications of directionality theory. These applications, which draw from the medical sciences and sociobiology, appeal to methods which lie outside the formalism described in this report. A companion review, Demetrius and Gundlach (submitted for publication), gives an account of these applications.An important aspect of this report pertains to the connection between statistical mechanics and evolutionary theory and its implications towards understanding the processes which underlie the emergence of living systems from inanimate matter-a problem which has recently attracted considerable attention, Morowitz (1992), Eigen (1992), Dyson (2000), Pross (2012).The connection between the two disciplines can be addressed by appealing to certain extremal principles which are considered the mainstay of the respective theories.The extremal principle in statistical mechanics can be stated as follows:

The status of evolutionary medicine education in North American medical schools.

PubMed

Hidaka, Brandon H; Asghar, Anila; Aktipis, C Athena; Nesse, Randolph M; Wolpaw, Terry M; Skursky, Nicole K; Bennett, Katelyn J; Beyrouty, Matthew W; Schwartz, Mark D

2015-03-08

Medical and public health scientists are using evolution to devise new strategies to solve major health problems. But based on a 2003 survey, medical curricula may not adequately prepare physicians to evaluate and extend these advances. This study assessed the change in coverage of evolution in North American medical schools since 2003 and identified opportunities for enriching medical education. In 2013, curriculum deans for all North American medical schools were invited to rate curricular coverage and perceived importance of 12 core principles, the extent of anticipated controversy from adding evolution, and the usefulness of 13 teaching resources. Differences between schools were assessed by Pearson's chi-square test, Student's t-test, and Spearman's correlation. Open-ended questions sought insight into perceived barriers and benefits. Despite repeated follow-up, 60 schools (39%) responded to the survey. There was no evidence of sample bias. The three evolutionary principles rated most important were antibiotic resistance, environmental mismatch, and somatic selection in cancer. While importance and coverage of principles were correlated (r = 0.76, P < 0.01), coverage (at least moderate) lagged behind importance (at least moderate) by an average of 21% (SD = 6%). Compared to 2003, a range of evolutionary principles were covered by 4 to 74% more schools. Nearly half (48%) of responders anticipated igniting controversy at their medical school if they added evolution to their curriculum. The teaching resources ranked most useful were model test questions and answers, case studies, and model curricula for existing courses/rotations. Limited resources (faculty expertise) were cited as the major barrier to adding more evolution, but benefits included a deeper understanding and improved patient care. North American medical schools have increased the evolution content in their curricula over the past decade. However, coverage is not commensurate with importance. At a few medical schools, anticipated controversy impedes teaching more evolution. Efforts to improve evolution education in medical schools should be directed toward boosting faculty expertise and crafting resources that can be easily integrated into existing curricula.

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.

TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants

PubMed Central

Sulak, Michael; Fong, Lindsey; Mika, Katelyn; Chigurupati, Sravanthi; Yon, Lisa; Mongan, Nigel P; Emes, Richard D; Lynch, Vincent J

2016-01-01

A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as 'Peto's Paradox'. Here, we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and a hyperactive TP53 signaling pathway in the elephant (Proboscidean) lineage. Furthermore, we show that several of the TP53 retrogenes (TP53RTGs) are transcribed and likely translated. While TP53RTGs do not appear to directly function as transcription factors, they do contribute to the enhanced sensitivity of elephant cells to DNA damage and the induction of apoptosis by regulating activity of the TP53 signaling pathway. These results suggest that an increase in the copy number of TP53 may have played a direct role in the evolution of very large body sizes and the resolution of Peto's paradox in Proboscideans. DOI: http://dx.doi.org/10.7554/eLife.11994.001 PMID:27642012

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

Modified unified kinetic scheme for all flow regimes.

PubMed

Liu, Sha; Zhong, Chengwen

2012-06-01

A modified unified kinetic scheme for the prediction of fluid flow behaviors in all flow regimes is described. The time evolution of macrovariables at the cell interface is calculated with the idea that both free transport and collision mechanisms should be considered. The time evolution of macrovariables is obtained through the conservation constraints. The time evolution of local Maxwellian distribution is obtained directly through the one-to-one mapping from the evolution of macrovariables. These improvements provide more physical realities in flow behaviors and more accurate numerical results in all flow regimes especially in the complex transition flow regime. In addition, the improvement steps introduce no extra computational complexity.

In vivo Elimination of Parental Clones in General and Site-directed Mutagenesis

PubMed Central

Holland, Erika G.; Acca, Felicity E.; Belanger, Kristina M.; Bylo, Mary E.; Kay, Brian K.; Weiner, Michael P.; Kiss, Margaret M.

2015-01-01

The Eco29k I restriction endonuclease is a Sac II isoschizomer that recognizes the sequence 5’-CCGCGG-3’ and is encoded, along with the Eco29k I methylase, in the Escherichia coli strain 29k. We have expressed the Eco29k I restriction-methylation system (RM2) in E. coli strain TG1 to produce the strain AXE688. We have developed a directed molecular evolution (DME) mutagenesis method that uses Eco29k I to restrict incoming parental DNA in transformed cells. Using our DME method, we have demonstrated that our AXE688 strain results in mutated directed molecular evolution libraries with diversity greater than 107 from a single transformation and with greater than 90% recombinant clones. PMID:25523926

In vivo elimination of parental clones in general and site-directed mutagenesis.

PubMed

Holland, Erika G; Acca, Felicity E; Belanger, Kristina M; Bylo, Mary E; Kay, Brian K; Weiner, Michael P; Kiss, Margaret M

2015-02-01

The Eco29k I restriction endonuclease is a Sac II isoschizomer that recognizes the sequence 5'-CCGCGG-3' and is encoded, along with the Eco29k I methylase, in the Escherichia coli strain 29k. We have expressed the Eco29k I restriction-methylation system (RM2) in E. coli strain TG1 to produce the strain AXE688. We have developed a directed molecular evolution (DME) mutagenesis method that uses Eco29k I to restrict incoming parental DNA in transformed cells. Using our DME method, we have demonstrated that our AXE688 strain results in mutated directed molecular evolution libraries with diversity greater than 10(7) from a single transformation and with greater than 90% recombinant clones. Copyright © 2014 Elsevier B.V. All rights reserved.

Dicationic ionic liquid mediated fabrication of Au@Pt nanoparticles supported on reduced graphene oxide with highly catalytic activity for oxygen reduction and hydrogen evolution

NASA Astrophysics Data System (ADS)

Shi, Ya-Cheng; Chen, Sai-Sai; Feng, Jiu-Ju; Lin, Xiao-Xiao; Wang, Weiping; Wang, Ai-Jun

2018-05-01

Ionic liquids as templates or directing agents have attracted great attention for shaping-modulated synthesis of advanced nanomaterials. In this work, reduced graphene oxide supported uniform core-shell Au@Pt nanoparticles (Au@Pt NPs/rGO) were fabricated by a simple one-pot aqueous approach, using N-methylimidazolium-based dicationic ionic liquid (1,1-bis(3-methylimadazoilum-1-yl)butylene bromide, [C4(Mim)2]2Br) as the shape-directing agent. The morphology evolution, structural information and formation mechanism of Au@Pt NPs anchored on rGO were investigated by a series of characterization techniques. The obtained nanocomposites displayed superior electrocatalytic features toward hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR) compared with commercial Pt/C catalyst. This approach provides a novel route for facile synthesis of nanocatalysts in fuel cells.

Was the Watchmaker Blind? Or Was She One-Eyed?

PubMed Central

Noble, Raymond; Noble, Denis

2017-01-01

The question whether evolution is blind is usually presented as a choice between no goals at all (‘the blind watchmaker’) and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are short-term goals within rather than external to organisms. Organisms and their interacting populations have evolved mechanisms by which they can harness blind stochasticity and so generate rapid functional responses to environmental challenges. They can achieve this by re-organising their genomes and/or their regulatory networks. Epigenetic as well as DNA changes are involved. Evolution may have no foresight, but it is at least partially directed by organisms themselves and by the populations of which they form part. Similar arguments support partial direction in the evolution of behavior. PMID:29261138

Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions

NASA Technical Reports Server (NTRS)

McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.

2002-01-01

Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(exp 406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5' yieldig 3' or a 3' yielding 5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.

Thermally Induced Structural Evolution and Performance of Mesoporous Block Copolymer-Directed Alumina Perovskite Solar Cells

PubMed Central

2015-01-01

Structure control in solution-processed hybrid perovskites is crucial to design and fabricate highly efficient solar cells. Here, we utilize in situ grazing incidence wide-angle X-ray scattering and scanning electron microscopy to investigate the structural evolution and film morphologies of methylammonium lead tri-iodide/chloride (CH3NH3PbI3–xClx) in mesoporous block copolymer derived alumina superstructures during thermal annealing. We show the CH3NH3PbI3–xClx material evolution to be characterized by three distinct structures: a crystalline precursor structure not described previously, a 3D perovskite structure, and a mixture of compounds resulting from degradation. Finally, we demonstrate how understanding the processing parameters provides the foundation needed for optimal perovskite film morphology and coverage, leading to enhanced block copolymer-directed perovskite solar cell performance. PMID:24684494

Key issues review: evolution on rugged adaptive landscapes

NASA Astrophysics Data System (ADS)

Obolski, Uri; Ram, Yoav; Hadany, Lilach

2018-01-01

Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.

Sherwood Washburn's New physical anthropology: rejecting the "religion of taxonomy".

PubMed

Mikels-Carrasco, Jessica

2012-01-01

Many physical anthropologists and nearly all of those studying primatology today can trace their academic genealogy to Sherwood Larned Washburn. His New physical anthropology, fully articulated in a 1951 paper, proposed that the study of hominid evolution must link understandings of form, function, and behavior along with the environment in order most accurately to reconstruct the evolution of our ancestors. This shift of concentration from strictly analyzing fossil remains to what Washburn termed adaptive complexes challenged not only Washburn's predecessors, but also led Washburn to critique the very system of academia within which he worked. Collaboration across multiple disciplines, linking the four fields of anthropology in order to understand humans and application of our understandings of human evolution to the betterment of society, are the hallmarks of Washburnian anthropology. In this paper I will explore how Washburn's New physical anthropology led him to not only change the research direction in physical anthropology, but also to challenge the academia within which he worked. I will conclude by reflecting on the prospects of continuing to practice Washburnian Anthropology.

Evolutionary Models of Cold, Magnetized, Interstellar Clouds

NASA Technical Reports Server (NTRS)

Gammie, Charles F.; Ostriker, Eve; Stone, James M.

2004-01-01

We modeled the long-term and small-scale evolution of molecular clouds using direct 2D and 3D magnetohydrodynamic (MHD) simulations. This work followed up on previous research by our group under auspices of the ATP in which we studied the energetics of turbulent, magnetized clouds and their internal structure on intermediate scales. Our new work focused on both global and smallscale aspects of the evolution of turbulent, magnetized clouds, and in particular studied the response of turbulent proto-cloud material to passage through the Galactic spiral potential, and the dynamical collapse of turbulent, magnetized (supercritical) clouds into fragments to initiate the formation of a stellar cluster. Technical advances under this program include developing an adaptive-mesh MHD code as a successor to ZEUS (ATHENA) in order to follow cloud fragmentation, developing a shearing-sheet MHD code which includes self-gravity and externally-imposed gravity to follow the evolution of clouds in the Galactic potential, and developing radiative transfer models to evaluate the internal ionization of clumpy clouds exposed to external photoionizing UV and CR radiation. Gammie's work at UIUC focused on the radiative transfer aspects of this program.

Phylogenomics of MADS-Box Genes in Plants - Two Opposing Life Styles in One Gene Family.

PubMed

Gramzow, Lydia; Theißen, Günter

2013-09-12

The development of multicellular eukaryotes, according to their body plan, is often directed by members of multigene families that encode transcription factors. MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR)-box genes form one of those families controlling nearly all major aspects of plant development. Knowing the complete complement of MADS-box genes in sequenced plant genomes will allow a better understanding of the evolutionary patterns of these genes and the association of their evolution with the evolution of plant morphologies. Here, we have applied a combination of automatic and manual annotations to identify the complete set of MADS-box genes in 17 plant genomes. Furthermore, three plant genomes were reanalyzed and published datasets were used for four genomes such that more than 2,600 genes from 24 species were classified into the two types of MADS-box genes, Type I and Type II. Our results extend previous studies, highlighting the remarkably different evolutionary patterns of Type I and Type II genes and provide a basis for further studies on the evolution and function of MADS-box genes.

Glycomics: revealing the dynamic ecology and evolution of sugar molecules.

PubMed

Springer, Stevan A; Gagneux, Pascal

2016-03-01

Sugars are the most functionally and structurally diverse molecules in the biological world. Glycan structures range from tiny single monosaccharide units to giant chains thousands of units long. Some glycans are branched, their monosaccharides linked together in many different combinations and orientations. Some exist as solitary molecules; others are conjugated to proteins and lipids and alter their collective functional properties. In addition to structural and storage roles, glycan molecules participate in and actively regulate physiological and developmental processes. Glycans also mediate cellular interactions within and between individuals. Their roles in ecology and evolution are pivotal, but not well studied because glycan biochemistry requires different methods than standard molecular biology practice. The properties of glycans are in some ways convenient, and in others challenging. Glycans vary on organismal timescales, and in direct response to physiological and ecological conditions. Their mature structures are physical records of both genetic and environmental influences during maturation. We describe the scope of natural glycan variation and discuss how studying glycans will allow researchers to further integrate the fields of ecology and evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Radiation-MHD models of elephant trunks and globules in HII regions

NASA Astrophysics Data System (ADS)

Mackey, Jonathan; Lim, Andrew J.

2011-01-01

We study the formation and evolution of pillars of dense gas, known as elephant trunks, at the boundaries of HII regions, formed by shadowing of ionising radiation by dense clumps. The effects of magnetic fields on this process are investigated using 3D radiation-magnetohydrodynamics simulations. For a simulation in which an initially uniform magnetic field of strength \\vert B\\vert≃50 μG is oriented perpendicular to the radiation propagation direction, the field is swept into alignment with the pillar during its dynamical evolution, in agreement with observations of the ``Pillars of Creation'' in M16, and of some cometary globules. This effect is significantly enhanced when the simulation is re-run with a weaker field of ≃18 μG. A stronger field with \\vert B\\vert≃ 160 μG is sufficient to prevent this evolution completely, also significantly affecting the photoionisation process. Using a larger simulation domain it is seen that the pillar formation models studied in Mackey & Lim (2010) ultimately evolve to cometary structures in the absence of dense gas further from the star.

Transition regime from step-flow to step-bunching in the growth of epitaxial SrRuO3 on (001) SrTiO3

NASA Astrophysics Data System (ADS)

Gura, Anna; Bertino, Giulia; Bein, Benjamin; Dawber, Matthew

2018-04-01

We present a study of the surface morphology of SrRuO3 thin films grown on TiO2 terminated (001) SrTiO3 substrates using an off-axis RF magnetron sputtering deposition technique. We investigated the step bunching formation and the evolution of the films by varying deposition parameters. The thin films were characterized using atomic force microscopy methods, allowing us to study the various growth regimes of SrRuO3 as a function of the growth parameters. We observe a strong influence of both the miscut angle and growth temperature on the evolution of the SrRuO3 surface morphology. In addition, a thickness dependence is present. Remarkably, the formation of a smooth, regular, and uniform "fish-skin" structure at the step-bunch transition is observed. The fish-skin morphology results from the merging of 2D flat islands predicted by previous models. The direct observation of surface evolution allows us to better understand the different growth regimes of SrRuO3 thin films.

Evolutionary developmental genetics of fruit morphological variation within the Solanaceae

PubMed Central

Wang, Li; Li, Jing; Zhao, Jing; He, Chaoying

2015-01-01

Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops. PMID:25918515

The Evolution of Sex Education and Students' Sexual Knowledge in Finland in the 2000s

ERIC Educational Resources Information Center

Kontula, Osmo

2010-01-01

Finland is probably the only country where sex education has been studied in two consecutive national surveys, in 1996 and 2006 directed at biology and health education teachers, and in 2000 and 2006 by measuring adolescents' sexual knowledge. In 2006, responses from teachers and students could be combined for 339 schools. The most important…

Girls in Science and Technology in Secondary and Post-Secondary Education: The Case of France

ERIC Educational Resources Information Center

Stevanovic, Biljana

2014-01-01

Based on surveys undertaken by the Institut national de la statistique et des études économiques (France's National Institute of Statistics and Economic Studies) and by the Direction de l'évaluation de la prospective et de la performance (Directorate of Evaluation, Forecasting and Performance), this article examines the evolution of female student…

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

Dogan, Fulya; Vaughey, John T.; Iddir, Hakim

Direct observations of local lattice aluminum environments have been a major challenge for aluminum -bearing Li ion battery materials, such as LiNi1-y-zCoyAlzO2 Al(NCA) and aluminum-doped LiNixMnyCozO2 (NMC). Al-27 magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy is the only structural probe currently available that can qualitatively and quantitatively characterize lattice and nonlattice (i.e., surface, coatings, segregation, secondary phase etc.) aluminum coordination and provide information that helps discern its effect in the lattice. In the present study, we use NMR to gain new insights into transition metal (TM)-O-Al coordination and evolution of lattice aluminum sites upon cycling. With the aidmore » of first-principles DFT calculations, we show direct evidence of lattice Al sites, nonpreferential Ni/Co-O-Al ordering in NCA, and the lack of bulk lattice aluminum in aluminum -"doped" NMC. Aluminum coordination of the paramagnetic (lattice) and diamagnetic (nonlattice) nature is investigated for Al-doped NMC and NCA. For the latter, the evolution of the lattice site(s) upon cycling is also studied. A clear reordering of lattice aluminum environments due to nickel migration is observed in NCA upon extended cycling.« less

Evolution of tag-based cooperation on Erdős-Rényi random graphs

NASA Astrophysics Data System (ADS)

Lima, F. W. S.; Hadzibeganovic, Tarik; Stauffer, Dietrich

2014-12-01

Here, we study an agent-based model of the evolution of tag-mediated cooperation on Erdős-Rényi random graphs. In our model, agents with heritable phenotypic traits play pairwise Prisoner's Dilemma-like games and follow one of the four possible strategies: Ethnocentric, altruistic, egoistic and cosmopolitan. Ethnocentric and cosmopolitan strategies are conditional, i.e. their selection depends upon the shared phenotypic similarity among interacting agents. The remaining two strategies are always unconditional, meaning that egoists always defect while altruists always cooperate. Our simulations revealed that ethnocentrism can win in both early and later evolutionary stages on directed random graphs when reproduction of artificial agents was asexual; however, under the sexual mode of reproduction on a directed random graph, we found that altruists dominate initially for a rather short period of time, whereas ethnocentrics and egoists suppress other strategists and compete for dominance in the intermediate and later evolutionary stages. Among our results, we also find surprisingly regular oscillations which are not damped in the course of time even after half a million Monte Carlo steps. Unlike most previous studies, our findings highlight conditions under which ethnocentrism is less stable or suppressed by other competing strategies.

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

Exploring the evolution of a trade-off between vigilance and foraging in group-living organisms

PubMed Central

Olson, Randal S.; Haley, Patrick B.; Dyer, Fred C.; Adami, Christoph

2015-01-01

Even though grouping behaviour has been actively studied for over a century, the relative importance of the numerous proposed fitness benefits of grouping remain unclear. We use a digital model of evolving prey under simulated predation to directly explore the evolution of gregarious foraging behaviour according to one such benefit, the ‘many eyes’ hypothesis. According to this hypothesis, collective vigilance allows prey in large groups to detect predators more efficiently by making alarm signals or behavioural cues to each other, thereby allowing individuals within the group to spend more time foraging. Here, we find that collective vigilance is sufficient to select for gregarious foraging behaviour as long there is not a direct cost for grouping (e.g. competition for limited food resources), even when controlling for confounding factors such as the dilution effect. Furthermore, we explore the role of the genetic relatedness and reproductive strategy of the prey and find that highly related groups of prey with a semelparous reproductive strategy are the most likely to evolve gregarious foraging behaviour mediated by the benefit of vigilance. These findings, combined with earlier studies with evolving digital organisms, further sharpen our understanding of the factors favouring grouping behaviour. PMID:26473039

Propagation of large-amplitude waves on dielectric liquid sheets in a tangential electric field: exact solutions in three-dimensional geometry.

PubMed

Zubarev, Nikolay M; Zubareva, Olga V

2010-10-01

Nonlinear waves on sheets of dielectric liquid in the presence of an external tangential electric field are studied theoretically. It is shown that waves of arbitrary shape in three-dimensional geometry can propagate along (or against) the electric field direction without distortion, i.e., the equations of motion admit a wide class of exact traveling wave solutions. This unusual situation occurs for nonconducting ideal liquids with high dielectric constants in the case of a sufficiently strong field strength. Governing equations for evolution of plane symmetric waves on fluid sheets are derived using conformal variables. A dispersion relation for the evolution of small perturbations of the traveling wave solutions is obtained. It follows from this relation that, regardless of the wave shape, the amplitudes of small-scale perturbations do not increase with time and, hence, the traveling waves are stable. We also study the interaction of counterpropagating symmetric waves with small but finite amplitudes. The corresponding solution of the equations of motion describes the nonlinear superposition of the oppositely directed waves. The results obtained are applicable for the description of long waves on fluid sheets in a horizontal magnetic field.

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.

Accumulation of dislocation loops in the α phase of Zr Excel alloy under heavy ion irradiation

NASA Astrophysics Data System (ADS)

Yu, Hongbing; Yao, Zhongwen; Idrees, Yasir; Zhang, He K.; Kirk, Mark A.; Daymond, Mark R.

2017-08-01

In-situ heavy ion irradiations were performed on the high Sn content Zr alloy 'Excel', measuring type dislocation loop accumulation up to irradiation damage doses of 10 dpa at a range of temperatures. The high content of Sn, which diffuses slowly, and the thin foil geometry of the sample provide a unique opportunity to study an extreme case where displacement cascades dominate the loop formation and evolution. The dynamic observation of dislocation loop evolution under irradiation at 200 °C reveals that type dislocation loops can form at very low dose (0.0025 dpa). The size of the dislocation loops increases slightly with irradiation damage dose. The mechanism controlling loop growth in this study is different from that in neutron irradiation; in this study, larger dislocation loops can condense directly from the interaction of displacement cascades and the high concentration of point defects in the matrix. The size of the dislocation loop is dependent on the point defect concentration in the matrix. A negative correlation between the irradiation temperature and the dislocation loop size was observed. A comparison between cascade dominated loop evolution (this study), diffusion dominated loop evolution (electron irradiation) and neutron irradiation suggests that heavy ion irradiation alone may not be enough to accurately reproduce neutron irradiation induced loop structures. An alternative method is proposed in this paper. The effects of Sn on the displacement cascades, defect yield, and the diffusion behavior of point defects are established.

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 extreme body size disparity in monitor lizards (Varanus).

PubMed

Collar, David C; Schulte, James A; Losos, Jonathan B

2011-09-01

Many features of species' biology, including life history, physiology, morphology, and ecology are tightly linked to body size. Investigation into the causes of size divergence is therefore critical to understanding the factors shaping phenotypic diversity within clades. In this study, we examined size evolution in monitor lizards (Varanus), a clade that includes the largest extant lizard species, the Komodo dragon (V. komodoensis), as well as diminutive species that are nearly four orders of magnitude smaller in adult body mass. We demonstrate that the remarkable body size disparity of this clade is a consequence of different selective demands imposed by three major habitat use patterns-arboreality, terrestriality, and rock-dwelling. We reconstructed phylogenetic relationships and ancestral habitat use and applied model selection to determine that the best-fitting evolutionary models for species' adult size are those that infer oppositely directed adaptive evolution associated with terrestriality and rock-dwelling, with terrestrial lineages evolving extremely large size and rock-dwellers becoming very small. We also show that habitat use affects the evolution of several ecologically important morphological traits independently of body size divergence. These results suggest that habitat use exerts a strong, multidimensional influence on the evolution of morphological size and shape disparity in monitor lizards. © 2011 The Author(s).

How does pollen versus seed dispersal affect niche evolution?

PubMed

Aguilée, Robin; Shaw, Frank H; Rousset, François; Shaw, Ruth G; Ronce, Ophélie

2013-03-01

In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed dispersal on the evolution of niche width in heterogeneous habitats, explicitly considering the feedback between maladaptation and demography. We consider two scenarios: the secondary contact of two subpopulations, in distinct, formerly isolated habitats, and the colonization of an empty habitat with dispersal between the new and ancestral habitat. With an analytical model, we identify critical levels of genetic variance leading to niche contraction (secondary contact scenario), or expansion (new habitat scenario). We confront these predictions with simulations where the genetic variance freely evolves. Niche contraction occurs when habitats are very different. It is faster as total gene flow increases or as pollen predominates in overall gene flow. Niche expansion occurs when habitat heterogeneity is not too high. Seed dispersal accelerates it, whereas pollen dispersal tends to retard it. In both scenarios very high seed dispersal leads to extinction. Overall, our results predict a wider niche for species dispersing seeds more than pollen. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Rapid evolution of reproductive isolation between incipient outcrossing and selfing Clarkia species.

PubMed

Briscoe Runquist, Ryan D; Chu, Eric; Iverson, Justin L; Kopp, Jason C; Moeller, David A

2014-10-01

A major goal of speciation research is to understand the processes involved in the earliest stages of the evolution of reproductive isolation (RI). One important challenge has been to identify systems where lineages have very recently diverged and opportunities for hybridization are present. We conducted a comprehensive examination of the components of RI across the life cycle of two subspecies of Clarkia xantiana, which diverged recently (ca. 65,000 bp). One subspecies is primarily outcrossing, but self-compatible, whereas the other is primarily selfing. The subspecies co-occur in a zone of sympatry but hybrids are rarely observed. Premating barriers resulted in nearly complete isolation in both subspecies with flowering time and pollinator preference (for the outcrosser over the selfer) as the strongest barriers. We found that the outcrosser had consistently more competitive pollen, facilitating hybridization in one direction, but no evidence for pollen-pistil interactions as an isolating barrier. Surprisingly, postzygotic isolation was detected at the stage of hybrid seed development, but in no subsequent life stages. This crossing barrier was asymmetric with crosses from the selfer to outcrosser most frequently failing. Collectively, the results provide evidence for rapid evolution of multiple premating and postzygotic barriers despite a very recent divergence time. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Preparation of NiS/ZnIn2S4 as a superior photocatalyst for hydrogen evolution under visible light irradiation

PubMed Central

Wei, Liang; Chen, Yongjuan; Zhao, Jialin

2013-01-01

Summary In this study, NiS/ZnIn2S4 nanocomposites were successfully prepared via a facile two-step hydrothermal process. The as-prepared samples were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HRTEM). Their photocatalytic performance for hydrogen evolution under visible light irradiation was also investigated. It was found that the photocatalytic hydrogen evolution activity over hexagonal ZnIn2S4 can be significantly increased by loading NiS as a co-catalyst. The formation of a good junction between ZnIn2S4 and NiS via the two step hydrothermal processes is beneficial for the directional migration of the photo-excited electrons from ZnIn2S4 to NiS. The highest photocatalytic hydrogen evolution rate (104.7 μmol/h), which is even higher than that over Pt/ZnIn2S4 nanocomposite (77.8 μmol/h), was observed over an optimum NiS loading amount of 0.5 wt %. This work demonstrates a high potential of the developing of environmental friendly, cheap noble-metal-free co-catalyst for semiconductor-based photocatalytic hydrogen evolution. PMID:24455453

Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering.

PubMed

Xie, Wenping; Lv, Xiaomei; Ye, Lidan; Zhou, Pingping; Yu, Hongwei

2015-07-01

Improved supply of farnesyl diphosphate (FPP) is often considered as a typical strategy for engineering Saccharomyces cerevisiae towards efficient terpenoid production. However, in the engineered strains with enhanced precursor supply, the production of the target metabolite is often impeded by insufficient capacity of the heterologous terpenoid pathways, which limits further conversion of FPP. Here, we tried to assemble an unimpeded biosynthesis pathway by combining directed evolution and metabolic engineering in S. cerevisiae for lycopene-overproduction. First, the catalytic ability of phytoene syntheses from different sources was investigated based on lycopene accumulation. Particularly, the lycopene cyclase function of the bifunctional enzyme CrtYB from Xanthophyllomyces dendrorhous was inactivated by deletion of functional domain and directed evolution to obtain mutants with solely phytoene synthase function. Coexpression of the resulting CrtYB11M mutant along with the CrtE and CrtI genes from X. dendrorhous, and the tHMG1 gene from S. cerevisiae led to production of 4.47 mg/g DCW (Dry cell weight) of lycopene and 25.66 mg/g DCW of the by-product squalene. To further increase the FPP competitiveness of the lycopene synthesis pathway, we tried to enhance the catalytic performance of CrtE by directed evolution and created a series of pathway variants by varying the copy number of Crt genes. Finally, fed-batch fermentation was conducted for the diploid strain YXWPD-14 resulting in accumulation of 1.61 g/L (24.41 mg/g DCW) of lycopene, meanwhile, the by-production of squalene was reduced to below 1 mg/g DCW. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Hydromechanical behavior of Estaillades carbonate : directional permeability, stress-path and microstructural heterogeneity effects, yield and failure envelopes

NASA Astrophysics Data System (ADS)

Dautriat, J.; Dimanov, A.; Gland, N.; Raphanel, J.

2009-04-01

The influence of stress paths representative of reservoir conditions on the mechanical behavior and the coupled permeability evolutions of a carbonate has been investigated. In order to predict the permeability evolutions under triaxial loading, we have developed a triaxial cell designed to allow the measurements of the permeability in three orthogonal directions, along and transverse to the maximum principal stress direction. A set of core specimens are mechanically loaded following different stress paths characterized by a constant ratio K between horizontal and vertical stress. Our experimental set-up allows the monitoring of the petrophysical and geomechanical parameters during loading, before and post sample damage. The tested rock is an analog reservoir carbonate, the Estaillades Limestone, characterized macroscopically by a porosity around 29% and a moderate permeability around 150mD. From our experimental results, the failure envelope of this carbonate is determined and the evolutions of the directional permeability are examined in the (p',q) diagram. According to the followed stress path, permeability reductions can be limited or drastic. In addition, we have performed microstructural analyses on deformed samples and in-situ observations during loading inside a SEM in order to identify the micromechanisms responsible for the evolutions of porosity and permeability. For instance, we show the importance of local heterogeneities on initiation of damage and of pore collapse. In the near-elastic domain, brittle damage induces limited directional permeability modifications; whereas, at higher stress, depending on the value of K, shear induced dilation or shear induced compaction mechanisms are activated. The highest permeability drop occurred for the hydrostatic compression (K=1), in the compaction regime, characterized by pore collapse mechanisms affecting preferentially the macroporosity. A failure model is proposed and the failure envelope is determined in the (p',q) plane. A new expression of the failure envelope is also discussed which includes a dependency of the deviatoric stress with the stress-path parameter.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

PubMed

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Phycoerythrin evolution and diversification of spectral phenotype in marine Synechococcus and related picocyanobacteria.

PubMed

Everroad, R Craig; Wood, A Michelle

2012-09-01

In marine Synechococcus there is evidence for the adaptive evolution of spectrally distinct forms of the major light harvesting pigment phycoerythrin (PE). Recent research has suggested that these spectral forms of PE have a different evolutionary history than the core genome. However, a lack of explicit statistical testing of alternative hypotheses or for selection on these genes has made it difficult to evaluate the evolutionary relationships between spectral forms of PE or the role horizontal gene transfer (HGT) may have had in the adaptive phenotypic evolution of the pigment system in marine Synechococcus. In this work, PE phylogenies of picocyanobacteria with known spectral phenotypes, including newly co-isolated strains of marine Synechococcus from the Gulf of Mexico, were constructed to explore the diversification of spectral phenotype and PE evolution in this group more completely. For the first time, statistical evaluation of competing evolutionary hypotheses and tests for positive selection on the PE locus in picocyanobacteria were performed. Genes for PEs associated with specific PE spectral phenotypes formed strongly supported monophyletic clades within the PE tree with positive directional selection driving evolution towards higher phycourobilin (PUB) content. The presence of the PUB-lacking phenotype in PE-containing marine picocyanobacteria from cyanobacterial lineages identified as Cyanobium is best explained by HGT into this group from marine Synechococcus. Taken together, these data provide strong examples of adaptive evolution of a single phenotypic trait in bacteria via mutation, positive directional selection and horizontal gene transfer. Copyright © 2012 Elsevier Inc. All rights reserved.

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

PubMed

Harms, Michael J; Thornton, Joseph W

2014-08-14

Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.

Generation and evolution of anisotropic turbulence and related energy transfer in a multi-species solar wind

NASA Astrophysics Data System (ADS)

Maneva, Yana; Poedts, Stefaan

2017-04-01

The electromagnetic fluctuations in the solar wind represent a zoo of plasma waves with different properties, whose wavelengths range from largest fluid scales to the smallest dissipation scales. By nature the power spectrum of the magnetic fluctuations is anisotropic with different spectral slopes in parallel and perpendicular directions with respect to the background magnetic field. Furthermore, the magnetic field power spectra steepen as one moves from the inertial to the dissipation range and we observe multiple spectral breaks with different slopes in parallel and perpendicular direction at the ion scales and beyond. The turbulent dissipation of magnetic field fluctuations at the sub-ion scales is believed to go into local ion heating and acceleration, so that the spectral breaks are typically associated with particle energization. The gained energy can be in the form of anisotropic heating, formation of non-thermal features in the particle velocity distributions functions, and redistribution of the differential acceleration between the different ion populations. To study the relation between the evolution of the anisotropic turbulent spectra and the particle heating at the ion and sub-ion scales we perform a series of 2.5D hybrid simulations in a collisionless drifting proton-alpha plasma. We neglect the fast electron dynamics and treat the electrons as an isothermal fluid electrons, whereas the protons and a minor population of alpha particles are evolved in a fully kinetic manner. We start with a given wave spectrum and study the evolution of the magnetic field spectral slopes as a function of the parallel and perpendicular wave¬numbers. Simultaneously, we track the particle response and the energy exchange between the parallel and perpendicular scales. We observe anisotropic behavior of the turbulent power spectra with steeper slopes along the dominant energy-containing direction. This means that for parallel and quasi-parallel waves we have steeper spectral slope in parallel direction, whereas for highly oblique waves the dissipation occurs predominantly in perpendicular direction and the spectral slopes are steeper across the background magnetic field. The value of the spectral slopes depends on the angle of propagation, the spectral range, as well as the plasma properties. In general the dissipation is stronger at small scales and the corresponding spectral slopes there are steeper. For parallel and quasi-parallel propagation the prevailing energy cascade remains along the magnetic field, whereas for initially isotropic oblique turbulence the cascade develops mainly in perpendicular direction.

Hormones and the Evolution of Complex Traits: Insights from Artificial Selection on Behavior

PubMed Central

Garland, Theodore; Zhao, Meng; Saltzman, Wendy

2016-01-01

Although behavior may often be a fairly direct target of natural or sexual selection, it cannot evolve without changes in subordinate traits that cause or permit its expression. In principle, changes in endocrine function could be a common mechanism underlying behavioral evolution because they are well positioned to mediate integrated responses to behavioral selection. More specifically, hormones can influence both motivational (e.g., brain) and performance (e.g., muscles) components of behavior simultaneously and in a coordinated fashion. If the endocrine system is often “used” as a general mechanism to effect responses to selection, then correlated responses in other aspects of behavior, life history, and organismal performance (e.g., locomotor abilities) should commonly occur because any cell with appropriate receptors could be affected. Ways in which behavior coadapts with other aspects of the phenotype can be studied directly through artificial selection and experimental evolution. Several studies have targeted rodent behavior for selective breeding and reported changes in other aspects of behavior, life history, and lower-level effectors of these organismal traits, including endocrine function. One example involves selection for high levels of voluntary wheel running, one aspect of physical activity, in four replicate High Runner (HR) lines of mice. Circulating levels of several hormones (including insulin, testosterone, thyroxine, triiodothyronine) have been characterized, three of which—corticosterone, leptin, and adiponectin—differ between HR and control lines, depending on sex, age, and generation. Potential changes in circulating levels of other behaviorally and metabolically relevant hormones, as well as in other components of the endocrine system (e.g., receptors), have yet to be examined. Overall, results to date identify promising avenues for further studies on the endocrine basis of activity levels. PMID:27252193

Combined MR direct thrombus imaging and non-contrast magnetic resonance venography reveal the evolution of deep vein thrombosis: a feasibility study.

PubMed

Mendichovszky, I A; Priest, A N; Bowden, D J; Hunter, S; Joubert, I; Hilborne, S; Graves, M J; Baglin, T; Lomas, D J

2017-06-01

Lower limb deep venous thrombosis (DVT) is a common condition with high morbidity and mortality. The aim of the study was to investigate the temporal evolution of the acute thrombus by magnetic resonance imaging (MRI) and its relationship to venous recanalization in patients with recurrent DVTs. Thirteen patients with newly diagnosed lower limb DVTs underwent MRI with non-contrast MR venography (NC-MRV) and MR direct thrombus imaging (MR-DTI), an inversion-recovery water-selective fast gradient-echo acquisition. Imaging was performed within 7 days of the acute thrombotic event, then at 3 and 6 months. By 3 months from the thrombotic event a third of the thrombi had resolved and by 6 months about half of the cases had resolved on the basis of vein recanalisation using NC-MRV. On the initial MR-DTI acute thrombus was clearly depicted by hyperintense signal, while the remaining thrombi were predominantly low signal at 3 and 6 months. Some residual thrombi contained small and fragmented persisting hyperintense areas at 3 months, clearing almost completely by 6 months. Our study suggests that synergistic venous assessment with combined NC-MRV and MR-DTI is able to distinguish acute venous thrombosis from the established (old) or evolving DVT detected by ultrasound. • MRI can distinguish between acute and evolving or chronic lower limb DVT • Two advanced MRI techniques can follow the evolution of lower limb DVT • MRI could be used to avoid an incorrect diagnosis of recurrent DVT • MRI could help avoid the risks and complications of lifelong anticoagulation therapy.

Effect of pre-straining on the evolution of material anisotropy in rolled magnesium alloy AZ31 sheet

NASA Astrophysics Data System (ADS)

Qiao, H.; Guo, X. Q.; Wu, P. D.

2013-12-01

The large strain Elastic Visco-Plastic Self-Consistent (EVPSC) model and the recently developed Twinning and De-Twinning (TDT) model are applied to study the mechanical behavior of rolled magnesium alloy AZ31 sheet. Three different specimen orientations with tilt angles of 0°, 45° and 90° between the rolling direction and longitudinal specimen axis are used to study the mechanical anisotropy under both uniaxial tension and compression. The effect of pre-strain in uniaxial compression along the rolling direction on subsequent uniaxial tension/compression along the three directions is also investigated. It is demonstrated that the twinning during pre-strain in compression and the detwinning in the subsequent deformation have a significant influence on the mechanical anisotropy. Numerical results are in good agreement with the experimental observations found in the literature.

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem.

PubMed

Zamdborg, Leonid; Holloway, David M; Merelo, Juan J; Levchenko, Vladimir F; Spirov, Alexander V

2015-06-10

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of "genomic parasites", such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators that adapt in response to an evolutionary problem in the course of co-evolution with their hosts.

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem

PubMed Central

Zamdborg, Leonid; Holloway, David M.; Merelo, Juan J.; Levchenko, Vladimir F.; Spirov, Alexander V.

2015-01-01

Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of “genomic parasites”, such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators that adapt in response to an evolutionary problem in the course of co-evolution with their hosts. PMID:25767296

The Hartman-Grobman theorem for semilinear hyperbolic evolution equations

NASA Astrophysics Data System (ADS)

Hein, Marie-Luise; Prüss, Jan

2016-10-01

The famous Hartman-Grobman theorem for ordinary differential equations is extended to abstract semilinear hyperbolic evolution equations in Banach spaces by means of simple direct proof. It is also shown that the linearising map is Hölder continuous. Several applications to abstract and specific damped wave equations are given, to demonstrate the strength of our results.

The Development, Evolution, and Status of Holland's Theory of Vocational Personalities: Reflections and Future Directions for Counseling Psychology

ERIC Educational Resources Information Center

Nauta, Margaret M.

2010-01-01

This article celebrates the 50th anniversary of the introduction of John L. Holland's (1959) theory of vocational personalities and work environments by describing the theory's development and evolution, its instrumentation, and its current status. Hallmarks of Holland's theory are its empirical testability and its user-friendliness. By…

Service, Comfort, or Emotional Support? The Evolution of Disability Law and Campus Housing

ERIC Educational Resources Information Center

Bauman, Mark; Davidson, Denise L.; Sachs, Michael C.; Kotarski, Tegan

2013-01-01

Comprehension and application of law in campus housing settings can be a daunting task. Though challenging, a basic understanding of law and how it applies to residence life and housing environments within institutions of higher education is crucial. This article provides an historical evolution of three laws that have direct bearing on campus…

Teaching the Theory of Evolution in Social, Intellectual, and Pedagogical Context

ERIC Educational Resources Information Center

Anderson, Ronald D.

2007-01-01

Teaching the theory of evolution in classrooms takes place in a social, intellectual, and pedagogical context which must be considered with care if students are to receive a complete and authentic education. In addition to the science education literature on this topic, attention is directed to the expanding literature on science and religion, as…

Mate Choice in Soldier Beetles: Field & Laboratory Experiments that Demonstrate Sexual Selection in Action

ERIC Educational Resources Information Center

Eason, Perri K.; Sherman, Peter T.

2003-01-01

Although the theory of evolution is the foundation of modern biology, students too rarely have an opportunity to watch selection operate in natural populations of animals. This lack may be partially responsible for the unfortunate ignorance of many people regarding the significance of evolution in biology. Laboratory exercises that directly study…

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.

Measurements of wind-waves under transient wind conditions.

NASA Astrophysics Data System (ADS)

Shemer, Lev; Zavadsky, Andrey

2015-11-01

Wind forcing in nature is always unsteady, resulting in a complicated evolution pattern that involves numerous time and space scales. In the present work, wind waves in a laboratory wind-wave flume are studied under unsteady forcing`. The variation of the surface elevation is measured by capacitance wave gauges, while the components of the instantaneous surface slope in across-wind and along-wind directions are determined by a regular or scanning laser slope gauge. The locations of the wave gauge and of the laser slope gauge are separated by few centimeters in across-wind direction. Instantaneous wind velocity was recorded simultaneously using Pitot tube. Measurements are performed at a number of fetches and for different patterns of wind velocity variation. For each case, at least 100 independent realizations were recorded for a given wind velocity variation pattern. The accumulated data sets allow calculating ensemble-averaged values of the measured parameters. Significant differences between the evolution patterns of the surface elevation and of the slope components were found. Wavelet analysis was applied to determine dominant wave frequency of the surface elevation and of the slope variation at each instant. Corresponding ensemble-averaged values acquired by different sensors were computed and compared. Analysis of the measured ensemble-averaged quantities at different fetches makes it possible to identify different stages in the wind-wave evolution and to estimate the appropriate time and length scales.

Gain-of-function mutations in beet DODA2 identify key residues for betalain pigment evolution.

PubMed

Bean, Alexander; Sunnadeniya, Rasika; Akhavan, Neda; Campbell, Annabelle; Brown, Matthew; Lloyd, Alan

2018-05-13

The key enzymatic step in betalain biosynthesis involves conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) to betalamic acid. One class of enzymes capable of this is 3,4-dihydroxyphenylalanine 4,5-dioxygenase (DODA). In betalain-producing species, multiple paralogs of this gene are maintained. This study demonstrates which paralogs function in the betalain pathway and determines the residue changes required to evolve a betalain-nonfunctional DODA into a betalain-functional DODA. Functionalities of two pairs of DODAs were tested by expression in beets, Arabidopsis and yeast, and gene silencing was performed by virus-induced gene silencing. Site-directed mutagenesis identified amino acid residues essential for betalamic acid production. Beta vulgaris and Mirabilis jalapa both possess a DODA1 lineage that functions in the betalain pathway and at least one other lineage, DODA2, that does not. Site-directed mutagenesis resulted in betalain biosynthesis by a previously nonfunctional DODA, revealing key residues required for evolution of the betalain pathway. Divergent functionality of DODA paralogs, one clade involved in betalain biosynthesis but others not, is present in various Caryophyllales species. A minimum of seven amino acid residue changes conferred betalain enzymatic activity to a betalain-nonfunctional DODA paralog, providing insight into the evolution of the betalain pigment pathway in plants. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

In situ multi-axial loading frame to probe elastomers using X-ray scattering.

PubMed

Pannier, Yannick; Proudhon, Henry; Mocuta, Cristian; Thiaudière, Dominique; Cantournet, Sabine

2011-11-01

An in situ tensile-shear loading device has been designed to study elastomer crystallization using synchrotron X-ray scattering at the Synchrotron Soleil on the DiffAbs beamline. Elastomer tape specimens of thickness 2 mm can be elongated by up to 500% in the longitudinal direction and sheared by up to 200% in the transverse direction. The device is fully automated and plugged into the TANGO control system of the beamline allowing synchronization between acquisition and loading sequences. Experimental results revealing the evolution of crystallization peaks under load are presented for several tension/shear loading sequences.

MEVTV Workshop on Early Tectonic and Volcanic Evolution of Mars

NASA Technical Reports Server (NTRS)

Frey, H. (Editor)

1988-01-01

Although not ignored, the problems of the early tectonic and volcanic evolution of Mars have generally received less attention than those later in the evolution of the planet. Specifically, much attention was devoted to the evolution of the Tharsis region of Mars and to the planet itself at the time following the establishment of this major tectonic and volcanic province. By contrast, little attention was directed at fundamental questions, such as the conditions that led to the development of Tharsis and the cause of the basic fundamental dichotomy of the Martian crust. It was to address these and related questions of the earliest evolution of Mars that a workshop was organized under the auspices of the Mars: Evolution of Volcanism, Tectonism, and Volatiles (MEVTV) Program. Four sessions were held: crustal dichotomy; crustal differentiation/volcanism; Tharsis, Elysium, and Valles Marineris; and ridges and fault tectonics.

Exobiology: The NASA program

NASA Technical Reports Server (NTRS)

Rummel, John D.; Harper, Lynn; Andersen, Dale

1992-01-01

The goal of NASA's Exobiology Program is to understand the origin, evolution, and distribution of life in the universe. To do this, the Exobiology Program seeks to provide a critical framework and some key research to allow NASA to bear the combined talents and capabilities of the agency and the scientific community, and the unique opportunities afforded by space exploration. To provide structure and direction to the quest for answers, the Exobiology Program has instituted a comprehensive research program divided into four elements which are being implemented at several of NASA's research centers and in the university community. These program elements correspond to the four major epochs in the evolution of living systems: (1) cosmic evolution of the biogenic compounds; (2) prebiotic evolution; (3) origin and early evolution of life; and (4) evolution of advanced life. The overall research program is designed to trace the pathways leading from the origin of the universe through the major epochs in the story of life.

Storytelling, behavior planning, and language evolution in context.

PubMed

McBride, Glen

2014-01-01

An attempt is made to specify the structure of the hominin bands that began steps to language. Storytelling could evolve without need for language yet be strongly subject to natural selection and could provide a major feedback process in evolving language. A storytelling model is examined, including its effects on the evolution of consciousness and the possible timing of language evolution. Behavior planning is presented as a model of language evolution from storytelling. The behavior programming mechanism in both directions provide a model of creating and understanding behavior and language. Culture began with societies, then family evolution, family life in troops, but storytelling created a culture of experiences, a final step in the long process of achieving experienced adults by natural selection. Most language evolution occurred in conversations where evolving non-verbal feedback ensured mutual agreements on understanding. Natural language evolved in conversations with feedback providing understanding of changes.

Storytelling, behavior planning, and language evolution in context

PubMed Central

McBride, Glen

2014-01-01

An attempt is made to specify the structure of the hominin bands that began steps to language. Storytelling could evolve without need for language yet be strongly subject to natural selection and could provide a major feedback process in evolving language. A storytelling model is examined, including its effects on the evolution of consciousness and the possible timing of language evolution. Behavior planning is presented as a model of language evolution from storytelling. The behavior programming mechanism in both directions provide a model of creating and understanding behavior and language. Culture began with societies, then family evolution, family life in troops, but storytelling created a culture of experiences, a final step in the long process of achieving experienced adults by natural selection. Most language evolution occurred in conversations where evolving non-verbal feedback ensured mutual agreements on understanding. Natural language evolved in conversations with feedback providing understanding of changes. PMID:25360123

Texture Development and Material Flow Behavior During Refill Friction Stir Spot Welding of AlMgSc

NASA Astrophysics Data System (ADS)

Shen, Junjun; Lage, Sara B. M.; Suhuddin, Uceu F. H.; Bolfarini, Claudemiro; dos Santos, Jorge F.

2018-01-01

The microstructural evolution during refill friction stir spot welding of an AlMgSc alloy was studied. The primary texture that developed in all regions, with the exception of the weld center, was determined to be 〈110〉 fibers and interpreted as a simple shear texture with the 〈110〉 direction aligned with the shear direction. The material flow is mainly driven by two components: the simple shear acting on the horizontal plane causing an inward-directed spiral flow and the extrusion acting on the vertical plane causing an upward-directed or downward-directed flow. Under such a complex material flow, the weld center, which is subjected to minimal local strain, is the least recrystallized. In addition to the geometric effects of strain and grain subdivision, thermally activated high-angle grain boundary migration, particularly continuous dynamic recrystallization, drives the formation of refined grains in the stirred zone.

Chemical and phase evolution of amorphous molybdenum sulfide catalysts for electrochemical hydrogen production [Chemical and phase evolution of amorphous molybdenum sulfide catalysts for electrochemical hydrogen production directly observed using environmental transmission electron microscopy

DOE PAGES

Lee, Sang Chul; Benck, Jesse D.; Tsai, Charlie; ...

2015-12-01

Amorphous MoS x is a highly active, earth-abundant catalyst for the electrochemical hydrogen evolution reaction. Previous studies have revealed that this material initially has a composition of MoS 3, but after electrochemical activation, the surface is reduced to form an active phase resembling MoS 2 in composition and chemical state. However, structural changes in the Mo Sx catalyst and the mechanism of the activation process remain poorly understood. In this study, we employ transmission electron microscopy (TEM) to image amorphous MoS x catalysts activated under two hydrogen-rich conditions: ex situ in an electrochemical cell and in situ in an environmentalmore » TEM. For the first time, we directly observe the formation of crystalline domains in the MoS x catalyst after both activation procedures as well as spatially localized changes in the chemical state detected via electron energy loss spectroscopy. Using density functional theory calculations, we investigate the mechanisms for this phase transformation and find that the presence of hydrogen is critical for enabling the restructuring process. Our results suggest that the surface of the amorphous MoS x catalyst is dynamic: while the initial catalyst activation forms the primary active surface of amorphous MoS 2, continued transformation to the crystalline phase during electrochemical operation could contribute to catalyst deactivation. Finally, these results have important implications for the application of this highly active electrocatalyst for sustainable H 2 generation.« less

A hybrid health service accreditation program model incorporating mandated standards and continuous improvement: interview study of multiple stakeholders in Australian health care.

PubMed

Greenfield, David; Hinchcliff, Reece; Hogden, Anne; Mumford, Virginia; Debono, Deborah; Pawsey, Marjorie; Westbrook, Johanna; Braithwaite, Jeffrey

2016-07-01

The study aim was to investigate the understandings and concerns of stakeholders regarding the evolution of health service accreditation programs in Australia. Stakeholder representatives from programs in the primary, acute and aged care sectors participated in semi-structured interviews. Across 2011-12 there were 47 group and individual interviews involving 258 participants. Interviews lasted, on average, 1 h, and were digitally recorded and transcribed. Transcriptions were analysed using textual referencing software. Four significant issues were considered to have directed the evolution of accreditation programs: altering underlying program philosophies; shifting of program content focus and details; different surveying expectations and experiences and the influence of external contextual factors upon accreditation programs. Three accreditation program models were noted by participants: regulatory compliance; continuous quality improvement and a hybrid model, incorporating elements of these two. Respondents noted the compatibility or incommensurability of the first two models. Participation in a program was reportedly experienced as ranging on a survey continuum from "malicious compliance" to "performance audits" to "quality improvement journeys". Wider contextual factors, in particular, political and community expectations, and associated media reporting, were considered significant influences on the operation and evolution of programs. A hybrid accreditation model was noted to have evolved. The hybrid model promotes minimum standards and continuous quality improvement, through examining the structure and processes of organisations and the outcomes of care. The hybrid model appears to be directing organisational and professional attention to enhance their safety cultures. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Measurement and potential barrier evolution analysis of cold field emission in fracture fabricated Si nanogap

NASA Astrophysics Data System (ADS)

Banerjee, Amit; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

2017-06-01

Cold field emission characteristics of a fracture fabricated Si nanogap (˜100 nm) were investigated with an ascending electric field (voltage) sweep. The nanogap was formed by controlled fracture of a free-standing silicon micro-beam along <111> direction by a microelectromechanical device, which results in flat, smooth, and conformal electrode pairs. This facilitates simultaneous large area emission, which gives rise to a significant current at low bias voltage, which usually remains indiscernible in nanogaps of this size. The measured emission current-voltage (I-V) characteristics clearly depict two distinct regimes: a linear (I ∝ V) regime at low bias voltage and a nonlinear [ln(I/V 2) ∝ V -1] regime at high bias voltage, separated by a transition point. We propose that the linear regime is owed to direct tunneling of electrons, whereas the nonlinear regime is due to Fowler-Nordheim type emission. This proposition essentially implies that the tunneling potential barrier gradually evolved from a rectangular shape to a triangular shape with increasing field (V). This type of evolution is usually observed in molecular size gaps. We have attempted to correlate the I-V curves acquired through the experiments with the electric field induced barrier shape evolution by numerical calculations involving standard quantum mechanics. The observed linear regime at low bias voltage (<5 V) in a relatively large size gap (˜100 nm) is attributed to the fabrication method adopted in this study. The reported study and the fabricated device are significant for developing a futuristic thermotunneling refrigerator that will find a wide range of application in nanoelectronic devices.