Mechanisms of stable lipid loss in a social insect.

PubMed

Ament, Seth A; Chan, Queenie W; Wheeler, Marsha M; Nixon, Scott E; Johnson, S Peir; Rodriguez-Zas, Sandra L; Foster, Leonard J; Robinson, Gene E

2011-11-15

Worker honey bees undergo a socially regulated, highly stable lipid loss as part of their behavioral maturation. We used large-scale transcriptomic and proteomic experiments, physiological experiments and RNA interference to explore the mechanistic basis for this lipid loss. Lipid loss was associated with thousands of gene expression changes in abdominal fat bodies. Many of these genes were also regulated in young bees by nutrition during an initial period of lipid gain. Surprisingly, in older bees, which is when maximum lipid loss occurs, diet played less of a role in regulating fat body gene expression for components of evolutionarily conserved nutrition-related endocrine systems involving insulin and juvenile hormone signaling. By contrast, fat body gene expression in older bees was regulated more strongly by evolutionarily novel regulatory factors, queen mandibular pheromone (a honey bee-specific social signal) and vitellogenin (a conserved yolk protein that has evolved novel, maturation-related functions in the bee), independent of nutrition. These results demonstrate that conserved molecular pathways can be manipulated to achieve stable lipid loss through evolutionarily novel regulatory processes.

The effect of travel loss on evolutionarily stable distributions of populations in space

USGS Publications Warehouse

DeAngelis, D.L.; Wolkowicz, G.S.K.; Lou, Y.; Jiang, Y.; Novak, M.; Svanback, R.; Araujo, M.S.; Jo, Y.S.; Cleary, E.A.

2011-01-01

A key assumption of the ideal free distribution (IFD) is that there are no costs in moving between habitat patches. However, because many populations exhibit more or less continuous population movement between patches and traveling cost is a frequent factor, it is important to determine the effects of costs on expected population movement patterns and spatial distributions. We consider a food chain (tritrophic or bitrophic) in which one species moves between patches, with energy cost or mortality risk in movement. In the two-patch case, assuming forced movement in one direction, an evolutionarily stable strategy requires bidirectional movement, even if costs during movement are high. In the N-patch case, assuming that at least one patch is linked bidirectionally to all other patches, optimal movement rates can lead to source-sink dynamics where patches with negative growth rates are maintained by other patches with positive growth rates. As well, dispersal between patches is not balanced (even in the two-patch case), leading to a deviation from the IFD. Our results indicate that cost-associated forced movement can have important consequences for spatial metapopulation dynamics. Relevance to marine reserve design and the study of stream communities subject to drift is discussed. ?? 2011 by The University of Chicago.

Evolution of proliferation and the angiogenic switch in tumors with high clonal diversity.

PubMed

Bickel, Scott T; Juliano, Joseph D; Nagy, John D

2014-01-01

Natural selection among tumor cell clones is thought to produce hallmark properties of malignancy. Efforts to understand evolution of one such hallmark--the angiogenic switch--has suggested that selection for angiogenesis can "run away" and generate a hypertumor, a form of evolutionary suicide by extreme vascular hypo- or hyperplasia. This phenomenon is predicted by models of tumor angiogenesis studied with the techniques of adaptive dynamics. These techniques also predict that selection drives tumor proliferative potential towards an evolutionarily stable strategy (ESS) that is also convergence-stable. However, adaptive dynamics are predicated on two key assumptions: (i) no more than two distinct clones or evolutionary strategies can exist in the tumor at any given time; and (ii) mutations cause small phenotypic changes. Here we show, using a stochastic simulation, that relaxation of these assumptions has no effect on the predictions of adaptive dynamics in this case. In particular, selection drives proliferative potential towards, and angiogenic potential away from, their respective ESSs. However, these simulations also show that tumor behavior is highly contingent on mutational history, particularly for angiogenesis. Individual tumors frequently grow to lethal size before the evolutionary endpoint is approached. In fact, most tumor dynamics are predicted to be in the evolutionarily transient regime throughout their natural history, so that clinically, the ESS is often largely irrelevant. In addition, we show that clonal diversity as measured by the Shannon Information Index correlates with the speed of approach to the evolutionary endpoint. This observation dovetails with results showing that clonal diversity in Barrett's esophagus predicts progression to malignancy.

The Hawk-Dove game in phenotypically homogeneous and heterogeneous populations of finite dimension

NASA Astrophysics Data System (ADS)

Laruelle, Annick; da Silva Rocha, André Barreira; Escobedo, Ramón

2018-02-01

The Hawk-Dove game played between individuals in populations of finite dimension is analyzed by means of a stochastic model. We take into account both cases when all individuals in the population are either phenotypically homogeneous or heterogeneous. A strategy in the model is a gene representing the probability of playing the Hawk strategy. Individual interactions at the microscopic level are described by a genetic algorithm where evolution results from the interplay among selection, mutation, drift and cross-over of genes. We show that the behavioral patterns observed at the macroscopic level can be reproduced as the emergent result of individual interactions governed by the rules of the Hawk-Dove game at the microscopic level. We study how the results of the genetic algorithm compare with those obtained in evolutionary game theory, finding that, although genes continuously change both their presence and frequency in the population over time, the population average behavior always achieves stationarity and, when this happens, the final average strategy played in the population oscillates around the evolutionarily stable strategy in the homogeneous population case or the neutrally stable set in the heterogeneous population case.

Evolutionary stability of egg trading and parceling in simultaneous hermaphrodites: the chalk bass revisited.

PubMed

Crowley, Philip H; Hart, Mary K

2007-06-07

Several species of simultaneously hermaphroditic seabasses living on coral reefs mate by alternating male and female roles with a partner. This is known as egg trading, one of the classic and most widely cited examples of social reciprocity among animals. Some of the egg-trading seabass species, including the chalk bass, Serranus tortugarum, switch mating roles repeatedly, having subdivided their clutch of eggs into parcels offered to the partner for fertilization. Here we attempt to understand these dynamics as a pair of evolutionary games, modifying some previous approaches to better reflect the biological system. We find that the trading of egg clutches is evolutionarily stable via byproduct mutualism and resistant to invasion by rare individuals that take the male role exclusively. We note why and how parceling may reflect sexual conflict between individuals in the mating pair. We estimate evolutionarily stable parcel numbers and show how they depend on parameter values. Typically, two or more sequential parcel numbers are evolutionarily stable, though the lowest of these yields the highest fitness. Assuming that parcel numbers are adjusted to local conditions, we predict that parcel numbers in nature are inversely related both to mating group density (except at low density) and predation risk.

Are there really no evolutionarily stable strategies in the iterated prisoner's dilemma?

PubMed

Lorberbaum, Jeffrey P; Bohning, Daryl E; Shastri, Ananda; Sine, Lauren E

2002-01-21

The evolutionary form of the iterated prisoner's dilemma (IPD) is a repeated game where players strategically choose whether to cooperate with or exploit opponents and reproduce in proportion to game success. It has been widely used to study the evolution of cooperation among selfish agents. In the past 15 years, researchers proved over a series of papers that there is no evolutionarily stable strategy (ESS) in the IPD when players maintain long-term relationships. This makes it difficult to make predictions about what strategies can actually persist as prevalent in a population over time. Here, we show that this no ESS finding may be a mathematical technicality, relying on implausible players who are "too perfect" in that their probability of cooperating on any move is arbitrarily close to either 0 or 1. Specifically, in the no ESS proof, all strategies were allowed, meaning that after a strategy X experiences any history H, X cooperates with an unrestricted probability p (X, H) where 0< or =p (X, H)< or =1. Here, we restrict strategies to the set S in which X is a member of S [corrected] if after any H, X cooperates with a restricted probability p (X, H) where e< or =p (X, H)< or =1-e and 0

Evolutionary stability concepts in a stochastic environment

NASA Astrophysics Data System (ADS)

Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi

2017-09-01

Over the past 30 years, evolutionary game theory and the concept of an evolutionarily stable strategy have been not only extensively developed and successfully applied to explain the evolution of animal behaviors, but also widely used in economics and social sciences. Nonetheless, the stochastic dynamical properties of evolutionary games in randomly fluctuating environments are still unclear. In this study, we investigate conditions for stochastic local stability of fixation states and constant interior equilibria in a two-phenotype model with random payoffs following pairwise interactions. Based on this model, we develop the concepts of stochastic evolutionary stability (SES) and stochastic convergence stability (SCS). We show that the condition for a pure strategy to be SES and SCS is more stringent than in a constant environment, while the condition for a constant mixed strategy to be SES is less stringent than the condition to be SCS, which is less stringent than the condition in a constant environment.

Evolution of extortion in the social-influenced prisoner’s dilemma

NASA Astrophysics Data System (ADS)

Wang, Zhipeng; Li, Miao; Wang, Dan; Chen, Qinghe

2016-01-01

The introduction of extortion strategy has attracted much attention since it dominates any evolutionary opponent in iterated prisoner’s dilemma games. Despite several studies argue that extortion is difficult to survive under strategy imitation and birth-death updating rules in well-mixed populations, it has recently been proven that a myopic best response rule facilitate the evolution of cooperation and extortion. However, such updating rules require a strong assumption of complete knowledge of all players, which is unlikely to hold in social networks in reality. To solve this problem, we introduce the concept of social influence into the model to limit players’ knowledge within their neighborhood. It turns out that this myopia initiated by social influence prevents players from observing superior strategies and therefore enables cooperators and extortioners to be evolutionarily stable. We also suggest that heterogeneous networks contribute to the evolution of cooperation and extortion under such social influence.

Polygyny, mate-guarding, and posthumous fertilization as alternative male mating strategies.

PubMed

Zamudio, K R; Sinervo, B

2000-12-19

Alternative male mating strategies within populations are thought to be evolutionarily stable because different behaviors allow each male type to successfully gain access to females. Although alternative male strategies are widespread among animals, quantitative evidence for the success of discrete male strategies is available for only a few systems. We use nuclear microsatellites to estimate the paternity rates of three male lizard strategies previously modeled as a rock-paper-scissors game. Each strategy has strengths that allow it to outcompete one morph, and weaknesses that leave it vulnerable to the strategy of another. Blue-throated males mate-guard their females and avoid cuckoldry by yellow-throated "sneaker" males, but mate-guarding is ineffective against aggressive orange-throated neighbors. The ultradominant orange-throated males are highly polygynous and maintain large territories; they overpower blue-throated neighbors and cosire offspring with their females, but are often cuckolded by yellow-throated males. Finally, yellow-throated sneaker males sire offspring via secretive copulations and often share paternity of offspring within a female's clutch. Sneaker males sire more offspring posthumously, indicating that sperm competition may be an important component of their strategy.

Evolutionarily stable range limits set by interspecific competition.

PubMed

Price, Trevor D; Kirkpatrick, Mark

2009-04-22

A combination of abiotic and biotic factors probably restricts the range of many species. Recent evolutionary models and tests of those models have asked how a gradual change in environmental conditions can set the range limit, with a prominent idea being that gene flow disrupts local adaptation. We investigate how biotic factors, explicitly competition for limited resources, result in evolutionarily stable range limits even in the absence of the disruptive effect of gene flow. We model two competing species occupying different segments of the resource spectrum. If one segment of the resource spectrum declines across space, a species that specializes on that segment can be driven to extinction, even though in the absence of competition it would evolve to exploit other abundant resources and so be saved. The result is that a species range limit is set in both evolutionary and ecological time, as the resources associated with its niche decline. Factors promoting this outcome include: (i) inherent gaps in the resource distribution, (ii) relatively high fitness of the species when in its own niche, and low fitness in the alternative niche, even when resource abundances are similar in each niche, (iii) strong interspecific competition, and (iv) asymmetric interspecific competition. We suggest that these features are likely to be common in multispecies communities, thereby setting evolutionarily stable range limits.

Evolutionarily stable range limits set by interspecific competition

PubMed Central

Price, Trevor D.; Kirkpatrick, Mark

2009-01-01

A combination of abiotic and biotic factors probably restricts the range of many species. Recent evolutionary models and tests of those models have asked how a gradual change in environmental conditions can set the range limit, with a prominent idea being that gene flow disrupts local adaptation. We investigate how biotic factors, explicitly competition for limited resources, result in evolutionarily stable range limits even in the absence of the disruptive effect of gene flow. We model two competing species occupying different segments of the resource spectrum. If one segment of the resource spectrum declines across space, a species that specializes on that segment can be driven to extinction, even though in the absence of competition it would evolve to exploit other abundant resources and so be saved. The result is that a species range limit is set in both evolutionary and ecological time, as the resources associated with its niche decline. Factors promoting this outcome include: (i) inherent gaps in the resource distribution, (ii) relatively high fitness of the species when in its own niche, and low fitness in the alternative niche, even when resource abundances are similar in each niche, (iii) strong interspecific competition, and (iv) asymmetric interspecific competition. We suggest that these features are likely to be common in multispecies communities, thereby setting evolutionarily stable range limits. PMID:19324813

Drought-related leaf phenology in tropical forests - Insights from a stochastic eco-hydrological approach

NASA Astrophysics Data System (ADS)

Vico, G.; Feng, X.; Dralle, D.; Thompson, S. E.; Manzoni, S.

2016-12-01

Drought deciduousness is a common phenological strategy to cope with water shortages during periodic dry spells or during the dry season in tropical forests. On one hand, shedding leaves allows avoiding drought stress, but implies leaf construction costs that evergreen species need to sustain less frequently. On the other hand, maintaining leaves during dry periods requires stable water sources, traits enabling leaves to remain active at low water potential, and carbon stores to sustain respiration costs in periods with little carbon uptake. Which of these strategies is the most competitive ultimately depends on the balance of carbon costs and gains in the long-term. In turn, this balance is affected by the hydro-climatic conditions, in terms of both length of the dry season and random rainfall occurrences during the wet season. To address the question as to which hydro-climatic conditions favor drought-deciduous vs. evergreen leaf habit in tropical forests, we develop a stochastic eco-hydrological framework that provides probability density functions of long-term carbon gain in tropical trees with a range of phenological strategies. From these distributions we compute the long-term mean carbon gain and use it as a measure of fitness and thus reproductive success. Finally, this measure is used to assess which phenological strategies are evolutionarily stable, providing an objective criterion to predict how likely a species with a certain phenological strategy is to invade a community dominated but another strategy. In general, we find that deciduous habit is evolutionary stable in more unpredictable climates for a given total rainfall, and in drier climates. However, a minimum annual rainfall is required for any strategy to have a positive carbon gain.

The rock-paper-scissors game

NASA Astrophysics Data System (ADS)

Zhou, Hai-Jun

2016-04-01

Rock-Paper-Scissors (RPS), a game of cyclic dominance, is not merely a popular children's game but also a basic model system for studying decision-making in non-cooperative strategic interactions. Aimed at students of physics with no background in game theory, this paper introduces the concepts of Nash equilibrium and evolutionarily stable strategy, and reviews some recent theoretical and empirical efforts on the non-equilibrium properties of the iterated RPS, including collective cycling, conditional response patterns and microscopic mechanisms that facilitate cooperation. We also introduce several dynamical processes to illustrate the applications of RPS as a simplified model of species competition in ecological systems and price cycling in economic markets.

Finite-size effects and switching times for Moran process with mutation.

PubMed

DeVille, Lee; Galiardi, Meghan

2017-04-01

We consider the Moran process with two populations competing under an iterated Prisoner's Dilemma in the presence of mutation, and concentrate on the case where there are multiple evolutionarily stable strategies. We perform a complete bifurcation analysis of the deterministic system which arises in the infinite population size. We also study the Master equation and obtain asymptotics for the invariant distribution and metastable switching times for the stochastic process in the case of large but finite population. We also show that the stochastic system has asymmetries in the form of a skew for parameter values where the deterministic limit is symmetric.

Fixation of strategies with the Moran and Fermi processes in evolutionary games

NASA Astrophysics Data System (ADS)

Liu, Xuesong; He, Mingfeng; Kang, Yibin; Pan, Qiuhui

2017-10-01

A model of stochastic evolutionary game dynamics with finite population was built. It combines the standard Moran and Fermi rules with two strategies cooperation and defection. We obtain the expressions of fixation probabilities and fixation times. The one-third rule which has been found in the frequency dependent Moran process also holds for our model. We obtain the conditions of strategy being an evolutionarily stable strategy in our model, and then make a comparison with the standard Moran process. Besides, the analytical results show that compared with the standard Moran process, fixation occurs with higher probabilities under a prisoner's dilemma game and coordination game, but with lower probabilities under a coexistence game. The simulation result shows that the fixation time in our mixed process is lower than that in the standard Fermi process. In comparison with the standard Moran process, fixation always takes more time on average in spatial populations, regardless of the game. In addition, the fixation time decreases with the growth of the number of neighbors.

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. Copyright © 2016 Elsevier Ltd. All rights reserved.

Beyond R0 Maximisation: On Pathogen Evolution and Environmental Dimensions.

PubMed

Lion, Sébastien; Metz, Johan A J

2018-06-01

A widespread tenet is that evolution of pathogens maximises their basic reproduction ratio, R 0 . The breakdown of this principle is typically discussed as exception. Here, we argue that a radically different stance is needed, based on evolutionarily stable strategy (ESS) arguments that take account of the 'dimension of the environmental feedback loop'. The R 0 maximisation paradigm requires this feedback loop to be one-dimensional, which notably excludes pathogen diversification. By contrast, almost all realistic ecological ingredients of host-pathogen interactions (density-dependent mortality, multiple infections, limited cross-immunity, multiple transmission routes, host heterogeneity, and spatial structure) will lead to multidimensional feedbacks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes

PubMed Central

Ślipiko, Monika; Buczkowska-Chmielewska, Katarzyna; Bączkiewicz, Alina; Szczecińska, Monika; Sawicki, Jakub

2017-01-01

Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida) contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts. PMID:29257096

Polygyny, mate-guarding, and posthumous fertilization as alternative male mating strategies

PubMed Central

Zamudio, Kelly R.; Sinervo, Barry

2000-01-01

Alternative male mating strategies within populations are thought to be evolutionarily stable because different behaviors allow each male type to successfully gain access to females. Although alternative male strategies are widespread among animals, quantitative evidence for the success of discrete male strategies is available for only a few systems. We use nuclear microsatellites to estimate the paternity rates of three male lizard strategies previously modeled as a rock-paper-scissors game. Each strategy has strengths that allow it to outcompete one morph, and weaknesses that leave it vulnerable to the strategy of another. Blue-throated males mate-guard their females and avoid cuckoldry by yellow-throated “sneaker” males, but mate-guarding is ineffective against aggressive orange-throated neighbors. The ultradominant orange-throated males are highly polygynous and maintain large territories; they overpower blue-throated neighbors and cosire offspring with their females, but are often cuckolded by yellow-throated males. Finally, yellow-throated sneaker males sire offspring via secretive copulations and often share paternity of offspring within a female's clutch. Sneaker males sire more offspring posthumously, indicating that sperm competition may be an important component of their strategy. PMID:11106369

Rational Design of Evolutionarily Stable Microbial Kill Switches.

PubMed

Stirling, Finn; Bitzan, Lisa; O'Keefe, Samuel; Redfield, Elizabeth; Oliver, John W K; Way, Jeffrey; Silver, Pamela A

2017-11-16

The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. Additionally, cryodeath was shown to control the growth environment of a population, with an escape frequency of less than 1 in 10 5 after 10 days of growth in the mammalian gut. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution of cooperation with shared costs and benefits

PubMed Central

Brown, Joel S; Vincent, Thomas L

2008-01-01

The quest to determine how cooperation evolves can be based on evolutionary game theory, in spite of the fact that evolutionarily stable strategies (ESS) for most non-zero-sum games are not cooperative. We analyse the evolution of cooperation for a family of evolutionary games involving shared costs and benefits with a continuum of strategies from non-cooperation to total cooperation. This cost–benefit game allows the cooperator to share in the benefit of a cooperative act, and the recipient to be burdened with a share of the cooperator's cost. The cost–benefit game encompasses the Prisoner's Dilemma, Snowdrift game and Partial Altruism. The models produce ESS solutions of total cooperation, partial cooperation, non-cooperation and coexistence between cooperation and non-cooperation. Cooperation emerges from an interplay between the nonlinearities in the cost and benefit functions. If benefits increase at a decelerating rate and costs increase at an accelerating rate with the degree of cooperation, then the ESS has an intermediate level of cooperation. The game also exhibits non-ESS points such as unstable minima, convergent-stable minima and unstable maxima. The emergence of cooperative behaviour in this game represents enlightened self-interest, whereas non-cooperative solutions illustrate the Tragedy of the Commons. Games having either a stable maximum or a stable minimum have the property that small changes in the incentive structure (model parameter values) or culture (starting frequencies of strategies) result in correspondingly small changes in the degree of cooperation. Conversely, with unstable maxima or unstable minima, small changes in the incentive structure or culture can result in a switch from non-cooperation to total cooperation (and vice versa). These solutions identify when human or animal societies have the potential for cooperation and whether cooperation is robust or fragile. PMID:18495622

Evolution of learning strategies in temporally and spatially variable environments: A review of theory

PubMed Central

Aoki, Kenichi; Feldman, Marcus W.

2013-01-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change – coevolutionary, two-timescale, and information decay – are compared and shown to sometimes yield contradictory results. The so-called Rogers’ paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers’ paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. PMID:24211681

Evolution of learning strategies in temporally and spatially variable environments: a review of theory.

PubMed

Aoki, Kenichi; Feldman, Marcus W

2014-02-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change--coevolutionary, two-timescale, and information decay--are compared and shown to sometimes yield contradictory results. The so-called Rogers' paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers' paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation.

PubMed

Martinez-Vaquero, Luis A; Cuesta, José A

2013-05-01

Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity is reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies; thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly, we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can resist the invasion of any other strategy. However, if actions are not always witnessed, cheaters (i.e., individuals with a probability of defecting regardless of the opponent's reputation) have a chance to defeat the stable strategies for some choices of the probabilities of cheating and of being witnessed. Remarkably, by analyzing this issue with adaptive dynamics we find that whether an honest population resists the invasion of cheaters is determined by a Hamilton-like rule, with the probability that the cheat is discovered playing the role of the relatedness parameter.

Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation

NASA Astrophysics Data System (ADS)

Martinez-Vaquero, Luis A.; Cuesta, José A.

2013-05-01

Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity is reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies; thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly, we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can resist the invasion of any other strategy. However, if actions are not always witnessed, cheaters (i.e., individuals with a probability of defecting regardless of the opponent's reputation) have a chance to defeat the stable strategies for some choices of the probabilities of cheating and of being witnessed. Remarkably, by analyzing this issue with adaptive dynamics we find that whether an honest population resists the invasion of cheaters is determined by a Hamilton-like rule, with the probability that the cheat is discovered playing the role of the relatedness parameter.

Adaptive evolution of defense ability leads to diversification of prey species.

PubMed

Zu, Jian; Wang, Jinliang; Du, Jianqiang

2014-06-01

In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey-two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex-concave-convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale.

Evolution of flowering strategies in Oenothera glazioviana: an integral projection model approach.

PubMed Central

Rees, Mark; Rose, Karen E

2002-01-01

The timing of reproduction is a key determinant of fitness. Here, we develop parameterized integral projection models of size-related flowering for the monocarpic perennial Oenothera glazioviana and use these to predict the evolutionarily stable strategy (ESS) for flowering. For the most part there is excellent agreement between the model predictions and the results of quantitative field studies. However, the model predicts a much steeper relationship between plant size and the probability of flowering than observed in the field, indicating selection for a 'threshold size' flowering function. Elasticity and sensitivity analysis of population growth rate lambda and net reproductive rate R(0) are used to identify the critical traits that determine fitness and control the ESS for flowering. Using the fitted model we calculate the fitness landscape for invading genotypes and show that this is characterized by a ridge of approximately equal fitness. The implications of these results for the maintenance of genetic variation are discussed. PMID:12137582

Evolution of flowering strategies in Oenothera glazioviana: an integral projection model approach.

PubMed

Rees, Mark; Rose, Karen E

2002-07-22

The timing of reproduction is a key determinant of fitness. Here, we develop parameterized integral projection models of size-related flowering for the monocarpic perennial Oenothera glazioviana and use these to predict the evolutionarily stable strategy (ESS) for flowering. For the most part there is excellent agreement between the model predictions and the results of quantitative field studies. However, the model predicts a much steeper relationship between plant size and the probability of flowering than observed in the field, indicating selection for a 'threshold size' flowering function. Elasticity and sensitivity analysis of population growth rate lambda and net reproductive rate R(0) are used to identify the critical traits that determine fitness and control the ESS for flowering. Using the fitted model we calculate the fitness landscape for invading genotypes and show that this is characterized by a ridge of approximately equal fitness. The implications of these results for the maintenance of genetic variation are discussed.

Arms races and the evolution of big fierce societies.

PubMed

Boswell, G P; Franks, N R; Britton, N F

2001-08-22

The causes of biological gigantism have received much attention, but only for individual organisms. What selection pressures might favour the evolution of gigantic societies? Here we consider the largest single-queen insect societies, those of the Old World army ant Dorylus, single colonies of which can have 20 million workers. We propose that colony gigantism in Dorylus arises as a result of an arms race and test this prediction by developing a size-structured mathematical model. We use this model for exploring and potentially explaining differences in colony size, colony aggression and colony propagation strategies in populations of New World army ants Eciton and Old World army ants Dorylus. The model shows that, by determining evolutionarily stable strategies (ESSs), differences in the trophic levels at which these army ants live feed forwards into differences in their densities and collision rates and, hence, into different strategies of growth, aggression and propagation. The model predicts large colony size and the occurrence of battles and a colony-propagation strategy involving highly asymmetrical divisions in Dorylus and that Eciton colonies should be smaller, non-combative and exhibit equitable binary fission. These ESSs are in excellent agreement with field observations and demonstrate that gargantuan societies can arise through arms races.

Evolutionarily stable strategy of carbon and nitrogen investments in forest leaves and its application in vegetation dynamic modeling

NASA Astrophysics Data System (ADS)

Weng, E.; Farrior, C.; Dybzinski, R.; Pacala, S. W.

2015-12-01

Leaf mass per area (LMA) and leaf lifespan (LL) are two highly correlated plant traits that are key to plant physiological and ecological properties. Usually, low LMA means short LL, high nitrogen (N) content per unit mass, and fast turnover rates of nutrients; high LMA leads to long LL, low N content, and slow turnover rates. Deciduous trees with low LMA and short lifespan leaves have low carbon cost but high nitrogen demand; and evergreen trees, with high LMA and long lifespan leaves, have high carbon cost but low nitrogen demand. These relationships lead to: 1) evergreen trees have higher leaf area index than deciduous trees; 2) evergreen trees' carbon use efficiency is lower than the deciduous trees' because of their thick leaves and therefore high maintenance respiration; 3) the advantage of evergreens trees brought by their extra leaves over deciduous trees diminishes with increase N in ecosystem. These facts determine who will win when trees compete with each other in a N-limited ecosystem. In this study, we formulate a mathematical model according to the relationships between LMA, LL, leaf nitrogen, and leaf building and maintenance cost, where LMA is the fundamental variable determining the other three. We analyze the evolutionarily stable strategies (ESSs) of LMA with this mathematical model by examining the benefits of carbon and nitrogen investments to leaves in ecosystems with different N. The model shows the ESS converges to low LMA at high N and high LMA at low N. At intermediate N, there are two ESSs at low and high ends of LMA, respectively. The ESS also leads to low forest productivity by outcompeting the possible high productive strategies. We design a simulation scheme in an individual-based competition model (LM3-PPA) to simulate forest dynamics as results of the competition between deciduous and evergreen trees in three different biomes, which are temperate deciduous forest, deciduous-evergreen mixed forest, and boreal evergreen forest. The simulated results are consistent with the actual forests. Our model and simulated results indicate the distribution of evergreen and deciduous forests can be explained by one single leaf trait (i.e., LMA) and associated physiological and biogeochemical processes.

An evolutionarily stable strategy and the critical point of hog futures trading entities based on replicator dynamic theory: 2006–2015 data for China’s 22 provinces

PubMed Central

Pang, Jinbo; Deng, Lingfei

2017-01-01

Although frequent fluctuations in domestic hog prices seriously affect the stability and robustness of the hog supply chain, hog futures (an effective hedging instrument) have not been listed in China. To better understand hog futures market hedging, it is important to study the steady state of intersubjective bidding. This paper uses evolutionary game theory to construct a game model between hedgers and speculators in the hog futures market, and replicator dynamic equations are then used to obtain the steady state between the two trading entities. The results show that the steady state is one in which hedgers adopt a “buy” strategy and speculators adopt a “do not speculate” strategy, but this type of extreme steady state is not easily realized. Thus, to explore the rational proportion of hedgers and speculators in the evolutionary stabilization strategy, bidding processes were simulated using weekly average hog prices from 2006 to 2015, such that the conditions under which hedgers and speculators achieve a steady state could be analyzed. This task was performed to achieve the stability critical point, and we show that only when the value of λ is satisfied and the conditions of hog futures price changes and futures price are satisfied can hedgers and speculators achieve a rational proportion and a stable hog futures market. This market can thus provide a valuable reference for the development of the Chinese hog futures market and the formulation and guidance of relevant departmental policies. PMID:28241024

An evolutionarily stable strategy and the critical point of hog futures trading entities based on replicator dynamic theory: 2006-2015 data for China's 22 provinces.

PubMed

Pang, Jinbo; Deng, Lingfei; Wang, Gangyi

2017-01-01

Although frequent fluctuations in domestic hog prices seriously affect the stability and robustness of the hog supply chain, hog futures (an effective hedging instrument) have not been listed in China. To better understand hog futures market hedging, it is important to study the steady state of intersubjective bidding. This paper uses evolutionary game theory to construct a game model between hedgers and speculators in the hog futures market, and replicator dynamic equations are then used to obtain the steady state between the two trading entities. The results show that the steady state is one in which hedgers adopt a "buy" strategy and speculators adopt a "do not speculate" strategy, but this type of extreme steady state is not easily realized. Thus, to explore the rational proportion of hedgers and speculators in the evolutionary stabilization strategy, bidding processes were simulated using weekly average hog prices from 2006 to 2015, such that the conditions under which hedgers and speculators achieve a steady state could be analyzed. This task was performed to achieve the stability critical point, and we show that only when the value of λ is satisfied and the conditions of hog futures price changes and futures price are satisfied can hedgers and speculators achieve a rational proportion and a stable hog futures market. This market can thus provide a valuable reference for the development of the Chinese hog futures market and the formulation and guidance of relevant departmental policies.

Diversity in times of adversity: probabilistic strategies in microbial survival games.

PubMed

Wolf, Denise M; Vazirani, Vijay V; Arkin, Adam P

2005-05-21

Population diversification strategies are ubiquitous among microbes, encompassing random phase-variation (RPV) of pathogenic bacteria, viral latency as observed in some bacteriophage and HIV, and the non-genetic diversity of bacterial stress responses. Precise conditions under which these diversification strategies confer an advantage have not been well defined. We develop a model of population growth conditioned on dynamical environmental and cellular states. Transitions among cellular states, in turn, may be biased by possibly noisy readings of the environment from cellular sensors. For various types of environmental dynamics and cellular sensor capability, we apply game-theoretic analysis to derive the evolutionarily stable strategy (ESS) for an organism and determine when that strategy is diversification. We find that: (1) RPV, effecting a sort of Parrondo paradox wherein random alternations between losing strategies produce a winning strategy, is selected when transitions between different selective environments cannot be sensed, (2) optimal RPV cell switching rates are a function of environmental lifecycle asymmetries and environmental autocorrelation, (3) probabilistic diversification upon entering a new environment is selected when sensors can detect environmental transitions but have poor precision in identifying new environments, and (4) in the presence of excess additive noise, low-pass filtering is required for evolutionary stability. We show that even when RPV is not the ESS, it may minimize growth rate variance and the risk of extinction due to 'unlucky' environmental dynamics.

Sex-specific mechanism of social hierarchy in mice.

PubMed

van den Berg, Wouter E; Lamballais, Sander; Kushner, Steven A

2015-05-01

The establishment of social hierarchies is a naturally occurring, evolutionarily conserved phenomenon with a well-established impact on fitness and health. Investigations of complex social group dynamics may offer novel opportunities for translational studies of autism spectrum disorder. Here we describe a robust behavioral paradigm using an automated version of the tube test. Isogenic groups of male and female mice establish linear social hierarchies that remain highly stable for at least 14 days, the longest interval tested. Remarkably, however, their social strategy is sex-specific: females primarily utilize intrinsic attributes, whereas males are strongly influenced by prior social experience. Using both genetic and pharmacological manipulations, we identify testosterone as a critical sex-specific factor for determining which social strategy is used. Males inheriting a null mutation of the sex-determining region Y (Sry) gene used a similar social cognitive strategy as females. In contrast, females with transgenic expression of Sry utilized a typically male social strategy. Analogously, castration of males and testosterone supplementation of females yielded similar outcomes, with a reversal of their social cognitive strategy. Together, our results demonstrate a sex-specific mechanism underlying social hierarchy, in which both males and females retain the functional capacity to adapt their social strategy. More generally, we expect the automated tube test to provide an important complementary approach for both fundamental and translational studies of social behavior.

Biological auctions with multiple rewards

PubMed Central

Reiter, Johannes G.; Kanodia, Ayush; Gupta, Raghav; Nowak, Martin A.; Chatterjee, Krishnendu

2015-01-01

The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards. PMID:26180069

A dynamic game-theoretic model of parental care.

PubMed

Mcnamara, J M; Székely, T; Webb, J N; Houston, A I

2000-08-21

We present a model in which members of a mated pair decide whether to care for their offspring or desert them. There is a breeding season of finite length during which it is possible to produce and raise several batches of offspring. On deserting its offspring, an individual can search for a new mate. The probability of finding a mate depends on the number of individuals of each sex that are searching, which in turn depends upon the previous care and desertion decisions of all population members. We find the evolutionarily stable pattern of care over the breeding season. The feedback between behaviour and mating opportunity can result in a pattern of stable oscillations between different forms of care over the breeding season. Oscillations can also arise because the best thing for an individual to do at a particular time in the season depends on future behaviour of all population members. In the baseline model, a pair splits up after a breeding attempt, even if they both care for the offspring. In a version of the model in which a pair stays together if they both care, the feedback between behaviour and mating opportunity can lead to more than one evolutionarily stable form of care. Copyright 2000 Academic Press.

Reconsideration of r/K Selection Theory Using Stochastic Control Theory and Nonlinear Structured Population Models.

PubMed

Oizumi, Ryo; Kuniya, Toshikazu; Enatsu, Yoichi

2016-01-01

Despite the fact that density effects and individual differences in life history are considered to be important for evolution, these factors lead to several difficulties in understanding the evolution of life history, especially when population sizes reach the carrying capacity. r/K selection theory explains what types of life strategies evolve in the presence of density effects and individual differences. However, the relationship between the life schedules of individuals and population size is still unclear, even if the theory can classify life strategies appropriately. To address this issue, we propose a few equations on adaptive life strategies in r/K selection where density effects are absent or present. The equations detail not only the adaptive life history but also the population dynamics. Furthermore, the equations can incorporate temporal individual differences, which are referred to as internal stochasticity. Our framework reveals that maximizing density effects is an evolutionarily stable strategy related to the carrying capacity. A significant consequence of our analysis is that adaptive strategies in both selections maximize an identical function, providing both population growth rate and carrying capacity. We apply our method to an optimal foraging problem in a semelparous species model and demonstrate that the adaptive strategy yields a lower intrinsic growth rate as well as a lower basic reproductive number than those obtained with other strategies. This study proposes that the diversity of life strategies arises due to the effects of density and internal stochasticity.

Evolutionary behavior of generalized zero-determinant strategies in iterated prisoner's dilemma

NASA Astrophysics Data System (ADS)

Liu, Jie; Li, Y.; Xu, C.; Hui, P. M.

2015-07-01

We study the competition and strategy selections between a class of generalized zero-determinant (ZD) strategies and the classic strategies of always cooperate (AllC), always defect (AllD), tit-for-tat (TFT), and win-stay-lose-shift (WSLS) strategies in an iterated prisoner's dilemma comprehensively. Using the generalized ZD strategy, a player could get a payoff that is χ (χ > 1) times that of his opponent's, when the payoff is measured with respect to a referencing baseline parameterized by 0 ≤ σ ≤ 1. Varying σ gives ZD strategies of tunable generosity from the extortionate-like ZD strategy for σ ≪ 1 to the compliance-like strategy at σ ≈ 1. Expected payoffs when ZD strategy competes with each one of the classic strategies are presented. Strategy evolution based on adopting the strategy of a better performing neighbor is studied in a well-mixed population of finite size and a population on a square lattice. Depending on the parameters, extortion-like strategies may not be evolutionarily stable despite a positive surplus over cooperative strategies, while extortion-like strategies may dominate or coexist with other strategies that tend to defect despite a negative surplus. The dependence of the equilibrium fraction of ZD strategy players on the model parameters in a well-mixed population can be understood analytically by comparing the average payoffs to the competing strategies. On a square lattice, the success of the ZD strategy can be qualitatively understood by focusing on the relative alignments of the finite number of payoff values that the two competing strategies could attain when the spatial structure is imposed. ZD strategies with properly chosen generosity could be more successful in evolutionary competing systems.

Nash Equilibrium of Social-Learning Agents in a Restless Multiarmed Bandit Game.

PubMed

Nakayama, Kazuaki; Hisakado, Masato; Mori, Shintaro

2017-05-16

We study a simple model for social-learning agents in a restless multiarmed bandit (rMAB). The bandit has one good arm that changes to a bad one with a certain probability. Each agent stochastically selects one of the two methods, random search (individual learning) or copying information from other agents (social learning), using which he/she seeks the good arm. Fitness of an agent is the probability to know the good arm in the steady state of the agent system. In this model, we explicitly construct the unique Nash equilibrium state and show that the corresponding strategy for each agent is an evolutionarily stable strategy (ESS) in the sense of Thomas. It is shown that the fitness of an agent with ESS is superior to that of an asocial learner when the success probability of social learning is greater than a threshold determined from the probability of success of individual learning, the probability of change of state of the rMAB, and the number of agents. The ESS Nash equilibrium is a solution to Rogers' paradox.

Social eavesdropping and the evolution of conditional cooperation and cheating strategies

PubMed Central

Earley, Ryan L.

2010-01-01

The response of bystanders to information available in their social environment can have a potent influence on the evolution of cooperation and signalling systems. In the presence of bystanders, individuals might be able to increase their payoff by exaggerating signals beyond their means (cheating) or investing to help others despite considerable costs. In doing so, animals can accrue immediate benefits by manipulating (or helping) individuals with whom they are currently interacting and delayed benefits by convincing bystanders that they are more fit or cooperative than perhaps is warranted. In this paper, I provide some illustrative examples of how bystanders could apply added positive selection pressure on both cooperative behaviour and dishonest signalling during courtship or conflict. I also discuss how the presence of bystanders might select for greater flexibility in behavioural strategies (e.g. conditional or condition dependence), which could maintain dishonesty at evolutionarily stable frequencies under some ecological conditions. By recognizing bystanders as a significant selection pressure, we might gain a more realistic approximation of what drives signalling and/or interaction dynamics in social animals. PMID:20679111

Payoff non-linearity sways the effect of mistakes on the evolution of reciprocity.

PubMed

Kurokawa, Shun

2016-09-01

The existence of cooperation is considered to require explanation, and reciprocity is a potential explanatory mechanism. Animals sometimes fail to cooperate even when they attempt to do so, and a reciprocator has an Achilles' heel: it is vulnerable to error (the interaction between two reciprocators can lead to an endless vendetta.). However, the strategy favored by natural selection is determined also by its interaction with other strategies. The relationship between two reciprocators leading to a collapse of cooperation through error does not straightforwardly imply that mistakes make the conditions under which reciprocity evolves stringent. Hence, mistakes may facilitate the evolution of reciprocity. However, it has been shown through the analysis of the interaction between reciprocators and unconditional defectors that the existence of mistakes makes the conditions for reciprocators stable against invasion by an unconditional defector more stringent, which indicates that mistakes discourage the evolution of reciprocity. However, this result is based on the assumption that the effects of cooperation are additive (payoff is linear), while the game played by real animals does not always display this feature. In such cases, the result may be swayed. In this paper, we remove this assumption, reexamining whether mistakes disturb the evolution of reciprocity. Using the analysis of an evolutionarily stable strategy (ESS), we show that when extra fitness costs are present in cases where mutual cooperation is established, mistakes can facilitate the evolution of reciprocity; whereas, when the effect of cooperation is additive, mistakes always disturb the evolution of reciprocity, as has been shown previously. Copyright © 2016. Published by Elsevier Inc.

The property 'instinct'.

PubMed Central

Stake, Jeffrey Evans

2004-01-01

Evolutionary theory and empirical studies suggest that many animals, including humans, have a genetic predisposition to acquire and retain property. This is hardly surprising because survival is closely bound up with the acquisition of things: food, shelter, tools and territory. But the root of these general urges may also run to quite specific and detailed rules about property acquisition, retention and disposition. The great variation in property-related behaviours across species may mask some important commonalities grounded in adaptive utility. Experiments and observations in the field and laboratory suggest that the legal rules of temporal priority and possession are grounded in what were evolutionarily stable strategies in the ancestral environment. Moreover, the preferences that humans exhibit in disposing of their property on their deaths, both by dispositions made in wills and by the laws of intestacy, tend to advance reproductive success as a result of inclusive fitness pay-offs. PMID:15590617

The property 'instinct'.

PubMed

Stake, Jeffrey Evans

2004-11-29

Evolutionary theory and empirical studies suggest that many animals, including humans, have a genetic predisposition to acquire and retain property. This is hardly surprising because survival is closely bound up with the acquisition of things: food, shelter, tools and territory. But the root of these general urges may also run to quite specific and detailed rules about property acquisition, retention and disposition. The great variation in property-related behaviours across species may mask some important commonalities grounded in adaptive utility. Experiments and observations in the field and laboratory suggest that the legal rules of temporal priority and possession are grounded in what were evolutionarily stable strategies in the ancestral environment. Moreover, the preferences that humans exhibit in disposing of their property on their deaths, both by dispositions made in wills and by the laws of intestacy, tend to advance reproductive success as a result of inclusive fitness pay-offs.

Population growth rates: issues and an application.

PubMed Central

Godfray, H Charles J; Rees, Mark

2002-01-01

Current issues in population dynamics are discussed in the context of The Royal Society Discussion Meeting 'Population growth rate: determining factors and role in population regulation'. In particular, different views on the centrality of population growth rates to the study of population dynamics and the role of experiments and theory are explored. Major themes emerging include the role of modern statistical techniques in bringing together experimental and theoretical studies, the importance of long-term experimentation and the need for ecology to have model systems, and the value of population growth rate as a means of understanding and predicting population change. The last point is illustrated by the application of a recently introduced technique, integral projection modelling, to study the population growth rate of a monocarpic perennial plant, its elasticities to different life-history components and the evolution of an evolutionarily stable strategy size at flowering. PMID:12396521

Deep ancestry of programmed genome rearrangement in lampreys.

PubMed

Timoshevskiy, Vladimir A; Lampman, Ralph T; Hess, Jon E; Porter, Laurie L; Smith, Jeramiah J

2017-09-01

In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma. Copyright © 2017 Elsevier Inc. All rights reserved.

The evolution of conformist transmission in social learning when the environment changes periodically.

PubMed

Nakahashi, Wataru

2007-08-01

Conformity is often observed in human social learning. Social learners preferentially imitate the majority or most common behavior in many situations, though the strength of conformity varies with the situation. Why has such a psychological tendency evolved? I investigate this problem by extending a standard model of social learning evolution with infinite environmental states (Feldman, M.W., Aoki, K., Kumm, J., 1996. Individual versus social learning: evolutionary analysis in a fluctuating environment. Anthropol. Sci. 104, 209-231) to include conformity bias. I mainly focus on the relationship between the strength of conformity bias that evolves and environmental stability, which is one of the most important factors in the evolution of social learning. Using the evolutionarily stable strategy (ESS) approach, I show that conformity always evolves when environmental stability and the cost of adopting a wrong behavior are small, though environmental stability and the cost of individual learning both negatively affect the strength of conformity.

Modeling Selection and Extinction Mechanisms of Biological Systems

NASA Astrophysics Data System (ADS)

Amirjanov, Adil

In this paper, the behavior of a genetic algorithm is modeled to enhance its applicability as a modeling tool of biological systems. A new description model for selection mechanism is introduced which operates on a portion of individuals of population. The extinction and recolonization mechanism is modeled, and solving the dynamics analytically shows that the genetic drift in the population with extinction/recolonization is doubled. The mathematical analysis of the interaction between selection and extinction/recolonization processes is carried out to assess the dynamics of motion of the macroscopic statistical properties of population. Computer simulations confirm that the theoretical predictions of described models are in good approximations. A mathematical model of GA dynamics was also examined, which describes the anti-predator vigilance in an animal group with respect to a known analytical solution of the problem, and showed a good agreement between them to find the evolutionarily stable strategies.

Efficiency in evolutionary games: Darwin, Nash and the secret handshake.

PubMed

Robson, A J

1990-06-07

This paper considers any evolutionary game possessing several evolutionarily stable strategies, or ESSs, with differing payoffs. A mutant is introduced which will "destroy" any ESS which yields a lower payoff than another. This mutant possesses a costless signal and also conditions on the presence of this signal in each opponent. The mutant then can protect itself against a population playing an inefficient ESS by matching this against these non-signalers. At the same time, the mutants can achieve the more efficient ESS against the signaling mutant population itself. This construction is illustrated by means of the simplest possible example, a co-ordination game. The one-shot prisoner's dilemma is used to illustrate how a superior outcome which is not induced by an ESS may be temporarily but not permanently attained. In the case of the repeated prisoner's dilemma, the present argument seems to render the "evolution of co-operation" ultimately inevitable.

Conservation and variability of West Nile virus proteins.

PubMed

Koo, Qi Ying; Khan, Asif M; Jung, Keun-Ok; Ramdas, Shweta; Miotto, Olivo; Tan, Tin Wee; Brusic, Vladimir; Salmon, Jerome; August, J Thomas

2009-01-01

West Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. This study, which used 2,746 WNV protein sequences collected from the NCBI GenPept database, focused on analysis of peptides of length 9 amino acids or more, which are immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences, revealed the presence of numerous evolutionarily stable nonamer positions across the proteome (entropy value of < or = 1). The representation (frequency) of nonamers variant to the predominant peptide at these stable positions was, generally, low (< or = 10% of the WNV sequences analyzed). Eighty-eight fragments of length 9-29 amino acids, representing approximately 34% of the WNV polyprotein length, were identified to be identical and evolutionarily stable in all analyzed WNV sequences. Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. Immunoinformatic analysis revealed that the majority (78/88) of conserved sequences are potentially immunogenic, while 44 contained experimentally confirmed human T-cell epitopes. This study identified a comprehensive catalogue of completely conserved WNV sequences, many of which are shared by other flaviviruses, and majority are potential epitopes. The complete conservation of these immunologically relevant sequences through the entire recorded WNV history suggests they will be valuable as components of peptide-specific vaccines or other therapeutic applications, for sequence-specific diagnosis of a wide-range of Flavivirus infections, and for studies of homologous sequences among other flaviviruses.

The importance of mechanisms for the evolution of cooperation

PubMed Central

van den Berg, Pieter; Weissing, Franz J.

2015-01-01

Studies aimed at explaining the evolution of phenotypic traits have often solely focused on fitness considerations, ignoring underlying mechanisms. In recent years, there has been an increasing call for integrating mechanistic perspectives in evolutionary considerations, but it is not clear whether and how mechanisms affect the course and outcome of evolution. To study this, we compare four mechanistic implementations of two well-studied models for the evolution of cooperation, the Iterated Prisoner's Dilemma (IPD) game and the Iterated Snowdrift (ISD) game. Behavioural strategies are either implemented by a 1 : 1 genotype–phenotype mapping or by a simple neural network. Moreover, we consider two different scenarios for the effect of mutations. The same set of strategies is feasible in all four implementations, but the probability that a given strategy arises owing to mutation is largely dependent on the behavioural and genetic architecture. Our individual-based simulations show that this has major implications for the evolutionary outcome. In the ISD, different evolutionarily stable strategies are predominant in the four implementations, while in the IPD each implementation creates a characteristic dynamical pattern. As a consequence, the evolved average level of cooperation is also strongly dependent on the underlying mechanism. We argue that our findings are of general relevance for the evolution of social behaviour, pleading for the integration of a mechanistic perspective in models of social evolution. PMID:26246554

The evolution of the competition-dispersal trade-off affects α- and β-diversity in a heterogeneous metacommunity.

PubMed

Laroche, Fabien; Jarne, Philippe; Perrot, Thomas; Massol, Francois

2016-04-27

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities. © 2016 The Author(s).

Individual variation and the resolution of conflict over parental care in penduline tits

PubMed Central

van Dijk, René E.; Székely, Tamás; Komdeur, Jan; Pogány, Ákos; Fawcett, Tim W.; Weissing, Franz J.

2012-01-01

Eurasian penduline tits (Remiz pendulinus) have an unusually diverse breeding system consisting of frequent male and female polygamy, and uniparental care by the male or the female. Intriguingly, 30 to 40 per cent of all nests are deserted by both parents. To understand the evolution of this diverse breeding system and frequent clutch desertion, we use 6 years of field data to derive fitness expectations for males and females depending on whether or not they care for their offspring. The resulting payoff matrix corresponds to an asymmetric Snowdrift Game with two alternative evolutionarily stable strategies (ESSs): female-only and male-only care. This, however, does not explain the polymorphism in care strategies and frequent biparental desertion, because theory predicts that one of the two ESSs should have spread to fixation. Using a bootstrapping approach, we demonstrate that taking account of individual variation in payoffs explains the patterns of care better than a model based on the average population payoff matrix. In particular, a model incorporating differences in male attractiveness closely predicts the observed frequencies of male and female desertion. Our work highlights the need for a new generation of individual-based evolutionary game-theoretic models. PMID:22189404

Individual variation and the resolution of conflict over parental care in penduline tits.

PubMed

van Dijk, René E; Székely, Tamás; Komdeur, Jan; Pogány, Akos; Fawcett, Tim W; Weissing, Franz J

2012-05-22

Eurasian penduline tits (Remiz pendulinus) have an unusually diverse breeding system consisting of frequent male and female polygamy, and uniparental care by the male or the female. Intriguingly, 30 to 40 per cent of all nests are deserted by both parents. To understand the evolution of this diverse breeding system and frequent clutch desertion, we use 6 years of field data to derive fitness expectations for males and females depending on whether or not they care for their offspring. The resulting payoff matrix corresponds to an asymmetric Snowdrift Game with two alternative evolutionarily stable strategies (ESSs): female-only and male-only care. This, however, does not explain the polymorphism in care strategies and frequent biparental desertion, because theory predicts that one of the two ESSs should have spread to fixation. Using a bootstrapping approach, we demonstrate that taking account of individual variation in payoffs explains the patterns of care better than a model based on the average population payoff matrix. In particular, a model incorporating differences in male attractiveness closely predicts the observed frequencies of male and female desertion. Our work highlights the need for a new generation of individual-based evolutionary game-theoretic models.

A paradox of cumulative culture.

PubMed

Kobayashi, Yutaka; Wakano, Joe Yuichiro; Ohtsuki, Hisashi

2015-08-21

Culture can grow cumulatively if socially learnt behaviors are improved by individual learning before being passed on to the next generation. Previous authors showed that this kind of learning strategy is unlikely to be evolutionarily stable in the presence of a trade-off between learning and reproduction. This is because culture is a public good that is freely exploited by any member of the population in their model (cultural social dilemma). In this paper, we investigate the effect of vertical transmission (transmission from parents to offspring), which decreases the publicness of culture, on the evolution of cumulative culture in both infinite and finite population models. In the infinite population model, we confirm that culture accumulates largely as long as transmission is purely vertical. It turns out, however, that introduction of even slight oblique transmission drastically reduces the equilibrium level of culture. Even more surprisingly, if the population size is finite, culture hardly accumulates even under purely vertical transmission. This occurs because stochastic extinction due to random genetic drift prevents a learning strategy from accumulating enough culture. Overall, our theoretical results suggest that introducing vertical transmission alone does not really help solve the cultural social dilemma problem. Copyright © 2015 Elsevier Ltd. All rights reserved.

Apology and forgiveness evolve to resolve failures in cooperative agreements.

PubMed

Martinez-Vaquero, Luis A; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

2015-06-09

Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas.

Apology and forgiveness evolve to resolve failures in cooperative agreements

PubMed Central

Martinez-Vaquero, Luis A.; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

2015-01-01

Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas. PMID:26057819

Competitive helping increases with the size of biological markets and invades defection.

PubMed

Barclay, Pat

2011-07-21

Cooperation between unrelated individuals remains a puzzle in evolutionary biology. Recent work indicates that partner choice can select for high levels of helping. More generally, helping can be seen as but one strategy used to compete for partners within a broader biological market, yet giving within such markets has received little mathematical investigation. In the present model, individuals help others to attract attention from them and thus receive a larger share of any help actively or passively provided by those others. The evolutionarily stable level of helping increases with the size of the biological market and the degree of partner choice. Furthermore, if individuals passively produce some no-cost help to partners, competitive helping can then invade populations of non-helpers because helpers directly benefit from increasing their access to potential partners. This framework of competitive helping demonstrates how high helping can be achieved and why different populations may differ in helping levels. Copyright © 2011 Elsevier Ltd. All rights reserved.

Preemptive spatial competition under a reproduction-mortality constraint.

PubMed

Allstadt, Andrew; Caraco, Thomas; Korniss, G

2009-06-21

Spatially structured ecological interactions can shape selection pressures experienced by a population's different phenotypes. We study spatial competition between phenotypes subject to antagonistic pleiotropy between reproductive effort and mortality rate. The constraint we invoke reflects a previous life-history analysis; the implied dependence indicates that although propagation and mortality rates both vary, their ratio is fixed. We develop a stochastic invasion approximation predicting that phenotypes with higher propagation rates will invade an empty environment (no biotic resistance) faster, despite their higher mortality rate. However, once population density approaches demographic equilibrium, phenotypes with lower mortality are favored, despite their lower propagation rate. We conducted a set of pairwise invasion analyses by simulating an individual-based model of preemptive competition. In each case, the phenotype with the lowest mortality rate and (via antagonistic pleiotropy) the lowest propagation rate qualified as evolutionarily stable among strategies simulated. This result, for a fixed propagation to mortality ratio, suggests that a selective response to spatial competition can extend the time scale of the population's dynamics, which in turn decelerates phenotypic evolution.

Life history consequences of mammal sibling rivalry.

PubMed

Stockley, P; Parker, G A

2002-10-01

Mammal life history traits relating to growth and reproduction are extremely diverse. Sibling rivalry may contribute to selection pressures influencing this diversity, because individuals that are relatively large at birth typically have an advantage in competition for milk. However, selection for increased growth rate is likely to be constrained by kin selection and physiological costs. Here, we present and test a model examining the ESS (evolutionarily stable strategy) balance between these constraints and advantages associated with increased prenatal growth in mammal sibling rivalry. Predictions of the model are supported by results of comparative analyses for the Carnivora and Insectivora, which demonstrate an increase in prenatal growth rate with increasing intensity of postnatal scramble competition, and a decrease in postnatal growth rate relative to size at birth. Because increased prenatal growth rates are predicted to select for reduced gestation length under certain conditions, our study also indicates that sibling rivalry may contribute to selection pressures influencing variation in altriciality and precociality among mammals.

Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

PubMed Central

Meng, Hao; Agbagwa, Ikechukwu O.; Wang, Ling-Xiang; Wang, Yingzhi; Yan, Shi; Ren, Shancheng; Sun, Yinghao; Pei, Gang; Liu, Xin; Liu, Jiang; Jin, Li; Li, Hui; Sun, Yingli

2016-01-01

DNA methylation plays an important role for mammalian development. However, it is unclear whether the DNA methylation pattern is evolutionarily conserved. The Y chromosome serves as a powerful tool for the study of human evolution because it is transferred between males. In this study, based on deep-rooted pedigrees and the latest Y chromosome phylogenetic tree, we performed epigenetic pattern analysis of the Y chromosome from 72 donors. By comparing their respective DNA methylation level, we found that the DNA methylation pattern on the Y chromosome was stable among family members and haplogroups. Interestingly, two haplogroup-specific methylation sites were found, which were both genotype-dependent. Moreover, the African and Asian samples also had similar DNA methylation pattern with a remote divergence time. Our findings indicated that the DNA methylation pattern on the Y chromosome was conservative during human male history. PMID:26760298

A theory for the evolution of other-regard integrating proximate and ultimate perspectives.

PubMed

Akçay, Erol; Van Cleve, Jeremy; Feldman, Marcus W; Roughgarden, Joan

2009-11-10

Although much previous work describes evolutionary mechanisms that promote or stabilize different social behaviors, we still have little understanding of the factors that drive animal behavior proximately. Here we present a modeling approach to answer this question. Our model rests on motivations to achieve objectives as the proximate determinants of behavior. We develop a two-tiered framework by first modeling the dynamics of a social interaction at the behavioral time scale and then find the evolutionarily stable objectives that result from the outcomes these dynamics produce. We use this framework to ask whether "other-regarding" motivations, which result from a kind of nonselfish objective, can evolve when individuals are engaged in a social interaction that entails a conflict between their material payoffs. We find that, at the evolutionarily stable state, individuals can be other-regarding in that they are motivated to increase their partners' payoff as well as their own. In contrast to previous theories, we find that such motivations can evolve because of their direct effect on fitness and do not require kin selection or a special group structure. We also derive general conditions for the evolutionary stability of other-regarding motivations. Our conditions indicate that other-regarding motivations are more likely to evolve when social interactions and behavioral objectives are both synergistic.

The price of being seen to be just: an intention signalling strategy for indirect reciprocity.

PubMed

Tanaka, Hiroki; Ohtsuki, Hisashi; Ohtsubo, Yohsuke

2016-07-27

Cooperation among strangers is a marked characteristic of human sociality. One prominent evolutionary explanation for this form of human cooperation is indirect reciprocity, whereby each individual selectively helps people with a 'good' reputation, but not those with a 'bad' reputation. Some evolutionary analyses have underscored the importance of second-order reputation information (the reputation of a current partner's previous partner) for indirect reciprocity as it allows players to discriminate justified 'good' defectors, who selectively deny giving help to 'bad' partners, from unjustified 'bad' defectors. Nevertheless, it is not clear whether people in fact make use of second-order information in indirect reciprocity settings. As an alternative, we propose the intention signalling strategy, whereby defectors are given the option to abandon a resource as a means of expunging their 'bad' reputation. Our model deviates from traditional modelling approaches in the indirect reciprocity literature in a crucial way-we show that first-order information is sufficient to maintain cooperation if players are given an option to signal their intention. Importantly, our model is robust against invasion by both unconditionally cooperative and uncooperative strategies, a first step towards demonstrating its viability as an evolutionarily stable strategy. Furthermore, in two behavioural experiments, when participants were given the option to abandon a resource so as to mend a tarnished reputation, participants not only spontaneously began to use this option, they also interpreted others' use of this option as a signal of cooperative intent. © 2016 The Author(s).

Optimal defense strategies in an idealized microbial food web under trade-off between competition and defense.

PubMed

Våge, Selina; Storesund, Julia E; Giske, Jarl; Thingstad, T Frede

2014-01-01

Trophic mechanisms that can generate biodiversity in food webs include bottom-up (growth rate regulating) and top-down (biomass regulating) factors. The top-down control has traditionally been analyzed using the concepts of "Keystone Predation" (KP) and "Killing-the-Winner" (KtW), predominately occuring in discussions of macro- and micro-biological ecology, respectively. Here we combine the classical diamond-shaped food web structure frequently discussed in KP analyses and the KtW concept by introducing a defense strategist capable of partial defense. A formalized description of a trade-off between the defense-strategist's competitive and defensive ability is included. The analysis reveals a complex topology of the steady state solution with strong relationships between food web structure and the combination of trade-off, defense strategy and the system's nutrient content. Among the results is a difference in defense strategies corresponding to maximum biomass, production, or net growth rate of invading individuals. The analysis thus summons awareness that biomass or production, parameters typically measured in field studies to infer success of particular biota, are not directly acted upon by natural selection. Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist. The findings of success of different defense strategies are discussed with respect to SAR11, a highly successful bacterial clade in the pelagic ocean.

Chaos and the evolution of cooperation.

PubMed

Nowak, M; Sigmund, K

1993-06-01

The "iterated prisoner's dilemma" is the most widely used model for the evolution of cooperation in biological societies. Here we show that a heterogeneous population consisting of simple strategies, whose behavior is totally specified by the outcome of the previous round, can lead to persistent periodic or highly irregular (chaotic) oscillations in the frequencies of the strategies and the overall level of cooperation. The levels of cooperation jump up and down in an apparently unpredictable fashion. Small recurrent and simultaneous invasion attempts (caused by mutation) can change the evolutionary dynamics from converging to an evolutionarily stable strategy to periodic oscillations and chaos. Evolution can be twisted away from defection, toward cooperation. Adding "generous tit-for-tat" greatly increases the overall level of cooperation and can lead to long periods of steady cooperation. Since May's paper [May, R. M. (1976) Nature (London) 261, 459-467], "simple mathematical models with very complicated dynamics" have been found in many biological applications, but here we provide an example of a biologically relevant evolutionary game whose dynamics display deterministic chaos. The simulations bear some resemblance to the irregular cycles displayed by the frequencies of host genotypes and specialized parasites in evolutionary "arms races" [Hamilton, W. D., Axelrod, R. & Tanese, R. (1990) Proc. Natl. Acad. Sci. USA 87, 3566-3573; Seger, J. (1988) Philos. Trans. R. Soc. London B 319, 541-555].

Evolution of acuteness in pathogen metapopulations: conflicts between “classical” and invasion-persistence trade-offs

PubMed Central

Shrestha, Sourya; Bjørnstad, Ottar N.; King, Aaron A.

2014-01-01

Classical life-history theory predicts that acute, immunizing pathogens should maximize between-host transmission. When such pathogens induce violent epidemic outbreaks, however, a pathogen’s short-term advantage at invasion may come at the expense of its ability to persist in the population over the long term. Here, we seek to understand how the classical and invasion-persistence trade-offs interact to shape pathogen life-history evolution as a function of the size and structure of the host population. We develop an individual-based infection model at three distinct levels of organization: within an individual host, among hosts within a local population, and among local populations within a metapopulation. We find a continuum of evolutionarily stable pathogen strategies. At one end of the spectrum—in large well-mixed populations—pathogens evolve to greater acuteness to maximize between-host transmission: the classical trade-off theory applies in this regime. At the other end of the spectrum—when the host population is broken into many small patches—selection favors less acute pathogens, which persist longer within a patch and thereby achieve enhanced between-patch transmission: the invasion-persistence tradeoff dominates in this regime. Between these extremes, we explore the effects of the size and structure of the host population in determining pathogen strategy. In general, pathogen strategies respond to evolutionary pressures arising at both scales. PMID:25214895

Site-specific selfish genes as tools for the control and genetic engineering of natural populations.

PubMed

Burt, Austin

2003-05-07

Site-specific selfish genes exploit host functions to copy themselves into a defined target DNA sequence, and include homing endonuclease genes, group II introns and some LINE-like transposable elements. If such genes can be engineered to target new host sequences, then they can be used to manipulate natural populations, even if the number of individuals released is a small fraction of the entire population. For example, a genetic load sufficient to eradicate a population can be imposed in fewer than 20 generations, if the target is an essential host gene, the knockout is recessive and the selfish gene has an appropriate promoter. There will be selection for resistance, but several strategies are available for reducing the likelihood of it evolving. These genes may also be used to genetically engineer natural populations, by means of population-wide gene knockouts, gene replacements and genetic transformations. By targeting sex-linked loci just prior to meiosis one may skew the population sex ratio, and by changing the promoter one may limit the spread of the gene to neighbouring populations. The proposed constructs are evolutionarily stable in the face of the mutations most likely to arise during their spread, and strategies are also available for reversing the manipulations.

An ESS maximum principle for matrix games.

PubMed

Vincent, T L; Cressman, R

2000-11-01

Previous work has demonstrated that for games defined by differential or difference equations with a continuum of strategies, there exists a G-function, related to individual fitness, that must take on a maximum with respect to a virtual variable v whenever v is one of the vectors in the coalition of vectors which make up the evolutionarily stable strategy (ESS). This result, called the ESS maximum principle, is quite useful in determining candidates for an ESS. This principle is reformulated here, so that it may be conveniently applied to matrix games. In particular, we define a matrix game to be one in which fitness is expressed in terms of strategy frequencies and a matrix of expected payoffs. It is shown that the G-function in the matrix game setting must again take on a maximum value at all the strategies which make up the ESS coalition vector. The reformulated maximum principle is applicable to both bilinear and nonlinear matrix games. One advantage in employing this principle to solve the traditional bilinear matrix game is that the same G-function is used to find both pure and mixed strategy solutions by simply specifying an appropriate strategy space. Furthermore we show how the theory may be used to solve matrix games which are not in the usual bilinear form. We examine in detail two nonlinear matrix games: the game between relatives and the sex ratio game. In both of these games an ESS solution is determined. These examples not only illustrate the usefulness of this approach to finding solutions to an expanded class of matrix games, but aids in understanding the nature of the ESS as well.

The extended reciprocity: Strong belief outperforms persistence.

PubMed

Kurokawa, Shun

2017-05-21

The existence of cooperation is a mysterious phenomenon and demands explanation, and direct reciprocity is one key potential explanation for the evolution of cooperation. Direct reciprocity allows cooperation to evolve for cooperators who switch their behavior on the basis of information about the opponent's behavior. Here, relevant to direct reciprocity is information deficiency. When the opponent's last move is unknown, how should players behave? One possibility is to choose cooperation with some default probability without using any further information. In fact, our previous paper (Kurokawa, 2016a) examined this strategy. However, there might be beneficial information other than the opponent's last move. A subsequent study of ours (Kurokawa, 2017) examined the strategy which uses the own last move when the opponent's last move is unknown, and revealed that referring to the own move and trying to imitate it when information is absent is beneficial. Is there any other beneficial information else? How about strong belief (i.e., have infinite memory and believe that the opponent's behavior is unchanged)? Here, we examine the evolution of strategies with strong belief. Analyzing the repeated prisoner's dilemma game and using evolutionarily stable strategy (ESS) analysis against an invasion by unconditional defectors, we find the strategy with strong belief is more likely to evolve than the strategy which does not use information other than the opponent player's last move and more likely to evolve than the strategy which uses not only the opponent player's last move but also the own last move. Strong belief produces the extended reciprocity and facilitates the evolution of cooperation. Additionally, we consider the two strategies game between strategies with strong belief and any strategy, and we consider the four strategies game in which unconditional cooperators, unconditional defectors, pessimistic reciprocators with strong belief, and optimistic reciprocators with strong belief are present. Copyright © 2017 Elsevier Ltd. All rights reserved.

Random and non-random mating populations: Evolutionary dynamics in meiotic drive.

PubMed

Sarkar, Bijan

2016-01-01

Game theoretic tools are utilized to analyze a one-locus continuous selection model of sex-specific meiotic drive by considering nonequivalence of the viabilities of reciprocal heterozygotes that might be noticed at an imprinted locus. The model draws attention to the role of viability selections of different types to examine the stable nature of polymorphic equilibrium. A bridge between population genetics and evolutionary game theory has been built up by applying the concept of the Fundamental Theorem of Natural Selection. In addition to pointing out the influences of male and female segregation ratios on selection, configuration structure reveals some noted results, e.g., Hardy-Weinberg frequencies hold in replicator dynamics, occurrence of faster evolution at the maximized variance fitness, existence of mixed Evolutionarily Stable Strategy (ESS) in asymmetric games, the tending evolution to follow not only a 1:1 sex ratio but also a 1:1 different alleles ratio at particular gene locus. Through construction of replicator dynamics in the group selection framework, our selection model introduces a redefining bases of game theory to incorporate non-random mating where a mating parameter associated with population structure is dependent on the social structure. Also, the model exposes the fact that the number of polymorphic equilibria will depend on the algebraic expression of population structure. Copyright © 2015 Elsevier Inc. All rights reserved.

The dynamics of strangling among forest trees.

PubMed

Okamoto, Kenichi W

2015-11-07

Strangler trees germinate and grow on other trees, eventually enveloping and potentially even girdling their hosts. This allows them to mitigate fitness costs otherwise incurred by germinating and competing with other trees on the forest floor, as well as minimize risks associated with host tree-fall. If stranglers can themselves host other strangler trees, they may not even seem to need non-stranglers to persist. Yet despite their high fitness potential, strangler trees neither dominate the communities in which they occur nor is the strategy particularly common outside of figs (genus Ficus). Here we analyze how dynamic interactions between strangling and non-strangling trees can shape the adaptive landscape for strangling mutants and mutant trees that have lost the ability to strangle. We find a threshold which strangler germination rates must exceed for selection to favor the evolution of strangling, regardless of how effectively hemiepiphytic stranglers may subsequently replace their hosts. This condition describes the magnitude of the phenotypic displacement in the ability to germinate on other trees necessary for invasion by a mutant tree that could potentially strangle its host following establishment as an epiphyte. We show how the relative abilities of strangling and non-strangling trees to occupy empty sites can govern whether strangling is an evolutionarily stable strategy, and obtain the conditions for strangler coexistence with non-stranglers. We then elucidate when the evolution of strangling can disrupt stable coexistence between commensal epiphytic ancestors and their non-strangling host trees. This allows us to highlight parallels between the invasion fitness of strangler trees arising from commensalist ancestors, and cases where strangling can arise in concert with the evolution of hemiepiphytism among free-standing ancestors. Finally, we discuss how our results can inform the evolutionary ecology of antagonistic interactions more generally. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-target drugs to address multiple checkpoints in complex inflammatory pathologies: evolutionary cues for novel "first-in-class" anti-inflammatory drug candidates: a reviewer's perspective.

PubMed

Mathew, Geetha; Unnikrishnan, M K

2015-10-01

Inflammation is a complex, metabolically expensive process involving multiple signaling pathways and regulatory mechanisms which have evolved over evolutionary timescale. Addressing multiple targets of inflammation holistically, in moderation, is probably a more evolutionarily viable strategy, as compared to current therapy which addresses drug targets in isolation. Polypharmacology, addressing multiple targets, is commonly used in complex ailments, suggesting the superior safety and efficacy profile of multi-target (MT) drugs. Phenotypic drug discovery, which generated successful MT and first-in-class drugs in the past, is now re-emerging. A multi-pronged approach, which modulates the evolutionarily conserved, robust and pervasive cellular mechanisms of tissue repair, with AMPK at the helm, regulating the complex metabolic/immune/redox pathways underlying inflammation, is perhaps a more viable strategy than addressing single targets in isolation. Molecules that modulate multiple molecular mechanisms of inflammation in moderation (modulating TH cells toward the anti-inflammatory phenotype, activating AMPK, stimulating Nrf2 and inhibiting NFκB) might serve as a model for a novel Darwinian "first-in-class" therapeutic category that holistically addresses immune, redox and metabolic processes associated with inflammatory repair. Such a multimodal biological activity is supported by the fact that several non-calorific pleiotropic natural products with anti-inflammatory action have been incorporated into diet (chiefly guided by the adaptive development of olfacto-gustatory preferences over evolutionary timescales) rendering such molecules, endowed with evolutionarily privileged molecular scaffolds, naturally oriented toward multiple targets.

Optimal Defense Strategies in an Idealized Microbial Food Web under Trade-Off between Competition and Defense

PubMed Central

Våge, Selina; Storesund, Julia E.; Giske, Jarl; Thingstad, T. Frede

2014-01-01

Trophic mechanisms that can generate biodiversity in food webs include bottom-up (growth rate regulating) and top-down (biomass regulating) factors. The top-down control has traditionally been analyzed using the concepts of “Keystone Predation” (KP) and “Killing-the-Winner” (KtW), predominately occuring in discussions of macro- and micro-biological ecology, respectively. Here we combine the classical diamond-shaped food web structure frequently discussed in KP analyses and the KtW concept by introducing a defense strategist capable of partial defense. A formalized description of a trade-off between the defense-strategist's competitive and defensive ability is included. The analysis reveals a complex topology of the steady state solution with strong relationships between food web structure and the combination of trade-off, defense strategy and the system's nutrient content. Among the results is a difference in defense strategies corresponding to maximum biomass, production, or net growth rate of invading individuals. The analysis thus summons awareness that biomass or production, parameters typically measured in field studies to infer success of particular biota, are not directly acted upon by natural selection. Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist. The findings of success of different defense strategies are discussed with respect to SAR11, a highly successful bacterial clade in the pelagic ocean. PMID:24999739

Sensitivity to Shared Information in Social Learning

ERIC Educational Resources Information Center

Whalen, Andrew; Griffiths, Thomas L.; Buchsbaum, Daphna

2018-01-01

Social learning has been shown to be an evolutionarily adaptive strategy, but it can be implemented via many different cognitive mechanisms. The adaptive advantage of social learning depends crucially on the ability of each learner to obtain relevant and accurate information from informants. The source of informants' knowledge is a particularly…

Comparative statics of games between relatives.

PubMed

Milchtaich, Igal

2006-03-01

According to Hamilton's theory of kin selection, species tend to evolve behavior such that each organism appears to be attempting to maximize its inclusive fitness. In particular, two neighbors are likely to help each other if the cost of doing so is less than the benefit multiplied by r, their coefficient of relatedness. Since the latter is less than unity, mutual altruism benefits both neighbors. However, is it theoretically possible that acting so as to maximize the inclusive, rather than personal, fitness may harm both parties. This may occur in strategic symmetric pairwise interactions (more specifically, nxn games), in which the outcome depends on both sides' actions. In this case, the equilibrium outcome may be less favorable to the interactants' personal fitness than if each of them acted so as to maximize the latter. This paper shows, however, that such negative effect of relatedness on fitness is incompatible with evolutionary stability. If the symmetric equilibrium strategies are evolutionarily stable, a higher coefficient of relatedness can only entail higher personal fitness for the two neighbors. This suggests that negative comparative statics as above are not likely to occur in nature.

Density-dependence interacts with extrinsic mortality in shaping life histories

PubMed Central

Burger, Oskar; Kozłowski, Jan

2017-01-01

The role of extrinsic mortality in shaping life histories is poorly understood. However, substantial evidence suggests that extrinsic mortality interacts with density-dependence in crucial ways. We develop a model combining Evolutionarily Stable Strategies with a projection matrix that allows resource allocation to growth, tissue repairs, and reproduction. Our model examines three cases, with density-dependence acting on: (i) mortality, (ii) fecundity, and (iii) production rate. We demonstrate that density-independent extrinsic mortality influences the rate of aging, age at maturity, growth rate, and adult size provided that density-dependence acts on fertility or juvenile mortality. However, density-independent extrinsic mortality has no effect on these life history traits when density-dependence acts on survival. We show that extrinsic mortality interacts with density-dependence via a compensation mechanism: the higher the extrinsic mortality the lower the strength of density-dependence. However, this compensation fully offsets the effect of extrinsic mortality only if density-dependence acts on survival independently of age. Both the age-pattern and the type of density-dependence are crucial for shaping life history traits. PMID:29049399

A theoretical model of the evolution of maternal effects under parent-offspring conflict.

PubMed

Uller, Tobias; Pen, Ido

2011-07-01

The evolution of maternal effects on offspring phenotype should depend on the extent of parent-offspring conflict and costs and constraints associated with maternal and offspring strategies. Here, we develop a model of maternal effects on offspring dispersal phenotype under parent-offspring conflict to evaluate such dependence. In the absence of evolutionary constraints and costs, offspring evolve dispersal rates from different patch types that reflect their own, rather than the maternal, optima. This result also holds true when offspring are unable to assess their own environment because the maternal phenotype provides an additional source of information. Consequently, maternal effects on offspring diapause, dispersal, and other traits that do not necessarily represent costly resource investment are more likely to maximize offspring than maternal fitness. However, when trait expression was costly, the evolutionarily stable dispersal rates tended to deviate from those under both maternal and offspring control. We use our results to (re)interpret some recent work on maternal effects and their adaptive value and provide suggestions for future work. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Resolving the iterated prisoner's dilemma: theory and reality.

PubMed

Raihani, N J; Bshary, R

2011-08-01

Pairs of unrelated individuals face a prisoner's dilemma if cooperation is the best mutual outcome, but each player does best to defect regardless of his partner's behaviour. Although mutual defection is the only evolutionarily stable strategy in one-shot games, cooperative solutions based on reciprocity can emerge in iterated games. Among the most prominent theoretical solutions are the so-called bookkeeping strategies, such as tit-for-tat, where individuals copy their partner's behaviour in the previous round. However, the lack of empirical data conforming to predicted strategies has prompted the suggestion that the iterated prisoner's dilemma (IPD) is neither a useful nor realistic basis for investigating cooperation. Here, we discuss several recent studies where authors have used the IPD framework to interpret their data. We evaluate the validity of their approach and highlight the diversity of proposed solutions. Strategies based on precise accounting are relatively uncommon, perhaps because the full set of assumptions of the IPD model are rarely satisfied. Instead, animals use a diverse array of strategies that apparently promote cooperation, despite the temptation to cheat. These include both positive and negative reciprocity, as well as long-term mutual investments based on 'friendships'. Although there are various gaps in these studies that remain to be filled, we argue that in most cases, individuals could theoretically benefit from cheating and that cooperation cannot therefore be explained with the concept of positive pseudo-reciprocity. We suggest that by incorporating empirical data into the theoretical framework, we may gain fundamental new insights into the evolution of mutual reciprocal investment in nature. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Hawks, doves, and mixed-symmetry games.

PubMed

Crowley, P H

2000-06-21

The hawk-dove game has proved to be an important tool for understanding the role of aggression in social interactions. Here, the game is presented in a more general form (GHD) to facilitate analyses of interactions between individuals that may differ in "size", where size is interpreted as a surrogate for resource holding power. Three different situations are considered, based on the availability and use of information that interacting individuals have about their sizes: the classical symmetric case, in which no information about sizes is used, the asymmetric case, in which the individuals know their relative sizes and thus their chances of prevailing in combat, and a mixed-symmetry case, in which each individual only knows its own size (or only knows its opponent's size). I describe and use some recently developed methods for multitype games-evolutionary games involving two or more categories of players. With these methods and others, the evolutionarily stable strategies (ESSs) that emerge for the three different cases are identified and compared. A proof of the form and uniqueness of the ESS for the mixed-symmetry case is presented. In this situation, one size category at most can play a mixed strategy; larger individuals are aggressive and smaller individuals are not. As the number of size categories approaches infinity and the size distribution becomes continuous, there is a threshold size, above which all individuals are aggressive, and below which they are not. Copyright 2000 Academic Press.

Cooperation induces other cooperation: Fruiting bodies promote the evolution of macrocysts in Dictyostelium discoideum.

PubMed

Shibasaki, Shota; Shirokawa, Yuka; Shimada, Masakazu

2017-05-21

Biological studies of the evolution of cooperation are challenging because this process is vulnerable to cheating. Many mechanisms, including kin discrimination, spatial structure, or by-products of self-interested behaviors, can explain this evolution. Here we propose that the evolution of cooperation can be induced by other cooperation. To test this idea, we used a model organism Dictyostelium discoideum because it exhibits two cooperative dormant phases, the fruiting body and the macrocyst. In both phases, the same chemoattractant, cyclic AMP (cAMP), is used to collect cells. This common feature led us to hypothesize that the evolution of macrocyst formation would be induced by coexistence with fruiting bodies. Before forming a mathematical model, we confirmed that macrocysts coexisted with fruiting bodies, at least under laboratory conditions. Next, we analyzed our evolutionary game theory-based model to investigate whether coexistence with fruiting bodies would stabilize macrocyst formation. The model suggests that macrocyst formation represents an evolutionarily stable strategy and a global invader strategy under this coexistence, but is unstable if the model ignores the fruiting body formation. This result indicates that the evolution of macrocyst formation and maintenance is attributable to coexistence with fruiting bodies. Therefore, macrocyst evolution can be considered as an example of evolution of cooperation induced by other cooperation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary Dynamics of Biological Auctions

PubMed Central

Chatterjee, Krishnendu; Reiter, Johannes G.; Nowak, Martin A.

2011-01-01

Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions” the costs are the bid for every participating individual. In “biological second price all-pay auctions” the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided. PMID:22120126

Evolutionary dynamics of a smoothed war of attrition game.

PubMed

Iyer, Swami; Killingback, Timothy

2016-05-07

In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tolerant indirect reciprocity can boost social welfare through solidarity with unconditional cooperators in private monitoring.

PubMed

Okada, Isamu; Sasaki, Tatsuya; Nakai, Yutaka

2017-08-29

Indirect reciprocity is an important mechanism for resolving social dilemmas. Previous studies explore several types of assessment rules that are evolutionarily stable for keeping cooperation regimes. However, little is known about the effects of private information on social systems. Most indirect reciprocity studies assume public monitoring in which individuals share a single assessment for each individual. Here, we consider a private monitoring system that loosens such an unnatural assumption. We explore the stable norms in the private system using an individual-based simulation. We have three main findings. First, narrow and unstable cooperation: cooperation in private monitoring becomes unstable and the restricted norms cannot maintain cooperative regimes while they can in public monitoring. Second, stable coexistence of discriminators and unconditional cooperators: under private monitoring, unconditional cooperation can play a role in keeping a high level of cooperation in tolerant norm situations. Finally, Pareto improvement: private monitoring can achieve a higher cooperation rate than does public monitoring.

Working dogs cooperate among one another by generalised reciprocity.

PubMed

Gfrerer, Nastassja; Taborsky, Michael

2017-03-06

Cooperation by generalised reciprocity implies that individuals apply the decision rule "help anyone if helped by someone". This mechanism has been shown to generate evolutionarily stable levels of cooperation, but as yet it is unclear how widely this cooperation mechanism is applied among animals. Dogs (Canis familiaris) are highly social animals with considerable cognitive potential and the ability to differentiate between individual social partners. But although dogs can solve complex problems, they may use simple rules for behavioural decisions. Here we show that dogs trained in an instrumental cooperative task to provide food to a social partner help conspecifics more often after receiving help from a dog before. Remarkably, in so doing they show no distinction between partners that had helped them before and completely unfamiliar conspecifics. Apparently, dogs use the simple decision rule characterizing generalised reciprocity, although they are probably capable of using the more complex decision rule of direct reciprocity: "help someone who has helped you". However, generalized reciprocity involves lower information processing costs and is therefore a cheaper cooperation strategy. Our results imply that generalised reciprocity might be applied more commonly than direct reciprocity also in other mutually cooperating animals.

Working dogs cooperate among one another by generalised reciprocity

PubMed Central

Gfrerer, Nastassja; Taborsky, Michael

2017-01-01

Cooperation by generalised reciprocity implies that individuals apply the decision rule “help anyone if helped by someone”. This mechanism has been shown to generate evolutionarily stable levels of cooperation, but as yet it is unclear how widely this cooperation mechanism is applied among animals. Dogs (Canis familiaris) are highly social animals with considerable cognitive potential and the ability to differentiate between individual social partners. But although dogs can solve complex problems, they may use simple rules for behavioural decisions. Here we show that dogs trained in an instrumental cooperative task to provide food to a social partner help conspecifics more often after receiving help from a dog before. Remarkably, in so doing they show no distinction between partners that had helped them before and completely unfamiliar conspecifics. Apparently, dogs use the simple decision rule characterizing generalised reciprocity, although they are probably capable of using the more complex decision rule of direct reciprocity: “help someone who has helped you”. However, generalized reciprocity involves lower information processing costs and is therefore a cheaper cooperation strategy. Our results imply that generalised reciprocity might be applied more commonly than direct reciprocity also in other mutually cooperating animals. PMID:28262722

Detection of Interaural Time Differences in the Alligator

PubMed Central

Carr, Catherine E.; Soares, Daphne; Smolders, Jean; Simon, Jonathan Z.

2011-01-01

The auditory systems of birds and mammals use timing information from each ear to detect interaural time difference (ITD). To determine whether the Jeffress-type algorithms that underlie sensitivity to ITD in birds are an evolutionarily stable strategy, we recorded from the auditory nuclei of crocodilians, who are the sister group to the birds. In alligators, precisely timed spikes in the first-order nucleus magnocellularis (NM) encode the timing of sounds, and NM neurons project to neurons in the nucleus laminaris (NL) that detect interaural time differences. In vivo recordings from NL neurons show that the arrival time of phase-locked spikes differs between the ipsilateral and contralateral inputs. When this disparity is nullified by their best ITD, the neurons respond maximally. Thus NL neurons act as coincidence detectors. A biologically detailed model of NL with alligator parameters discriminated ITDs up to 1 kHz. The range of best ITDs represented in NL was much larger than in birds, however, and extended from 0 to 1000 μs contralateral, with a median ITD of 450 μs. Thus, crocodilians and birds employ similar algorithms for ITD detection, although crocodilians have larger heads. PMID:19553438

Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors.

PubMed

Schradin, Carsten

2013-05-19

Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation.

Cognitive Adaptations for n-person Exchange: The Evolutionary Roots of Organizational Behavior.

PubMed

Tooby, John; Cosmides, Leda; Price, Michael E

2006-03-01

Organizations are composed of stable, predominantly cooperative interactions or n -person exchanges. Humans have been engaging in n -person exchanges for a great enough period of evolutionary time that we appear to have evolved a distinct constellation of species-typical mechanisms specialized to solve the adaptive problems posed by this form of social interaction. These mechanisms appear to have been evolutionarily elaborated out of the cognitive infrastructure that initially evolved for dyadic exchange. Key adaptive problems that these mechanisms are designed to solve include coordination among individuals, and defense against exploitation by free riders. Multi-individual cooperation could not have been maintained over evolutionary time if free riders reliably benefited more than contributors to collective enterprises, and so outcompeted them. As a result, humans evolved mechanisms that implement an aversion to exploitation by free riding, and a strategy of conditional cooperation, supplemented by punitive sentiment towards free riders. Because of the design of these mechanisms, how free riding is treated is a central determinant of the survival and health of cooperative organizations. The mapping of the evolved psychology of n -party exchange cooperation may contribute to the construction of a principled theoretical foundation for the understanding of human behavior in organizations.

Resource Allocation and Seed Size Selection in Perennial Plants under Pollen Limitation.

PubMed

Huang, Qiaoqiao; Burd, Martin; Fan, Zhiwei

2017-09-01

Pollen limitation may affect resource allocation patterns in plants, but its role in the selection of seed size is not known. Using an evolutionarily stable strategy model of resource allocation in perennial iteroparous plants, we show that under density-independent population growth, pollen limitation (i.e., a reduction in ovule fertilization rate) should increase the optimal seed size. At any level of pollen limitation (including none), the optimal seed size maximizes the ratio of juvenile survival rate to the resource investment needed to produce one seed (including both ovule production and seed provisioning); that is, the optimum maximizes the fitness effect per unit cost. Seed investment may affect allocation to postbreeding adult survival. In our model, pollen limitation increases individual seed size but decreases overall reproductive allocation, so that pollen limitation should also increase the optimal allocation to postbreeding adult survival. Under density-dependent population growth, the optimal seed size is inversely proportional to ovule fertilization rate. However, pollen limitation does not affect the optimal allocation to postbreeding adult survival and ovule production. These results highlight the importance of allocation trade-offs in the effect pollen limitation has on the ecology and evolution of seed size and postbreeding adult survival in perennial plants.

Some dynamics of signaling games.

PubMed

Huttegger, Simon; Skyrms, Brian; Tarrès, Pierre; Wagner, Elliott

2014-07-22

Information transfer is a basic feature of life that includes signaling within and between organisms. Owing to its interactive nature, signaling can be investigated by using game theory. Game theoretic models of signaling have a long tradition in biology, economics, and philosophy. For a long time the analyses of these games has mostly relied on using static equilibrium concepts such as Pareto optimal Nash equilibria or evolutionarily stable strategies. More recently signaling games of various types have been investigated with the help of game dynamics, which includes dynamical models of evolution and individual learning. A dynamical analysis leads to more nuanced conclusions as to the outcomes of signaling interactions. Here we explore different kinds of signaling games that range from interactions without conflicts of interest between the players to interactions where their interests are seriously misaligned. We consider these games within the context of evolutionary dynamics (both infinite and finite population models) and learning dynamics (reinforcement learning). Some results are specific features of a particular dynamical model, whereas others turn out to be quite robust across different models. This suggests that there are certain qualitative aspects that are common to many real-world signaling interactions.

Some dynamics of signaling games

PubMed Central

Huttegger, Simon; Skyrms, Brian; Tarrès, Pierre; Wagner, Elliott

2014-01-01

Information transfer is a basic feature of life that includes signaling within and between organisms. Owing to its interactive nature, signaling can be investigated by using game theory. Game theoretic models of signaling have a long tradition in biology, economics, and philosophy. For a long time the analyses of these games has mostly relied on using static equilibrium concepts such as Pareto optimal Nash equilibria or evolutionarily stable strategies. More recently signaling games of various types have been investigated with the help of game dynamics, which includes dynamical models of evolution and individual learning. A dynamical analysis leads to more nuanced conclusions as to the outcomes of signaling interactions. Here we explore different kinds of signaling games that range from interactions without conflicts of interest between the players to interactions where their interests are seriously misaligned. We consider these games within the context of evolutionary dynamics (both infinite and finite population models) and learning dynamics (reinforcement learning). Some results are specific features of a particular dynamical model, whereas others turn out to be quite robust across different models. This suggests that there are certain qualitative aspects that are common to many real-world signaling interactions. PMID:25024209

Cognitive Adaptations for n-person Exchange: The Evolutionary Roots of Organizational Behavior

PubMed Central

Tooby, John; Cosmides, Leda; Price, Michael E.

2013-01-01

Organizations are composed of stable, predominantly cooperative interactions or n-person exchanges. Humans have been engaging in n-person exchanges for a great enough period of evolutionary time that we appear to have evolved a distinct constellation of species-typical mechanisms specialized to solve the adaptive problems posed by this form of social interaction. These mechanisms appear to have been evolutionarily elaborated out of the cognitive infrastructure that initially evolved for dyadic exchange. Key adaptive problems that these mechanisms are designed to solve include coordination among individuals, and defense against exploitation by free riders. Multi-individual cooperation could not have been maintained over evolutionary time if free riders reliably benefited more than contributors to collective enterprises, and so outcompeted them. As a result, humans evolved mechanisms that implement an aversion to exploitation by free riding, and a strategy of conditional cooperation, supplemented by punitive sentiment towards free riders. Because of the design of these mechanisms, how free riding is treated is a central determinant of the survival and health of cooperative organizations. The mapping of the evolved psychology of n-party exchange cooperation may contribute to the construction of a principled theoretical foundation for the understanding of human behavior in organizations. PMID:23814325

Sneaker "jack" males outcompete dominant "hooknose" males under sperm competition in Chinook salmon (Oncorhynchus tshawytscha).

PubMed

Young, Brent; Conti, David V; Dean, Matthew D

2013-12-01

In a variety of taxa, males deploy alternative reproductive tactics to secure fertilizations. In many species, small "sneaker" males attempt to steal fertilizations while avoiding encounters with larger, more aggressive, dominant males. Sneaker males usually face a number of disadvantages, including reduced access to females and the higher likelihood that upon ejaculation, their sperm face competition from other males. Nevertheless, sneaker males represent an evolutionarily stable strategy under a wide range of conditions. Game theory suggests that sneaker males compensate for these disadvantages by investing disproportionately in spermatogenesis, by producing more sperm per unit body mass (the "fair raffle") and/or by producing higher quality sperm (the "loaded raffle"). Here, we test these models by competing sperm from sneaker "jack" males against sperm from dominant "hooknose" males in Chinook salmon. Using two complementary approaches, we reject the fair raffle in favor of the loaded raffle and estimate that jack males were ∼1.35 times as likely as hooknose males to fertilize eggs under controlled competitive conditions. Interestingly, the direction and magnitude of this skew in paternity shifted according to individual female egg donors, suggesting cryptic female choice could moderate the outcomes of sperm competition in this externally fertilizing species.

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game

PubMed Central

Sasaki, Tatsuya; Okada, Isamu

2015-01-01

It is well known that in contrast to the Prisoner’s Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. PMID:25868940

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game.

PubMed

Sasaki, Tatsuya; Okada, Isamu

2015-05-01

It is well known that in contrast to the Prisoner's Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Inter-progenitor pool wiring: An evolutionarily conserved strategy that expands neural circuit diversity.

PubMed

Suzuki, Takumi; Sato, Makoto

2017-11-15

Diversification of neuronal types is key to establishing functional variations in neural circuits. The first critical step to generate neuronal diversity is to organize the compartmental domains of developing brains into spatially distinct neural progenitor pools. Neural progenitors in each pool then generate a unique set of diverse neurons through specific spatiotemporal specification processes. In this review article, we focus on an additional mechanism, 'inter-progenitor pool wiring', that further expands the diversity of neural circuits. After diverse types of neurons are generated in one progenitor pool, a fraction of these neurons start migrating toward a remote brain region containing neurons that originate from another progenitor pool. Finally, neurons of different origins are intermingled and eventually form complex but precise neural circuits. The developing cerebral cortex of mammalian brains is one of the best examples of inter-progenitor pool wiring. However, Drosophila visual system development has revealed similar mechanisms in invertebrate brains, suggesting that inter-progenitor pool wiring is an evolutionarily conserved strategy that expands neural circuit diversity. Here, we will discuss how inter-progenitor pool wiring is accomplished in mammalian and fly brain systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution of long-term coloration trends with biochemically unstable ingredients

PubMed Central

Davis, Sarah N.; Andrews, John E.; Badyaev, Alexander V.

2016-01-01

The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins. Here, we examine evolutionary lability and transitions between the two strategies across 126 species of birds. We report that species that express mostly unmodified, fast-degrading, carotenoids have pre-breeding moults, and a particularly short time between carotenoid deposition and the subsequent breeding season. Species that expressed mostly slow-degrading carotenoids in their plumage accomplished this through increased metabolic modification of dietary carotenoids, and the selective expression of these slow-degrading compounds. In these species, the timing of moult was not associated with carotenoid composition of plumage displays. Using repeated samples from individuals of one species, we found that metabolic modification of dietary carotenoids significantly slowed their degradation between moult and breeding season. Thus, the most complex and colourful ornamentation is likely the most biochemically stable in birds, and depends less on ecological factors, such as moult timing and migration tendency. We suggest that coevolution of metabolic modification, selective expression and biochemical stability of plumage carotenoids enables the use of unstable pigments in long-term evolutionary trends in plumage coloration. PMID:27194697

Tubulin Dimer Reversible Dissociation

PubMed Central

Schuck, Peter; Sackett, Dan L.

2016-01-01

Tubulins are evolutionarily conserved proteins that reversibly polymerize and direct intracellular traffic. Of the tubulin family only αβ-tubulin forms stable dimers. We investigated the monomer-dimer equilibrium of rat brain αβ-tubulin using analytical ultracentrifugation and fluorescence anisotropy, observing tubulin in virtually fully monomeric and dimeric states. Monomeric tubulin was stable for a few hours and exchanged into preformed dimers, demonstrating reversibility of dimer dissociation. Global analysis combining sedimentation velocity and fluorescence anisotropy yielded Kd = 84 (54–123) nm. Dimer dissociation kinetics were measured by analyzing the shape of the sedimentation boundary and by the relaxation of fluorescence anisotropy following rapid dilution of labeled tubulin, yielding koff in the range 10−3–10−2 s−1. Thus, tubulin dimers reversibly dissociate with moderately fast kinetics. Monomer-monomer association is much less sensitive than dimer-dimer association to solution changes (GTP/GDP, urea, and trimethylamine oxide). PMID:26934918

The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

PubMed

Moore, Jason R; Varricchio, David J

2016-01-01

Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care, paternal care evolved in the saurischian line, prior to derived theropod dinosaurs, and the most basal neognaths likely exhibited biparental care. Overall, the evolution of parental care among diapsids shows a persistent trend towards increased care of offspring, and more complex care strategies and behaviors with time. Reversions to reduced care are infrequent.

Structures of pyruvate kinases display evolutionarily divergent allosteric strategies

PubMed Central

Morgan, Hugh P.; Zhong, Wenhe; McNae, Iain W.; Michels, Paul A. M.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

2014-01-01

The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (kcat/S0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (kcat/S0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors. PMID:26064527

The evolution of cooperation by negotiation in a noisy world.

PubMed

Ito, K; McNamara, J M; Yamauchi, A; Higginson, A D

2017-03-01

Cooperative interactions among individuals are ubiquitous despite the possibility of exploitation by selfish free riders. One mechanism that may promote cooperation is 'negotiation': individuals altering their behaviour in response to the behaviour of others. Negotiating individuals decide their actions through a recursive process of reciprocal observation, thereby reducing the possibility of free riding. Evolutionary games with response rules have shown that infinitely many forms of the rule can be evolutionarily stable simultaneously, unless there is variation in individual quality. This potentially restricts the conditions under which negotiation could maintain cooperation. Organisms interact with one another in a noisy world in which cooperative effort and the assessment of effort may be subject to error. Here, we show that such noise can make the number of evolutionarily stable rules finite, even without quality variation, and so noise could help maintain cooperative behaviour. We show that the curvature of the benefit function is the key factor determining whether individuals invest more or less as their partner's investment increases, investing less when the benefit to investment has diminishing returns. If the benefits of low investment are very small then behavioural flexibility tends to promote cooperation, because negotiation enables cooperators to reach large benefits. Under some conditions, this leads to a repeating cycle in which cooperative behaviour rises and falls over time, which may explain between-population differences in cooperative behaviour. In other conditions, negotiation leads to extremely high levels of cooperative behaviour, suggesting that behavioural flexibility could facilitate the evolution of eusociality in the absence of high relatedness. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway.

PubMed

Malinovsky, Frederikke Gro; Thomsen, Marie-Louise F; Nintemann, Sebastian J; Jagd, Lea Møller; Bourgine, Baptiste; Burow, Meike; Kliebenstein, Daniel J

2017-12-12

To optimize fitness a plant should monitor its metabolism to appropriately control growth and defense. Primary metabolism can be measured by the universally conserved TOR (Target of Rapamycin) pathway to balance growth and development with the available energy and nutrients. Recent work suggests that plants may measure defense metabolites to potentially provide a strategy ensuring fast reallocation of resources to coordinate plant growth and defense. There is little understanding of mechanisms enabling defense metabolite signaling. To identify mechanisms of defense metabolite signaling, we used glucosinolates, an important class of plant defense metabolites. We report novel signaling properties specific to one distinct glucosinolate, 3-hydroxypropylglucosinolate across plants and fungi. This defense metabolite, or derived compounds, reversibly inhibits root growth and development. 3-hydroxypropylglucosinolate signaling functions via genes in the ancient TOR pathway. If this event is not unique, this raises the possibility that other evolutionarily new plant metabolites may link to ancient signaling pathways.

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway

PubMed Central

Malinovsky, Frederikke Gro; Thomsen, Marie-Louise F; Nintemann, Sebastian J; Jagd, Lea Møller; Bourgine, Baptiste; Burow, Meike

2017-01-01

To optimize fitness a plant should monitor its metabolism to appropriately control growth and defense. Primary metabolism can be measured by the universally conserved TOR (Target of Rapamycin) pathway to balance growth and development with the available energy and nutrients. Recent work suggests that plants may measure defense metabolites to potentially provide a strategy ensuring fast reallocation of resources to coordinate plant growth and defense. There is little understanding of mechanisms enabling defense metabolite signaling. To identify mechanisms of defense metabolite signaling, we used glucosinolates, an important class of plant defense metabolites. We report novel signaling properties specific to one distinct glucosinolate, 3-hydroxypropylglucosinolate across plants and fungi. This defense metabolite, or derived compounds, reversibly inhibits root growth and development. 3-hydroxypropylglucosinolate signaling functions via genes in the ancient TOR pathway. If this event is not unique, this raises the possibility that other evolutionarily new plant metabolites may link to ancient signaling pathways. PMID:29231169

Crown depth as a result of evolutionary games: decreasing solar angle should lead to shallower, not deeper crowns.

PubMed

Vermeulen, Peter Johannes

2014-06-01

There is a general notion in the literature that, with increasing latitude, trees have deeper crowns as a result of a lower solar elevation angle. However, these predictions are based on models that did not include the effects of competition for light between individuals. Here, I argue that there should be selection for trees to increase the height of the crown base, as this decreases shading by neighbouring trees, leading to an evolutionarily stable strategy (ESS). Because the level of between-tree shading increases with decreasing solar angle, the predicted ESS will shift to higher crown base height. This argument is supported by a simulation model to check for the effects of crown shape and the change of light intensity that occurs with changing solar angle on model outcomes. So, the lower solar angle at higher latitudes would tend to select for shallower, and not deeper, crowns. This casts doubt on the common belief that a decreasing solar angle increases crown depth. More importantly, it shows that different assumptions about what should be optimized can lead to different predictions, not just for absolute trait values, but for the direction of selection itself. © 2014 The Author. New Phytologist © 2014 New Phytologist Trust.

Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles.

PubMed

Massol, François; Débarre, Florence

2015-07-01

Spatiotemporal variability of the environment is bound to affect the evolution of dispersal, and yet model predictions strongly differ on this particular effect. Recent studies on the evolution of local adaptation have shown that the life cycle chosen to model the selective effects of spatiotemporal variability of the environment is a critical factor determining evolutionary outcomes. Here, we investigate the effect of the order of events in the life cycle on the evolution of unconditional dispersal in a spatially heterogeneous, temporally varying landscape. Our results show that the occurrence of intermediate singular strategies and disruptive selection are conditioned by the temporal autocorrelation of the environment and by the life cycle. Life cycles with dispersal of adults versus dispersal of juveniles, local versus global density regulation, give radically different evolutionary outcomes that include selection for total philopatry, evolutionary bistability, selection for intermediate stable states, and evolutionary branching points. Our results highlight the importance of accounting for life-cycle specifics when predicting the effects of the environment on evolutionarily selected trait values, such as dispersal, as well as the need to check the robustness of model conclusions against modifications of the life cycle. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Global biogeography of seed dormancy is determined by seasonality and seed size: a case study in the legumes.

PubMed

Rubio de Casas, Rafael; Willis, Charles G; Pearse, William D; Baskin, Carol C; Baskin, Jerry M; Cavender-Bares, Jeannine

2017-06-01

Seed dormancy is expected to provide ecological advantages by adjusting germination to the favorable growth period. However, many species produce nondormant seeds, particularly in wet tropical forests, a biogeographic pattern that is not well accounted for in current models. We hypothesized that the global distribution of dormant seeds derives from their adaptive value in predictably fluctuating (i.e. seasonal) environments. However, the advantage conferred by dormancy might ultimately depend on other seed attributes, particularly size. This general model was tested within a phylogenetically informed framework using a data set comprising > 216 000 world-wide observations of Fabaceae, spanning three orders of magnitude in seed size and including both dormant and nondormant seeds. Our results confirmed our hypothesis: nondormant seeds can only evolve in climates with long growing seasons and/or in lineages that produce larger seeds. Conversely, dormancy should be evolutionarily stable in temperate lineages with small seeds. When the favorable season is fleeting, seed dormancy is the only adaptive strategy. Based on these results, we predict that, within a given lineage, taxa producing larger, nondormant seeds will necessarily predominate in aseasonal environments, while plants bearing small, dormant seeds will be dominant under short growing seasons. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Dioecy and the evolution of sex ratios in ants

PubMed Central

Wiernasz, Diane C.; Cole, Blaine J.

2009-01-01

Split sex ratios, when some colonies produce only male and others only female reproductives, is a common feature of social insects, especially ants. The most widely accepted explanation for split sex ratios was proposed by Boomsma and Grafen, and is driven by conflicts of interest among colonies that vary in relatedness. The predictions of the Boomsma–Grafen model have been confirmed in many cases, but contradicted in several others. We adapt a model for the evolution of dioecy in plants to make predictions about the evolution of split sex ratios in social insects. Reproductive specialization results from the instability of the evolutionarily stable strategy (ESS) sex ratio, and is independent of variation in relatedness. We test predictions of the model with data from a long-term study of harvester ants, and show that it correctly predicts the intermediate sex ratios we observe in our study species. The dioecy model provides a comprehensive framework for sex allocation that is based on the pay-offs to the colony via production of males and females, and is independent of the genetic variation among colonies. However, in populations where the conditions for the Boomsma–Grafen model hold, kin selection will still lead to an association between sex ratio and relatedness. PMID:19324757

The world's biomes and primary production as a triple tragedy of the commons foraging game played among plants

PubMed Central

Gonzalez-Meler, Miquel A.; Lynch, Douglas J.; Baltzer, Jennifer L.

2016-01-01

Plants appear to produce an excess of leaves, stems and roots beyond what would provide the most efficient harvest of available resources. One way to understand this overproduction of tissues is that excess tissue production provides a competitive advantage. Game theoretic models predict overproduction of all tissues compared with non-game theoretic models because they explicitly account for this indirect competitive benefit. Here, we present a simple game theoretic model of plants simultaneously competing to harvest carbon and nitrogen. In the model, a plant's fitness is influenced by its own leaf, stem and root production, and the tissue production of others, which produces a triple tragedy of the commons. Our model predicts (i) absolute net primary production when compared with two independent global datasets; (ii) the allocation relationships to leaf, stem and root tissues in one dataset; (iii) the global distribution of biome types and the plant functional types found within each biome; and (iv) ecosystem responses to nitrogen or carbon fertilization. Our game theoretic approach removes the need to define allocation or vegetation type a priori but instead lets these emerge from the model as evolutionarily stable strategies. We believe this to be the simplest possible model that can describe plant production. PMID:28120794

The world's biomes and primary production as a triple tragedy of the commons foraging game played among plants.

PubMed

McNickle, Gordon G; Gonzalez-Meler, Miquel A; Lynch, Douglas J; Baltzer, Jennifer L; Brown, Joel S

2016-11-16

Plants appear to produce an excess of leaves, stems and roots beyond what would provide the most efficient harvest of available resources. One way to understand this overproduction of tissues is that excess tissue production provides a competitive advantage. Game theoretic models predict overproduction of all tissues compared with non-game theoretic models because they explicitly account for this indirect competitive benefit. Here, we present a simple game theoretic model of plants simultaneously competing to harvest carbon and nitrogen. In the model, a plant's fitness is influenced by its own leaf, stem and root production, and the tissue production of others, which produces a triple tragedy of the commons. Our model predicts (i) absolute net primary production when compared with two independent global datasets; (ii) the allocation relationships to leaf, stem and root tissues in one dataset; (iii) the global distribution of biome types and the plant functional types found within each biome; and (iv) ecosystem responses to nitrogen or carbon fertilization. Our game theoretic approach removes the need to define allocation or vegetation type a priori but instead lets these emerge from the model as evolutionarily stable strategies. We believe this to be the simplest possible model that can describe plant production. © 2016 The Author(s).

Sneaker “jack” males outcompete dominant “hooknose” males under sperm competition in Chinook salmon (Oncorhynchus tshawytscha)

PubMed Central

Young, Brent; Conti, David V; Dean, Matthew D

2013-01-01

In a variety of taxa, males deploy alternative reproductive tactics to secure fertilizations. In many species, small “sneaker” males attempt to steal fertilizations while avoiding encounters with larger, more aggressive, dominant males. Sneaker males usually face a number of disadvantages, including reduced access to females and the higher likelihood that upon ejaculation, their sperm face competition from other males. Nevertheless, sneaker males represent an evolutionarily stable strategy under a wide range of conditions. Game theory suggests that sneaker males compensate for these disadvantages by investing disproportionately in spermatogenesis, by producing more sperm per unit body mass (the “fair raffle”) and/or by producing higher quality sperm (the “loaded raffle”). Here, we test these models by competing sperm from sneaker “jack” males against sperm from dominant “hooknose” males in Chinook salmon. Using two complementary approaches, we reject the fair raffle in favor of the loaded raffle and estimate that jack males were ∼1.35 times as likely as hooknose males to fertilize eggs under controlled competitive conditions. Interestingly, the direction and magnitude of this skew in paternity shifted according to individual female egg donors, suggesting cryptic female choice could moderate the outcomes of sperm competition in this externally fertilizing species. PMID:24455130

High Female Survival Promotes Evolution of Protogyny and Sexual Conflict

PubMed Central

Degen, Tobias; Hovestadt, Thomas; Mitesser, Oliver; Hölker, Franz

2015-01-01

Existing models explaining the evolution of sexual dimorphism in the timing of emergence (SDT) in Lepidoptera assume equal mortality rates for males and females. The limiting assumption of equal mortality rates has the consequence that these models are only able to explain the evolution of emergence of males before females, i.e. protandry—the more common temporal sequence of emergence in Lepidoptera. The models fail, however, in providing adaptive explanations for the evolution of protogyny, where females emerge before males, but protogyny is not rare in insects. The assumption of equal mortality rates seems too restrictive for many insects, such as butterflies. To investigate the influence of unequal mortality rates on the evolution of SDT, we present a generalised version of a previously published model where we relax this assumption. We find that longer life-expectancy of females compared to males can indeed favour the evolution of protogyny as a fitness enhancing strategy. Moreover, the encounter rate between females and males and the sex-ratio are two important factors that also influence the evolution of optimal SDT. If considered independently for females and males the predicted strategies can be shown to be evolutionarily stable (ESS). Under the assumption of equal mortality rates the difference between the females’ and males’ ESS remains typically very small. However, female and male ESS may be quite dissimilar if mortality rates are different. This creates the potential for an ‘evolutionary conflict’ between females and males. Bagworm moths (Lepidoptera: Psychidae) provide an exemplary case where life-history attributes are such that protogyny should indeed be the optimal emergence strategy from the males’ and females’ perspectives: (i) Female longevity is considerably larger than that of males, (ii) encounter rates between females and males are presumably low, and (iii) females mate only once. Protogyny is indeed the general mating strategy found in the bagworm family. PMID:25775473

Range expansion of heterogeneous populations.

PubMed

Reiter, Matthias; Rulands, Steffen; Frey, Erwin

2014-04-11

Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast-growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.

Localization of an evolutionarily conserved protein proton pyrophosphatase in evolutionarily distant plants oryza sativa and physcomitrella patens

USDA-ARS?s Scientific Manuscript database

Proton Pyrophosphatase (H+-PPase) is a highly evolutionarily conserved protein that is prevalent in the plant kingdom. One of the salient features of H+-PPase expression pattern, at least in vascular plants like Arabidopsis, is its conspicuous localization in both actively dividing cells and the phl...

Through the Immune Looking Glass: A Model for Brain Memory Strategies

PubMed Central

Sánchez-Ramón, Silvia; Faure, Florence

2016-01-01

The immune system (IS) and the central nervous system (CNS) are complex cognitive networks involved in defining the identity (self) of the individual through recognition and memory processes that enable one to anticipate responses to stimuli. Brain memory has traditionally been classified as either implicit or explicit on psychological and anatomical grounds, with reminiscences of the evolutionarily-based innate-adaptive IS responses. Beyond the multineuronal networks of the CNS, we propose a theoretical model of brain memory integrating the CNS as a whole. This is achieved by analogical reasoning between the operational rules of recognition and memory processes in both systems, coupled to an evolutionary analysis. In this new model, the hippocampus is no longer specifically ascribed to explicit memory but rather it both becomes part of the innate (implicit) memory system and tightly controls the explicit memory system. Alike the antigen presenting cells for the IS, the hippocampus would integrate transient and pseudo-specific (i.e., danger-fear) memories and would drive the formation of long-term and highly specific or explicit memories (i.e., the taste of the Proust’s madeleine cake) by the more complex and recent, evolutionarily speaking, neocortex. Experimental and clinical evidence is provided to support the model. We believe that the singularity of this model’s approximation could help to gain a better understanding of the mechanisms operating in brain memory strategies from a large-scale network perspective. PMID:26869886

Stationary stability for evolutionary dynamics in finite populations

DOE PAGES

Harper, Marc; Fryer, Dashiell

2016-08-25

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISSmore » candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.« less

Bacterial toxin-antitoxin systems: more than selfish entities?

PubMed

Van Melderen, Laurence; Saavedra De Bast, Manuel

2009-03-01

Bacterial toxin-antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes.

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

PubMed Central

Van Melderen, Laurence; Saavedra De Bast, Manuel

2009-01-01

Bacterial toxin–antitoxin (TA) systems are diverse and widespread in the prokaryotic kingdom. They are composed of closely linked genes encoding a stable toxin that can harm the host cell and its cognate labile antitoxin, which protects the host from the toxin's deleterious effect. TA systems are thought to invade bacterial genomes through horizontal gene transfer. Some TA systems might behave as selfish elements and favour their own maintenance at the expense of their host. As a consequence, they may contribute to the maintenance of plasmids or genomic islands, such as super-integrons, by post-segregational killing of the cell that loses these genes and so suffers the stable toxin's destructive effect. The function of the chromosomally encoded TA systems is less clear and still open to debate. This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes. PMID:19325885

Game dynamic model for yeast development.

PubMed

Huang, Yuanyuan; Wu, Zhijun

2012-07-01

Game theoretic models, along with replicator equations, have been applied successfully to the study of evolution of populations of competing species, including the growth of a population, the reaching of the population to an equilibrium state, and the evolutionary stability of the state. In this paper, we analyze a game model proposed by Gore et al. (Nature 456:253-256, 2009) in their recent study on the co-development of two mixed yeast strains. We examine the mathematical properties of this model with varying experimental parameters. We simulate the growths of the yeast strains and compare them with the experimental results. We also compute and analyze the equilibrium state of the system and prove that it is asymptotically and evolutionarily stable.

A simple fitness proxy for structured populations with continuous traits, with case studies on the evolution of haplo-diploids and genetic dimorphisms.

PubMed

Metz, J A J; Leimar, O

2011-03-01

For structured populations in equilibrium with everybody born equal, ln(R (0)) is a useful fitness proxy for evolutionarily steady strategy (ESS) and most adaptive dynamics calculations, with R (0) the average lifetime number of offspring in the clonal and haploid cases, and half the average lifetime number of offspring fathered or mothered for Mendelian diploids. When individuals have variable birth states, as is, for example, the case in spatial models, R (0) is itself an eigenvalue, which usually cannot be expressed explicitly in the trait vectors under consideration. In that case, Q(Y| X):=-det (I-L(Y| X)) can often be used as fitness proxy, with L the next-generation matrix for a potential mutant characterized by the trait vector Y in the (constant) environment engendered by a resident characterized by X. If the trait space is connected, global uninvadability can be determined from it. Moreover, it can be used in all the usual local calculations like the determination of evolutionarily singular trait vectors and their local invadability and attractivity. We conclude with three extended case studies demonstrating the usefulness of Q: the calculation of ESSs under haplo-diploid genetics (I), of evolutionarily steady genetic dimorphisms (ESDs) with a priori proportionality of macro- and micro-gametic outputs (an assumption that is generally made but the fulfilment of which is a priori highly exceptional) (II), and of ESDs without such proportionality (III). These case studies should also have some interest in their own right for the spelled out calculation recipes and their underlying modelling methodology.

Lymphatic filarial species differentiation using evolutionarily modified tandem repeats: generation of new genetic markers.

PubMed

Sakthidevi, Moorthy; Murugan, Vadivel; Hoti, Sugeerappa Laxmanappa; Kaliraj, Perumal

2010-05-01

Polymerase chain reaction based methods are promising tools for the monitoring and evaluation of the Global Program for the Elimination of Lymphatic Filariasis. The currently available PCR methods do not differentiate the DNA of Wuchereria bancrofti or Brugia malayi by a single PCR and hence are cumbersome. Therefore, we designed a single step PCR strategy for differentiating Bancroftian infection from Brugian infection based on a newly identified gene from the W. bancrofti genome, abundant larval transcript-2 (alt-2), which is abundantly expressed. The difference in PCR product sizes generated from the presence or absence of evolutionarily altered tandem repeats in alt-2 intron-3 differentiated W. bancrofti from B. malayi. The analysis was performed on the genomic DNA of microfilariae from a number of patient blood samples or microfilariae positive slides from different Indian geographical regions. The assay gave consistent results, differentiating the two filarial parasite species accurately. This alt-2 intron-3 based PCR assay can be a potential tool for the diagnosis and differentiation of co-infections by lymphatic filarial parasites. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Evolution and manipulation of parasitoid egg load.

PubMed

Gandon, Sylvain; Varaldi, Julien; Fleury, Frédéric; Rivero, Ana

2009-11-01

In proovigenic parasitoids such as Leptopilina boulardi, the female emerges with a limited egg load and no further eggs are produced during its adult life. A female thus runs the risk of exhausting this limited supply of eggs before the end of her life. Given that the production of an egg is costly, what is the evolutionarily stable egg load at emergence? This question has attracted a lot of attention in the last decade. Here, we analyze a model that allows us to track both the evolution and the population dynamics of a solitary, proovigenic parasitoid. First, we show how host-parasitoid dynamics feedbacks on the evolution of parasitoid egg load. Second, we use this model to consider the situation in which the parasitoid can be infected by a virus that manipulates the oviposition behavior of the females. In particular, we model the effect of the LbFV virus in L. boulardi, a virus that is known to enhance its horizontal transmission by increasing superparasitism (i.e., the laying of eggs in a host already parasitized). Specifically, we model (1) the effect of the virus on parasitoid egg load strategies, and (2) the evolution of egg load manipulation by the virus. This analysis yields two alternative, yet not mutually exclusive, adaptive explanations for the observation that females infected by the virus harbor higher egg loads than uninfected females. Infected females could either respond plastically to the infection status, or be manipulated by the virus. Further experimental work is required to distinguish between these two hypotheses. In a broader context, we present a general theoretical framework that allows us to study the epidemiology, the evolution, the coevolution, and the evolution of manipulation of various reproductive strategies of parasitoids.

The patch distributed producer-scrounger game.

PubMed

Ohtsuka, Yasunori; Toquenaga, Yukihiko

2009-09-21

Grouping in animals is ubiquitous and thought to provide group members antipredatory advantages and foraging efficiency. However, parasitic foraging strategy often emerges in a group. The optimal parasitic policy has given rise to the producer-scrounger (PS) game model, in which producers search for food patches, and scroungers parasitize the discovered patches. The N-persons PS game model constructed by Vickery et al. (1991. Producers, scroungers, and group foraging. American Naturalist 137, 847-863) predicts the evolutionarily stable strategy (ESS) of frequency of producers (q;) that depends on the advantage of producers and the number of foragers in a group. However, the model assumes that the number of discovered patches in one time unit never exceeds one. In reality, multiple patches could be found in one time unit. In the present study, we relax this assumption and assumed that the number of discovered patches depends on the producers' variable encounter rate with patches (lambda). We show that q; strongly depends on lambda within a feasible range, although it still depends on the advantage of producer and the number of foragers in a group. The basic idea of PS game is the same as the information sharing (parasitism), because scroungers are also thought to parasitize informations of locations of food patches. Horn (1968) indicated the role of information-parasitism in animal aggregation (Horn, H.S., 1968. The adaptive significance of colonial nesting in the Brewer's blackbird (euphagus cyanocephalus). Ecology 49, 682-646). Our modified PS game model shows the same prediction as the Horn's graphical animal aggregation model; the proportion of scroungers will increase or animals should adopt colonial foraging when resource is spatiotemporally clumped, but scroungers will decrease or animals should adopt territorial foraging if the resource is evenly distributed.

Formal Darwinism, the individual-as-maximizing-agent analogy and bet-hedging

PubMed Central

Grafen, A.

1999-01-01

The central argument of The origin of species was that mechanical processes (inheritance of features and the differential reproduction they cause) can give rise to the appearance of design. The 'mechanical processes' are now mathematically represented by the dynamic systems of population genetics, and the appearance of design by optimization and game theory in which the individual plays the part of the maximizing agent. Establishing a precise individual-as-maximizing-agent (IMA) analogy for a population-genetics system justifies optimization approaches, and so provides a modern formal representation of the core of Darwinism. It is a hitherto unnoticed implication of recent population-genetics models that, contrary to a decades-long consensus, an IMA analogy can be found in models with stochastic environments (subject to a convexity assumption), in which individuals maximize expected reproductive value. The key is that the total reproductive value of a species must be considered as constant, so therefore reproductive value should always be calculated in relative terms. This result removes a major obstacle from the theoretical challenge to find a unifying framework which establishes the IMA analogy for all of Darwinian biology, including as special cases inclusive fitness, evolutionarily stable strategies, evolutionary life-history theory, age-structured models and sex ratio theory. This would provide a formal, mathematical justification of fruitful and widespread but 'intentional' terms in evolutionary biology, such as 'selfish', 'altruism' and 'conflict'.

Small and poor females change sex: a theoretical and empirical study on protogynous sex change in a triggerfish under varying resource abundance.

PubMed

Yamaguchi, Sachi; Seki, Satoko; Sawada, Kota; Takahashi, Satoshi

2013-01-21

Sex change is known from various fish species. In many polygynous species, the largest female usually changes sex to male when the dominant male disappeared, as predicted by the classical size-advantage model. However, in some fishes, the disappearance of male often induces sex change by a smaller female, instead of the largest one. The halfmoon triggerfish Sufflamen chrysopterum is one of such species. We conducted both field investigation and theoretical analysis to test the hypothesis that variation in female fecundity causes the sex change by less-fertile females, even if they are not the largest. We estimated the effect of body length and residual body width (an indicator of nutrition status) on clutch size based on field data. Sex-specific growth rates were also estimated from our investigation and a previous study. We incorporated these estimated value into an evolutionarily stable strategy model for status-dependent size at sex change. As a result, we predict that rich females change sex at a larger size than poor ones, since a rich fish can achieve high reproductive success as a female. In some situations, richer females no longer change sex (i.e. lifelong females), and poorer fish changes sex just after maturation (i.e. primary males). We also analyzed the effect of size-specific growth and mortality. Copyright © 2012 Elsevier Ltd. All rights reserved.

The evolutionary psychology of left and right: costs and benefits of lateralization.

PubMed

Vallortigara, Giorgio

2006-09-01

Why do the left and right sides of the vertebrate brain play different functions? Having a lateralized brain, in which each hemisphere carries out different functions, is ubiquitous among vertebrates. The different specialization of the left and right side of the brain may increase brain efficiency--and some evidence for that is reported here. However, lateral biases due to brain lateralization (such as preferences in the use of a limb or, in animals with laterally placed eyes, of a visual hemifield) usually occur at the population level, with most individuals showing similar direction of bias. Individual brain efficiency does not require the alignment of lateralization in the population. Why then are not left--and right-type individuals equally common? Not only humans, but most vertebrates show a similar pattern. For instance, in the paper I report evidence that most toads, chickens, and fish react faster when a predator approaches from the left. I argue that invoking individual brain efficiency (lateralization may increase fitness), evolutionary chance or direct genetic mechanisms cannot explain this widespread pattern. Instead, using concepts from mathematical theory of games, I show that alignment of lateralization at the population level may arise as an "evolutionarily stable strategy" when individually asymmetrical organisms must coordinate their behavior with that of other asymmetrical organisms. Thus, the population structure of lateralization may result from genes specifying the direction of asymmetries which have been selected under "social" pressures.

Learning to Cooperate: The Evolution of Social Rewards in Repeated Interactions.

PubMed

Dridi, Slimane; Akçay, Erol

2018-01-01

Understanding the behavioral and psychological mechanisms underlying social behaviors is one of the major goals of social evolutionary theory. In particular, a persistent question about animal cooperation is to what extent it is supported by other-regarding preferences-the motivation to increase the welfare of others. In many situations, animals adjust their behaviors through learning by responding to the rewards they experience as a consequence of their actions. Therefore, we may ask whether learning in social situations can be driven by evolved other-regarding rewards. Here we develop a mathematical model in order to ask whether the mere act of cooperating with a social partner will evolve to be inherently rewarding. Individuals interact repeatedly in pairs and adjust their behaviors through reinforcement learning. We assume that individuals associate with each game outcome an internal reward value. These perceived rewards are genetically evolving traits. We find that conditionally cooperative rewards that value mutual cooperation positively but the sucker's outcome negatively tend to be evolutionarily stable. Purely other-regarding rewards can evolve only under special parameter combinations. On the other hand, selfish rewards that always lead to pure defection are also evolutionarily successful. These findings are consistent with empirical observations showing that humans tend to display conditionally cooperative behavior and also exhibit a diversity of preferences. Our model also demonstrates the need to further integrate multiple levels of biological causation of behavior.

Uncertain pollination environment promotes the evolution of a stable mixed reproductive system in the self-incompatible Hypochaeris salzmanniana (Asteraceae).

PubMed

Arista, M; Berjano, R; Viruel, J; Ortiz, M Á; Talavera, M; Ortiz, P L

2017-09-01

The transition from outcrossing to selfing is a repeated pattern in angiosperm diversification and according to general theory this transition should occur quickly and mixed reproductive systems should be infrequent. However, a large proportion of flowering plants have mixed reproductive systems, even showing inbreeding depression. Recently, several theoretical studies have shown that mixed mating systems can be stable, but empirical studies supporting these assumptions are still scarce. Hypochaeris salzmanniana, an annual species with populations differing in their self-incompatibility expression, was used as a study case to assess the stability of its mixed reproductive system. Here a descriptive study of the pollination environment was combined with measurements of the stability of the self-incompatibility system, outcrossing rate, reproductive assurance and inbreeding depression in four populations for two consecutive years. The reproductive system of populations exhibited a geographical pattern: the proportion of plants decreased from west to east. Pollinator environment also varied geographically, being less favourable from west to east. The self-incompatibility expression of some populations changed markedly in only one year. After selfing, progeny was mainly self-compatible, while after outcrossing both self-incompatible and self-compatible plants were produced. In general, both reproductive assurance and high inbreeding depression were found in all populations and years. The lowest values of inbreeding depression were found in 2014 in the easternmost populations, which experienced a marked increase in self-compatibility in 2015. The mixed reproductive system of H. salzmanniana seems to be an evolutionarily stable strategy, with selfing conferring reproductive assurance when pollinator attendance is low, but strongly limited by inbreeding depression. The fact that the highest frequencies of self-compatible plants appeared in the environments most unfavourable to pollination suggests that these plants are selected in these sites, although high rates of inbreeding depression should impede the complete loss of self-incompatibility. In H. salzmanniana, year-to-year changes in the frequency of self-incompatible individuals are directly derived from the balance between reproductive assurance and inbreeding depression. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please email: journals.permissions@oup.com

Evolutionary relevance facilitates visual information processing.

PubMed

Jackson, Russell E; Calvillo, Dusti P

2013-11-03

Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

PubMed

Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

2015-05-01

Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels.

PubMed

Zhang, Ruijie; Lv, Wenhua; Luan, Meiwei; Zheng, Jiajia; Shi, Miao; Zhu, Hongjie; Li, Jin; Lv, Hongchao; Zhang, Mingming; Shang, Zhenwei; Duan, Lian; Jiang, Yongshuai

2015-11-24

Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had lower SNP densities, and higher degrees of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.

Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation

PubMed Central

Gsponer, Jörg; Babu, M. Madan

2012-01-01

Summary Growing evidence suggests that aggregation-prone proteins are both harmful and functional for a cell. How do cellular systems balance the detrimental and beneficial effect of protein aggregation? We reveal that aggregation-prone proteins are subject to differential transcriptional, translational, and degradation control compared to nonaggregation-prone proteins, which leads to their decreased synthesis, low abundance, and high turnover. Genetic modulators that enhance the aggregation phenotype are enriched in genes that influence expression homeostasis. Moreover, genes encoding aggregation-prone proteins are more likely to be harmful when overexpressed. The trends are evolutionarily conserved and suggest a strategy whereby cellular mechanisms specifically modulate the availability of aggregation-prone proteins to (1) keep concentrations below the critical ones required for aggregation and (2) shift the equilibrium between the monomeric and oligomeric/aggregate form, as explained by Le Chatelier’s principle. This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control. PMID:23168257

Euryhaline ecology of early tetrapods revealed by stable isotopes.

PubMed

Goedert, Jean; Lécuyer, Christophe; Amiot, Romain; Arnaud-Godet, Florent; Wang, Xu; Cui, Linlin; Cuny, Gilles; Douay, Guillaume; Fourel, François; Panczer, Gérard; Simon, Laurent; Steyer, J-Sébastien; Zhu, Min

2018-06-01

The fish-to-tetrapod transition-followed later by terrestrialization-represented a major step in vertebrate evolution that gave rise to a successful clade that today contains more than 30,000 tetrapod species. The early tetrapod Ichthyostega was discovered in 1929 in the Devonian Old Red Sandstone sediments of East Greenland (dated to approximately 365 million years ago). Since then, our understanding of the fish-to-tetrapod transition has increased considerably, owing to the discovery of additional Devonian taxa that represent early tetrapods or groups evolutionarily close to them. However, the aquatic environment of early tetrapods and the vertebrate fauna associated with them has remained elusive and highly debated. Here we use a multi-stable isotope approach (δ 13 C, δ 18 O and δ 34 S) to show that some Devonian vertebrates, including early tetrapods, were euryhaline and inhabited transitional aquatic environments subject to high-magnitude, rapid changes in salinity, such as estuaries or deltas. Euryhalinity may have predisposed the early tetrapod clade to be able to survive Late Devonian biotic crises and then successfully colonize terrestrial environments.

Game theory as a conceptual framework for managing insect pests.

PubMed

Brown, Joel S; Staňková, Kateřina

2017-06-01

For over 100 years it has been recognized that insect pests evolve resistance to chemical pesticides. More recently, managers have advocated restrained use of pesticides, crop rotation, the use of multiple pesticides, and pesticide-free sanctuaries as resistance management practices. Game theory provides a conceptual framework for combining the resistance strategies of the insects and the control strategies of the pest manager into a unified conceptual and modelling framework. Game theory can contrast an ecologically enlightened application of pesticides with an evolutionarily enlightened one. In the former case the manager only considers ecological consequences whereas the latter anticipates the evolutionary response of the pests. Broader applications of this game theory approach include anti-biotic resistance, fisheries management and therapy resistance in cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

A norm knockout method on indirect reciprocity to reveal indispensable norms

PubMed Central

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-01-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out. PMID:28276485

A norm knockout method on indirect reciprocity to reveal indispensable norms

NASA Astrophysics Data System (ADS)

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-03-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out.

Evolutionary game theory and multiple chemical sensitivity.

PubMed

Newlin, D B

1999-01-01

Newlin's [Newlin D.B. Evolutionary game theory of tolerance and sensitization in substance abuse. Paper presented to the Research Society on Alcoholism, Hilton Head, SC, 1998] evolutionary game theory of addictive behavior specifies how evolutionarily stable strategies for survival and reproduction may lead to addiction. The game theory of multiple chemical sensitivity (MCS) assumes that: (1) the MCS patient responds to low-level toxicants as stressors or as direct threats to their survival and reproductive fitness, (2) this activates the cortico-mesolimbic dopamine system, (3) this system is a survival motivation center--not a 'reward center', (4) the subject emits a counter-response that is in the same direction as the naive response to the chemicals, (5) previously neutral stimuli associated with chemicals also trigger conditioned responses that mimic those to the chemicals, (6) these counter-responses further activate the dopaminergic survival motivation system, and (7) this produces a positive feedback loop that leads to strong neural sensitization in these structures and in behavior controlled by this system, despite a small initial response. Psychologically, the MCS patient with a sensitized cortico-mesolimbic dopamine system is behaving as though his/her survival is directly threatened by these chemicals. Non-MCS subjects have counter-responses opposite in direction to those of the chemicals and show tolerance. An autoshaping/sign-tracking model of this game is discussed. This evolutionary game makes several specific, testable predictions about differences between MCS subjects, non-MCS controls, and substance abusers in laboratory experiments, and between sensitized and nonsensitized animals.

Seven and up: individual differences in male voice fundamental frequency emerge before puberty and remain stable throughout adulthood

NASA Astrophysics Data System (ADS)

Fouquet, Meddy; Pisanski, Katarzyna; Mathevon, Nicolas; Reby, David

2016-10-01

Voice pitch (the perceptual correlate of fundamental frequency, F0) varies considerably even among individuals of the same sex and age, communicating a host of socially and evolutionarily relevant information. However, due to the almost exclusive utilization of cross-sectional designs in previous studies, it remains unknown whether these individual differences in voice pitch emerge before, during or after sexual maturation, and whether voice pitch remains stable into adulthood. Here, we measured the F0 parameters of men who were recorded once every 7 years from age 7 to 56 as they participated in the British television documentary Up Series. Linear mixed models revealed significant effects of age on all F0 parameters, wherein F0 mean, minimum, maximum and the standard deviation of F0 showed sharp pubertal decreases between age 7 and 21, yet remained remarkably stable after age 28. Critically, men's pre-pubertal F0 at age 7 strongly predicted their F0 at every subsequent adult age, explaining up to 64% of the variance in post-pubertal F0. This finding suggests that between-individual differences in voice pitch that are known to play an important role in men's reproductive success are in fact largely determined by age 7, and may therefore be linked to prenatal and/or pre-pubertal androgen exposure.

Ecology shapes the evolutionary trade-off between predator avoidance and defence in coral reef butterflyfishes.

PubMed

Hodge, Jennifer R; Alim, Chidera; Bertrand, Nick G; Lee, Wesley; Price, Samantha A; Tran, Binh; Wainwright, Peter C

2018-07-01

Antipredator defensive traits are thought to trade-off evolutionarily with traits that facilitate predator avoidance. However, complexity and scale have precluded tests of this prediction in many groups, including fishes. Using a macroevolutionary approach, we test this prediction in butterflyfishes, an iconic group of coral reef inhabitants with diverse social behaviours, foraging strategies and antipredator adaptations. We find that several antipredator traits have evolved adaptively, dependent primarily on foraging strategy. We identify a previously unrecognised axis of diversity in butterflyfishes where species with robust morphological defences have riskier foraging strategies and lack sociality, while species with reduced morphological defences feed in familiar territories, have adaptations for quick escapes and benefit from the vigilance provided by sociality. Furthermore, we find evidence for the constrained evolution of fin spines among species that graze solely on corals, highlighting the importance of corals, as both prey and structural refuge, in shaping fish morphology. © 2018 John Wiley & Sons Ltd/CNRS.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms.

PubMed

Bogdanov, Yuri F; Dadashev, Sergei Y; Grishaeva, Tatiana M

2003-01-01

Evolutionarily distant organisms have not only orthologs, but also nonhomologous proteins that build functionally similar subcellular structures. For instance, this is true with protein components of the synaptonemal complex (SC), a universal ultrastructure that ensures the successful pairing and recombination of homologous chromosomes during meiosis. We aimed at developing a method to search databases for genes that code for such nonhomologous but functionally analogous proteins. Advantage was taken of the ultrastructural parameters of SC and the conformation of SC proteins responsible for these. Proteins involved in SC central space are known to be similar in secondary structure. Using published data, we found a highly significant correlation between the width of the SC central space and the length of rod-shaped central domain of mammalian and yeast intermediate proteins forming transversal filaments in the SC central space. Basing on this, we suggested a method for searching genome databases of distant organisms for genes whose virtual proteins meet the above correlation requirement. Our recent finding of the Drosophila melanogaster CG17604 gene coding for synaptonemal complex transversal filament protein received experimental support from another lab. With the same strategy, we showed that the Arabidopsis thaliana and Caenorhabditis elegans genomes contain unique genes coding for such proteins.

Applying a Dynamic Stomatal Optimization to Predict Shifts in the Functional Composition of Tropical Forests Under Increased Drought And CO2

NASA Astrophysics Data System (ADS)

Bartlett, M. K.; Detto, M.; Pacala, S. W.

2017-12-01

The accurate prediction of tropical forest carbon fluxes is key to forecasting global climate, but forest responses to projected increases in CO2 and drought are highly uncertain. Here we present a dynamic optimization that derives the trajectory of stomatal conductance (gs) during drought, a key source of model uncertainty, from plant and soil water relations and the carbon economy of the plant hydraulic system. This optimization scheme is novel in two ways. First, by accounting for the ability of capacitance (i.e., the release of water from plant storage tissue; C) to buffer evaporative water loss and maintain gs during drought, this optimization captures both drought tolerant and avoidant hydraulic strategies. Second, by determining the optimal trajectory of plant and soil water potentials, this optimization quantifies species' impacts on the water available to competing plants. These advances allowed us to apply this optimization across the range of physiology trait values observed in tropical species to evaluate shifts in the competitively optimal trait values, or evolutionarily stable hydraulic strategy (ESS), under increased drought and CO2. Increasing the length of the dry season shifted the ESS towards more drought tolerant, rather than avoidant, trait values, and these shifts were larger for longer individual drought periods (i.e., more consecutive days without rainfall), even if the total time spent in drought was the same. Concurrently doubling the CO2 level reduced the magnitude of these shifts and slightly favored drought avoidant strategies under wet conditions. Overall, these analyses predicted that short, frequent droughts would allow elevated CO2 to shift the functional composition in tropical forests towards more drought avoidant species, while infrequent but long drought periods would shift the ESS to more drought tolerant trait values, despite increased CO2. Overall, these analyses quantified the impact of physiology traits on plant performance and competitive ability, and provide a mechanistic, trait-based approach to predict shifts in the functional composition of tropical forests under projected climatic conditions.

Money and trust among strangers

PubMed Central

Camera, Gabriele; Casari, Marco; Bigoni, Maria

2013-01-01

What makes money essential for the functioning of modern society? Through an experiment, we present evidence for the existence of a relevant behavioral dimension in addition to the standard theoretical arguments. Subjects faced repeated opportunities to help an anonymous counterpart who changed over time. Cooperation required trusting that help given to a stranger today would be returned by a stranger in the future. Cooperation levels declined when going from small to large groups of strangers, even if monitoring and payoffs from cooperation were invariant to group size. We then introduced intrinsically worthless tokens. Tokens endogenously became money: subjects took to reward help with a token and to demand a token in exchange for help. Subjects trusted that strangers would return help for a token. Cooperation levels remained stable as the groups grew larger. In all conditions, full cooperation was possible through a social norm of decentralized enforcement, without using tokens. This turned out to be especially demanding in large groups. Lack of trust among strangers thus made money behaviorally essential. To explain these results, we developed an evolutionary model. When behavior in society is heterogeneous, cooperation collapses without tokens. In contrast, the use of tokens makes cooperation evolutionarily stable. PMID:23980139

Money and trust among strangers.

PubMed

Camera, Gabriele; Casari, Marco; Bigoni, Maria

2013-09-10

What makes money essential for the functioning of modern society? Through an experiment, we present evidence for the existence of a relevant behavioral dimension in addition to the standard theoretical arguments. Subjects faced repeated opportunities to help an anonymous counterpart who changed over time. Cooperation required trusting that help given to a stranger today would be returned by a stranger in the future. Cooperation levels declined when going from small to large groups of strangers, even if monitoring and payoffs from cooperation were invariant to group size. We then introduced intrinsically worthless tokens. Tokens endogenously became money: subjects took to reward help with a token and to demand a token in exchange for help. Subjects trusted that strangers would return help for a token. Cooperation levels remained stable as the groups grew larger. In all conditions, full cooperation was possible through a social norm of decentralized enforcement, without using tokens. This turned out to be especially demanding in large groups. Lack of trust among strangers thus made money behaviorally essential. To explain these results, we developed an evolutionary model. When behavior in society is heterogeneous, cooperation collapses without tokens. In contrast, the use of tokens makes cooperation evolutionarily stable.

Genomic reassortment of influenza A virus in North American swine, 1998–2011

PubMed Central

Detmer, Susan E.; Wentworth, David E.; Tan, Yi; Schwartzbard, Aaron; Halpin, Rebecca A.; Stockwell, Timothy B.; Lin, Xudong; Vincent, Amy L.; Gramer, Marie R.; Holmes, Edward C.

2012-01-01

Revealing the frequency and determinants of reassortment among RNA genome segments is fundamental to understanding basic aspects of the biology and evolution of the influenza virus. To estimate the extent of genomic reassortment in influenza viruses circulating in North American swine, we performed a phylogenetic analysis of 139 whole-genome viral sequences sampled during 1998–2011 and representing seven antigenically distinct viral lineages. The highest amounts of reassortment were detected between the H3 and the internal gene segments (PB2, PB1, PA, NP, M and NS), while the lowest reassortment frequencies were observed among the H1γ, H1pdm and neuraminidase segments, particularly N1. Less reassortment was observed among specific haemagglutinin–neuraminidase combinations that were more prevalent in swine, suggesting that some genome constellations may be evolutionarily more stable. PMID:22993190

NREL, International Colleagues Propose Strategy for Stable, Commercial

Science.gov Websites

, Commercial Perovskite Solar Cells News Release: NREL, International Colleagues Propose Strategy for Stable , Commercial Perovskite Solar Cells October 17, 2016 Photo of two men in a lab. NREL Scientists Keith Emery and stable commercial PSCs-that includes the following: Developing a reproducible manufacturing method that

An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game.

PubMed

Hoffman, Moshe; Suetens, Sigrid; Gneezy, Uri; Nowak, Martin A

2015-03-06

Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium (NE), which is motivated by perfect rationality. NE specifies a strategy for everyone, such that no one would benefit by deviating unilaterally from his/her strategy. Another powerful tool available to game theorists are evolutionary dynamics (ED). Motivated by evolutionary and learning processes, ED specify changes in strategies over time in a population, such that more successful strategies typically become more frequent. A simple game that illustrates interesting ED is the generalized Rock-Paper-Scissors (RPS) game. The RPS game extends the children's game to situations where winning or losing can matter more or less relative to tying. Here we investigate experimentally three RPS games, where the NE is always to randomize with equal probability, but the evolutionary stability of this strategy changes. Consistent with the prediction of ED we find that aggregate behavior is far away from NE when it is evolutionarily unstable. Our findings add to the growing literature that demonstrates the predictive validity of ED in large-scale incentivized laboratory experiments with human subjects.

Correlation of Positive and Negative Reciprocity Fails to Confer an Evolutionary Advantage: Phase Transitions to Elementary Strategies

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž

2013-10-01

Economic experiments reveal that humans value cooperation and fairness. Punishing unfair behavior is therefore common, and according to the theory of strong reciprocity, it is also directly related to rewarding cooperative behavior. However, empirical data fail to confirm that positive and negative reciprocity are correlated. Inspired by this disagreement, we determine whether the combined application of reward and punishment is evolutionarily advantageous. We study a spatial public goods game, where in addition to the three elementary strategies of defection, rewarding, and punishment, a fourth strategy that combines the latter two competes for space. We find rich dynamical behavior that gives rise to intricate phase diagrams where continuous and discontinuous phase transitions occur in succession. Indirect territorial competition, spontaneous emergence of cyclic dominance, as well as divergent fluctuations of oscillations that terminate in an absorbing phase are observed. Yet, despite the high complexity of solutions, the combined strategy can survive only in very narrow and unrealistic parameter regions. Elementary strategies, either in pure or mixed phases, are much more common and likely to prevail. Our results highlight the importance of patterns and structure in human cooperation, which should be considered in future experiments.

Siderophore production and the evolution of investment in a public good: An adaptive dynamics approach to kin selection.

PubMed

Lee, William; van Baalen, Minus; Jansen, Vincent A A

2016-01-07

Like many other bacteria, Pseudomonas aeruginosa sequesters iron from the environment through the secretion, and subsequent uptake, of iron-binding molecules. As these molecules can be taken up by other bacteria in the population than those who secreted them, this is a form of cooperation through a public good. Traditionally, this problem has been studied by comparing the relative fitnesses of siderophore-producing and non-producing strains, but this gives no information about the fate of strains that do produce intermediate amounts of siderophores. Here, we investigate theoretically how the amount invested in this form of cooperation evolves. We use a mechanistic description of the laboratory protocols used in experimental evolution studies to describe the competition and cooperation of the bacteria. From this dynamical model we derive the fitness following the adaptive dynamics method. The results show how selection is driven by local siderophore production and local competition. Because siderophore production reduces the growth rate, local competition decreases with the degree of relatedness (which is a dynamical variable in our model). Our model is not restricted to the analysis of small phenotypic differences and allows for theoretical exploration of the effects of large phenotypic differences between cooperators and cheats. We predict that an intermediate ESS level of cooperation (molecule production) should exist. The adaptive dynamics approach allows us to assess evolutionary stability, which is often not possible in other kin-selection models. We found that selection can lead to an intermediate strategy which in our model is always evolutionarily stable, yet can allow invasion of strategies that are much more cooperative. Our model describes the evolution of a public good in the context of the ecology of the microorganism, which allows us to relate the extent of production of the public good to the details of the interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Commentary: Should Gender Differences Be Included in the Evolutionary Upgrade to Cognitive Load Theory?

ERIC Educational Resources Information Center

Bevilacqua, Andy

2017-01-01

Recent upgrades to cognitive load theory suggest that evolutionary processes have shaped the way that working memory processes cultural and social information. According to evolutionarily educational psychologists, some forms of information are processed with lower working memory loads than other forms. The former are evolutionarily salient and…

76 FR 50448 - Endangered and Threatened Species; 5-Year Reviews for 17 Evolutionarily Significant Units and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-15

... 11 evolutionarily significant units (ESUs) of Pacific salmon (Oncorhynchus sp.) and 6 distinct... and 6 DPSs of steelhead in Oregon, Washington, and Idaho shall remain listed as determined in 2005... Sound Chinook salmon; (4) Lower Columbia River Chinook salmon; (5) Upper Willamette Chinook salmon; (6...

Oxidative stress-induced autophagy: Role in pulmonary toxicity

PubMed Central

Malaviya, Rama; Laskin, Jeffrey D.; Laskin, Debra L.

2015-01-01

Autophagy is an evolutionarily conserved catabolic process important in regulating the turnover of essential proteins and in elimination of damaged organelles and protein aggregates. Autophagy is observed in the lung in response to oxidative stress generated as a consequence of exposure to environmental toxicants. Whether autophagy plays role in promoting cell survival or cytotoxicity is unclear. In this article recent findings on oxidative stress-induced autophagy in the lung are reviewed; potential mechanisms initiating autophagy are also discussed. A better understanding of autophagy and its role in pulmonary toxicity may lead to the development of new strategies to treat lung injury associated with oxidative stress. PMID:24398106

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

PubMed Central

Long, Hannah K.; King, Hamish W.; Patient, Roger K.; Odom, Duncan T.; Klose, Robert J.

2016-01-01

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. PMID:27084945

Modulation of host cell function by Legionella pneumophila type IV effectors.

PubMed

Hubber, Andree; Roy, Craig R

2010-01-01

Macrophages and protozoa ingest bacteria by phagocytosis and destroy these microbes using a conserved pathway that mediates fusion of the phagosome with lysosomes. To survive within phagocytic host cells, bacterial pathogens have evolved a variety of strategies to avoid fusion with lysosomes. A virulence strategy used by the intracellular pathogen Legionella pneumophila is to manipulate host cellular processes using bacterial proteins that are delivered into the cytosolic compartment of the host cell by a specialized secretion system called Dot/Icm. The proteins delivered by the Dot/Icm system target host factors that play evolutionarily conserved roles in controlling membrane transport in eukaryotic cells, which enables L. pneumophila to create an endoplasmic reticulum-like vacuole that supports intracellular replication in both protozoan and mammalian host cells. This review focuses on intracellular trafficking of L. pneumophila and describes how bacterial proteins contribute to modulation of host processes required for survival within host cells.

Studies in the Theory of Quantum Games

NASA Astrophysics Data System (ADS)

Iqbal, Azhar

2005-03-01

Theory of quantum games is a new area of investigation that has gone through rapid development during the last few years. Initial motivation for playing games, in the quantum world, comes from the possibility of re-formulating quantum communication protocols, and algorithms, in terms of games between quantum and classical players. The possibility led to the view that quantum games have a potential to provide helpful insight into working of quantum algorithms, and even in finding new ones. This thesis analyzes and compares some interesting games when played classically and quantum mechanically. A large part of the thesis concerns investigations into a refinement notion of the Nash equilibrium concept. The refinement, called an evolutionarily stable strategy (ESS), was originally introduced in 1970s by mathematical biologists to model an evolving population using techniques borrowed from game theory. Analysis is developed around a situation when quantization changes ESSs without affecting corresponding Nash equilibria. Effects of quantization on solution-concepts other than Nash equilibrium are presented and discussed. For this purpose the notions of value of coalition, backwards-induction outcome, and subgame-perfect outcome are selected. Repeated games are known to have different information structure than one-shot games. Investigation is presented into a possible way where quantization changes the outcome of a repeated game. Lastly, two new suggestions are put forward to play quantum versions of classical matrix games. The first one uses the association of De Broglie's waves, with travelling material objects, as a resource for playing a quantum game. The second suggestion concerns an EPR type setting exploiting directly the correlations in Bell's inequalities to play a bi-matrix game.

Reassessing the roles of PIN proteins and anticlinal microtubules during pavement cell morphogenesis

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

Belteton, Samuel; Sawchuk, Megan G.; Donohoe, Bryon S.

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxinmore » gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here we used Arabidopsis reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells, and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls.« less

Novel Approaches to Manipulating Bacterial Pathogen Biofilms: Whole-Systems Design Philosophy and Steering Microbial Evolution.

PubMed

Penn, Alexandra S

2016-01-01

Understanding and manipulating bacterial biofilms is crucial in medicine, ecology and agriculture and has potential applications in bioproduction, bioremediation and bioenergy. Biofilms often resist standard therapies and the need to develop new means of intervention provides an opportunity to fundamentally rethink our strategies. Conventional approaches to working with biological systems are, for the most part, "brute force", attempting to effect control in an input and effort intensive manner and are often insufficient when dealing with the inherent non-linearity and complexity of living systems. Biological systems, by their very nature, are dynamic, adaptive and resilient and require management tools that interact with dynamic processes rather than inert artefacts. I present an overview of a novel engineering philosophy which aims to exploit rather than fight those properties, and hence provide a more efficient and robust alternative. Based on a combination of evolutionary theory and whole-systems design, its essence is what I will call systems aikido; the basic principle of aikido being to interact with the momentum of an attacker and redirect it with minimal energy expenditure, using the opponent's energy rather than one's own. In more conventional terms, this translates to a philosophy of equilibrium engineering, manipulating systems' own self-organisation and evolution so that the evolutionarily or dynamically stable state corresponds to a function which we require. I illustrate these ideas with a description of a proposed manipulation of environmental conditions to alter the stability of co-operation in the context of Pseudomonas aeruginosa biofilm infection of the cystic fibrosis lung.

The evolution of parental care in the context of sexual selection: a critical reassessment of parental investment theory.

PubMed

Wade, Michael J; Shuster, Stephen M

2002-09-01

Males and females are often defined by differences in their energetic investment in gametes. In most sexual species, females produce few large ova, whereas males produce many tiny sperm. This difference in initial parental investment is presumed to exert a fundamental influence on sex differences in mating and parental behavior, resulting in a taxonomic bias toward parental care in females and away from parental care in males. In this article, we reexamine the logic of this argument as well as the evolutionarily stable strategy (ESS) theory often used to substantiate it. We show that the classic ESS model, which contrasts parental care with offspring desertion, violates the necessary relationship between mean male and female fitness. When the constraint of equal male and female mean fitness is correctly incorporated into the ESS model, its results are congruent with those of evolutionary genetic theory for the evolution of genes with direct and indirect effects. Male parental care evolves whenever half the magnitude of the indirect effect of paternal care on offspring viability exceeds the direct effect of additional mating success gained by desertion. When the converse is true, desertion invades and spreads. In the absence of a genetic correlation between the sexes, the evolution of paternal care is independent of maternal care. Theories based on sex differences in gametic investment make no such specific predictions. We discuss whether inferences about the evolution of sex differences in parental care can hold if the ESS theory on which they are based contains internal contradictions.

Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis1[OPEN

PubMed Central

Sawchuk, Megan G.; Scarpella, Enrico

2018-01-01

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxin gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here, we used Arabidopsis (Arabidopsis thaliana) reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor long-lived microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls. PMID:29192026

Landscape-level model to predict spawning habitat for Lower Columbia River fall Chinook salmon (Oncorhynchus tshawytscha)

Treesearch

D. Shallin Busch; Mindi Sheer; Kelly Burnett; Paul McElhany; Tom Cooney

2013-01-01

We developed an intrinsic potential (IP) model to estimate the potential of streams to provide habitat for spawning fall Chinook salmon (Oncorhynchus tshawytscha) in the Lower Columbia River evolutionarily significant unit. This evolutionarily significant unit is a threatened species, and both fish abundance and distribution are reduced from...

Validation of Reference Genes for Quantitative Expression Analysis by Real-Time RT-PCR in Four Lepidopteran Insects

PubMed Central

Teng, Xiaolu; Zhang, Zan; He, Guiling; Yang, Liwen; Li, Fei

2012-01-01

Quantitative real-time polymerase chain reaction (qPCR) is an efficient and widely used technique to monitor gene expression. Housekeeping genes (HKGs) are often empirically selected as the reference genes for data normalization. However, the suitability of HKGs used as the reference genes has been seldom validated. Here, six HKGs were chosen (actin A3, actin A1, GAPDH, G3PDH, E2F, rp49) in four lepidopteran insects Bombyx mori L. (Lepidoptera: Bombycidae), Plutella xylostella L. (Plutellidae), Chilo suppressalis Walker (Crambidae), and Spodoptera exigua Hübner (Noctuidae) to study their expression stability. The algorithms of geNorm, NormFinder, stability index, and ΔCt analysis were used to evaluate these HKGs. Across different developmental stages, actin A1 was the most stable in P. xylostella and C. suppressalis, but it was the least stable in B. mori and S. exigua. Rp49 and GAPDH were the most stable in B. mori and S. exigua, respectively. In different tissues, GAPDH, E2F, and Rp49 were the most stable in B. mori, S. exigua, and C. suppressalis, respectively. The relative abundances of Siwi genes estimated by 2-ΔΔCt method were tested with different HKGs as the reference gene, proving the importance of internal controls in qPCR data analysis. The results not only presented a list of suitable reference genes in four lepidopteran insects, but also proved that the expression stabilities of HKGs were different among evolutionarily close species. There was no single universal reference gene that could be used in all situations. It is indispensable to validate the expression of HKGs before using them as the internal control in qPCR. PMID:22938136

Validation of reference genes for quantitative expression analysis by real-time rt-PCR in four lepidopteran insects.

PubMed

Teng, Xiaolu; Zhang, Zan; He, Guiling; Yang, Liwen; Li, Fei

2012-01-01

Quantitative real-time polymerase chain reaction (qPCR) is an efficient and widely used technique to monitor gene expression. Housekeeping genes (HKGs) are often empirically selected as the reference genes for data normalization. However, the suitability of HKGs used as the reference genes has been seldom validated. Here, six HKGs were chosen (actin A3, actin A1, GAPDH, G3PDH, E2F, rp49) in four lepidopteran insects Bombyx mori L. (Lepidoptera: Bombycidae), Plutella xylostella L. (Plutellidae), Chilo suppressalis Walker (Crambidae), and Spodoptera exigua Hübner (Noctuidae) to study their expression stability. The algorithms of geNorm, NormFinder, stability index, and ΔCt analysis were used to evaluate these HKGs. Across different developmental stages, actin A1 was the most stable in P. xylostella and C. suppressalis, but it was the least stable in B. mori and S. exigua. Rp49 and GAPDH were the most stable in B. mori and S. exigua, respectively. In different tissues, GAPDH, E2F, and Rp49 were the most stable in B. mori, S. exigua, and C. suppressalis, respectively. The relative abundances of Siwi genes estimated by 2(-ΔΔCt) method were tested with different HKGs as the reference gene, proving the importance of internal controls in qPCR data analysis. The results not only presented a list of suitable reference genes in four lepidopteran insects, but also proved that the expression stabilities of HKGs were different among evolutionarily close species. There was no single universal reference gene that could be used in all situations. It is indispensable to validate the expression of HKGs before using them as the internal control in qPCR.

Stability of miRNA 5′terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy

PubMed Central

Hibio, Naoki; Hino, Kimihiro; Shimizu, Eigo; Nagata, Yoshiro; Ui-Tei, Kumiko

2012-01-01

MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly understood. Here we mathematized base-pairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity. The results are consistent with the previous findings that an RNA strand with unstable 5′ terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and miRNA recognizes target mRNAs with seed-complementary sequences to direct posttranscriptional repression. Our results suggested that both the unwinding and target recognition processes of miRNAs could be proficiently controlled by the thermodynamics of base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might be evolutionarily well adapted to the body temperatures of various species. PMID:23251782

The evolution of mimicry under constraints.

PubMed

Holen, Øistein Haugsten; Johnstone, Rufus A

2004-11-01

The resemblance between mimetic organisms and their models varies from near perfect to very crude. One possible explanation, which has received surprisingly little attention, is that evolution can improve mimicry only at some cost to the mimetic organism. In this article, an evolutionary game theory model of mimicry is presented that incorporates such constraints. The model generates novel and testable predictions. First, Batesian mimics that are very common and/or mimic very weakly defended models should evolve either inaccurate mimicry (by stabilizing selection) or mimetic polymorphism. Second, Batesian mimics that are very common and/or mimic very weakly defended models are more likely to evolve mimetic polymorphism if they encounter predators at high rates and/or are bad at evading predator attacks. The model also examines how cognitive constraints acting on signal receivers may help determine evolutionarily stable levels of mimicry. Surprisingly, improved discrimination abilities among signal receivers may sometimes select for less accurate mimicry.

Floral advertisement and the competition for pollination services.

PubMed

Fishman, Michael A; Hadany, Lilach

2015-06-01

Flowering plants are a major component of terrestrial ecosystems, and most of them depend on animal pollinators for reproduction. Thus, the mutualism between flowering plants and their pollinators is a keystone ecological relationship in both natural and agricultural ecosystems. Though plant-pollinator interactions have received considerable amount of attention, there are still many unanswered questions. In this paper, we use methods of evolutionary game theory to investigate the co-evolution of floral advertisement and pollinator preferences Our results indicate that competition for pollination services among plant species can in some cases lead to specialization of the pollinator population to a single plant species (oligolecty). However, collecting pollen from multiple plants - at least at the population level - is evolutionarily stable under a wider parameter range. Finally, we show that, in the presence of pollinators, plants that optimize their investment in attracting vs. rewarding visiting pollinators outcompete plants that do not. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Self-organized sorting limits behavioral variability in swarms

PubMed Central

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-01-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters. PMID:27550316

The organization and control of an evolving interdependent population

PubMed Central

Vural, Dervis C.; Isakov, Alexander; Mahadevan, L.

2015-01-01

Starting with Darwin, biologists have asked how populations evolve from a low fitness state that is evolutionarily stable to a high fitness state that is not. Specifically of interest is the emergence of cooperation and multicellularity where the fitness of individuals often appears in conflict with that of the population. Theories of social evolution and evolutionary game theory have produced a number of fruitful results employing two-state two-body frameworks. In this study, we depart from this tradition and instead consider a multi-player, multi-state evolutionary game, in which the fitness of an agent is determined by its relationship to an arbitrary number of other agents. We show that populations organize themselves in one of four distinct phases of interdependence depending on one parameter, selection strength. Some of these phases involve the formation of specialized large-scale structures. We then describe how the evolution of independence can be manipulated through various external perturbations. PMID:26040593

Transcription coactivator SAYP combines chromatin remodeler Brahma and transcription initiation factor TFIID into a single supercomplex

PubMed Central

Vorobyeva, Nadezhda E.; Soshnikova, Nataliya V.; Nikolenko, Julia V.; Kuzmina, Julia L.; Nabirochkina, Elena N.; Georgieva, Sofia G.; Shidlovskii, Yulii V.

2009-01-01

Transcription activation by RNA polymerase II is a complicated process driven by combined, precisely coordinated action of a wide array of coactivator complexes, which carry out chromatin-directed activities and nucleate the assembly of the preinitiation complex on the promoter. Using various techniques, we have shown the existence of a stable coactivator supercomplex consisting of the chromatin-remodeling factor Brahma (SWI/SNF) and the transcription initiation factor TFIID, named BTFly (Brahma and TFIID in one assembly). The coupling of Brahma and TFIID is mediated by the SAYP factor, whose evolutionarily conserved activation domain SAY can directly bind to both BAP170 subunit of Brahma and TAF5 subunit of TFIID. The integrity of BTFly is crucial for its ability to activate transcription. BTFly is distributed genome-wide and appears to be a means of effective transcription activation. PMID:19541607

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

PubMed

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

2012-10-09

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

The hitchhiker's guide to altruism: gene-culture coevolution, and the internalization of norms.

PubMed

Gintis, Herbert

2003-02-21

An internal norm is a pattern of behavior enforced in part by internal sanctions, such as shame, guilt and loss of self-esteem, as opposed to purely external sanctions, such as material rewards and punishment. The ability to internalize norms is widespread among humans, although in some so-called "sociopaths", this capacity is diminished or lacking. Suppose there is one genetic locus that controls the capacity to internalize norms. This model shows that if an internal norm is fitness enhancing, then for plausible patterns of socialization, the allele for internalization of norms is evolutionarily stable. This framework can be used to model Herbert Simon's (1990) explanation of altruism, showing that altruistic norms can "hitchhike" on the general tendency of internal norms to be personally fitness-enhancing. A multi-level selection, gene-culture coevolution argument then explains why individually fitness-reducing internal norms are likely to be prosocial as opposed to socially harmful.

Self-organized sorting limits behavioral variability in swarms

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-08-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

PubMed Central

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

2012-01-01

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans. PMID:23012415

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

PubMed

Long, Hannah K; King, Hamish W; Patient, Roger K; Odom, Duncan T; Klose, Robert J

2016-08-19

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leaf-cutting ants.

PubMed

Fernández-Marín, Hermógenes; Nash, David R; Higginbotham, Sarah; Estrada, Catalina; van Zweden, Jelle S; d'Ettorre, Patrizia; Wcislo, William T; Boomsma, Jacobus J

2015-05-22

Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little investigated antimicrobial agent. We show that particularly the smallest workers greatly reduce germination rates of Escovopsis and Metarhizium spores after actively applying PAA to experimental infection targets in garden fragments and transferring the spores to the ants' infrabuccal cavities. In vitro assays further indicated that Escovopsis strains isolated from evolutionarily derived leaf-cutting ants are less sensitive to PAA than strains from phylogenetically more basal fungus-farming ants, consistent with the dynamics of an evolutionary arms race between virulence and control for Escovopsis, but not Metarhizium. Atta ants form larger colonies with more extreme caste differentiation relative to other attines, in societies characterized by an almost complete absence of reproductive conflicts. We hypothesize that these changes are associated with unique evolutionary innovations in chemical pest management that appear robust against selection pressure for resistance by specialized mycopathogens. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Functional Similarity of Medial Superior Parietal Areas for Shift-Selective Attention Signals in Humans and Monkeys.

PubMed

Caspari, Natalie; Arsenault, John T; Vandenberghe, Rik; Vanduffel, Wim

2018-06-01

We continually shift our attention between items in the visual environment. These attention shifts are usually based on task relevance (top-down) or the saliency of a sudden, unexpected stimulus (bottom-up), and are typically followed by goal-directed actions. It could be argued that any species that can covertly shift its focus of attention will rely on similar, evolutionarily conserved neural substrates for processing such shift-signals. To address this possibility, we performed comparative fMRI experiments in humans and monkeys, combining traditional, and novel, data-driven analytical approaches. Specifically, we examined correspondences between monkey and human brain areas activated during covert attention shifts. When "shift" events were compared with "stay" events, the medial (superior) parietal lobe (mSPL) and inferior parietal lobes showed similar shift sensitivities across species, whereas frontal activations were stronger in monkeys. To identify, in a data-driven manner, monkey regions that corresponded with human shift-selective SPL, we used a novel interspecies beta-correlation strategy whereby task-related beta-values were correlated across voxels or regions-of-interest in the 2 species. Monkey medial parietal areas V6/V6A most consistently correlated with shift-selective human mSPL. Our results indicate that both species recruit corresponding, evolutionarily conserved regions within the medial superior parietal lobe for shifting spatial attention.

Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leaf-cutting ants

PubMed Central

Fernández-Marín, Hermógenes; Nash, David R.; Higginbotham, Sarah; Estrada, Catalina; van Zweden, Jelle S.; d'Ettorre, Patrizia; Wcislo, William T.; Boomsma, Jacobus J.

2015-01-01

Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little investigated antimicrobial agent. We show that particularly the smallest workers greatly reduce germination rates of Escovopsis and Metarhizium spores after actively applying PAA to experimental infection targets in garden fragments and transferring the spores to the ants' infrabuccal cavities. In vitro assays further indicated that Escovopsis strains isolated from evolutionarily derived leaf-cutting ants are less sensitive to PAA than strains from phylogenetically more basal fungus-farming ants, consistent with the dynamics of an evolutionary arms race between virulence and control for Escovopsis, but not Metarhizium. Atta ants form larger colonies with more extreme caste differentiation relative to other attines, in societies characterized by an almost complete absence of reproductive conflicts. We hypothesize that these changes are associated with unique evolutionary innovations in chemical pest management that appear robust against selection pressure for resistance by specialized mycopathogens. PMID:25925100

Phylogenetic analysis of conservation priorities for aquatic mammals and their terrestrial relatives, with a comparison of methods.

PubMed

May-Collado, Laura J; Agnarsson, Ingi

2011-01-01

Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all 'high priority' species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct--and thus 'biodiverse'--species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders.

Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface

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

Shao, Xiangqiang; Kang, Hyunook; Loveless, Timothy

Stable tissue integrity during embryonic development relies on the function of the cadherin·catenin complex (CCC). The Caenorhabditis elegans CCC is a useful paradigm for analyzing in vivo requirements for specific interactions among the core components of the CCC, and it provides a unique opportunity to examine evolutionarily conserved mechanisms that govern the interaction between α- and β-catenin. HMP-1, unlike its mammalian homolog α-catenin, is constitutively monomeric, and its binding affinity for HMP-2/β-catenin is higher than that of α-catenin for β-catenin. A crystal structure shows that the HMP-1·HMP-2 complex forms a five-helical bundle structure distinct from the structure of the mammalianmore » α-catenin·β-catenin complex. Deletion analysis based on the crystal structure shows that the first helix of HMP-1 is necessary for binding HMP-2 avidly in vitro and for efficient recruitment of HMP-1 to adherens junctions in embryos. HMP-2 Ser-47 and Tyr-69 flank its binding interface with HMP-1, and we show that phosphomimetic mutations at these two sites decrease binding affinity of HMP-1 to HMP-2 by 40–100-fold in vitro. In vivo experiments using HMP-2 S47E and Y69E mutants showed that they are unable to rescue hmp-2(zu364) mutants, suggesting that phosphorylation of HMP-2 on Ser-47 and Tyr-69 could be important for regulating CCC formation in C. elegans. Our data provide novel insights into how cadherin-dependent cell–cell adhesion is modulated in metazoans by conserved elements as well as features unique to specific organisms.« less

Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface

DOE PAGES

Shao, Xiangqiang; Kang, Hyunook; Loveless, Timothy; ...

2017-08-25

Stable tissue integrity during embryonic development relies on the function of the cadherin·catenin complex (CCC). The Caenorhabditis elegans CCC is a useful paradigm for analyzing in vivo requirements for specific interactions among the core components of the CCC, and it provides a unique opportunity to examine evolutionarily conserved mechanisms that govern the interaction between α- and β-catenin. HMP-1, unlike its mammalian homolog α-catenin, is constitutively monomeric, and its binding affinity for HMP-2/β-catenin is higher than that of α-catenin for β-catenin. A crystal structure shows that the HMP-1·HMP-2 complex forms a five-helical bundle structure distinct from the structure of the mammalianmore » α-catenin·β-catenin complex. Deletion analysis based on the crystal structure shows that the first helix of HMP-1 is necessary for binding HMP-2 avidly in vitro and for efficient recruitment of HMP-1 to adherens junctions in embryos. HMP-2 Ser-47 and Tyr-69 flank its binding interface with HMP-1, and we show that phosphomimetic mutations at these two sites decrease binding affinity of HMP-1 to HMP-2 by 40–100-fold in vitro. In vivo experiments using HMP-2 S47E and Y69E mutants showed that they are unable to rescue hmp-2(zu364) mutants, suggesting that phosphorylation of HMP-2 on Ser-47 and Tyr-69 could be important for regulating CCC formation in C. elegans. Our data provide novel insights into how cadherin-dependent cell–cell adhesion is modulated in metazoans by conserved elements as well as features unique to specific organisms.« less

Symbiotic Bacteria Direct Expression of an Intestinal Bactericidal Lectin

PubMed Central

Cash, Heather L.; Whitham, Cecilia V.; Behrendt, Cassie L.; Hooper, Lora V.

2009-01-01

The mammalian intestine harbors complex societies of beneficial bacteria that are maintained in the lumen with minimal penetration of mucosal surfaces. Microbial colonization of germ-free mice triggers epithelial expression of RegIIIγ, a secreted C-type lectin. RegIIIγ binds intestinal bacteria but lacks the complement recruitment domains present in other microbe-binding mammalian C-type lectins. We show that RegIIIγ and its human counterpart, HIP/PAP, are directly antimicrobial proteins that bind their bacterial targets via interactions with peptidoglycan carbohydrate. We propose that these proteins represent an evolutionarily primitive form of lectin-mediated innate immunity, and that they reveal intestinal strategies for maintaining symbiotic host-microbial relationships. PMID:16931762

A model for the coevolution of immunity and immune evasion in vector-borne diseases with implications for the epidemiology of malaria.

PubMed

Koella, Jacob C; Boëte, C

2003-05-01

We describe a model of host-parasite coevolution, where the interaction depends on the investments by the host in its immune response and by the parasite in its ability to suppress (or evade) its host's immune response. We base our model on the interaction between malaria parasites and their mosquito hosts and thus describe the epidemiological dynamics with the Macdonald-Ross equation of malaria epidemiology. The qualitative predictions of the model are most sensitive to the cost of the immune response and to the intensity of transmission. If transmission is weak or the cost of immunity is low, the system evolves to a coevolutionarily stable equilibrium at intermediate levels of investment (and, generally, at a low frequency of resistance). At a higher cost of immunity and as transmission intensifies, the system is not evolutionarily stable but rather cycles around intermediate levels of investment. At more intense transmission, neither host nor parasite invests any resources in dominating its partner so that no resistance is observed in the population. These results may help to explain the lack of encapsulated malaria parasites generally observed in natural populations of mosquito vectors, despite strong selection pressure for resistance in areas of very intense transmission.

Construction of a hybrid β-hexosaminidase subunit capable of forming stable homodimers that hydrolyze GM2 ganglioside in vivo.

PubMed

Tropak, Michael B; Yonekawa, Sayuri; Karumuthil-Melethil, Subha; Thompson, Patrick; Wakarchuk, Warren; Gray, Steven J; Walia, Jagdeep S; Mark, Brian L; Mahuran, Don

2016-01-01

Tay-Sachs or Sandhoff disease result from mutations in either the evolutionarily related HEXA or HEXB genes encoding respectively, the α- or β-subunits of β-hexosaminidase A (HexA). Of the three Hex isozymes, only HexA can interact with its cofactor, the GM2 activator protein (GM2AP), and hydrolyze GM2 ganglioside. A major impediment to establishing gene or enzyme replacement therapy based on HexA is the need to synthesize both subunits. Thus, we combined the critical features of both α- and β-subunits into a single hybrid µ-subunit that contains the α-subunit active site, the stable β-subunit interface and unique areas in each subunit needed to interact with GM2AP. To facilitate intracellular analysis and the purification of the µ-homodimer (HexM), CRISPR-based genome editing was used to disrupt the HEXA and HEXB genes in a Human Embryonic Kidney 293 cell line stably expressing the µ-subunit. In association with GM2AP, HexM was shown to hydrolyze a fluorescent GM2 ganglioside derivative both in cellulo and in vitro. Gene transfer studies in both Tay-Sachs and Sandhoff mouse models demonstrated that HexM expression reduced brain GM2 ganglioside levels.

Construction of a hybrid β-hexosaminidase subunit capable of forming stable homodimers that hydrolyze GM2 ganglioside in vivo

PubMed Central

Tropak, Michael B; Yonekawa, Sayuri; Karumuthil-Melethil, Subha; Thompson, Patrick; Wakarchuk, Warren; Gray, Steven J; Walia, Jagdeep S; Mark, Brian L; Mahuran, Don

2016-01-01

Tay-Sachs or Sandhoff disease result from mutations in either the evolutionarily related HEXA or HEXB genes encoding respectively, the α- or β-subunits of β-hexosaminidase A (HexA). Of the three Hex isozymes, only HexA can interact with its cofactor, the GM2 activator protein (GM2AP), and hydrolyze GM2 ganglioside. A major impediment to establishing gene or enzyme replacement therapy based on HexA is the need to synthesize both subunits. Thus, we combined the critical features of both α- and β-subunits into a single hybrid µ-subunit that contains the α-subunit active site, the stable β-subunit interface and unique areas in each subunit needed to interact with GM2AP. To facilitate intracellular analysis and the purification of the µ-homodimer (HexM), CRISPR-based genome editing was used to disrupt the HEXA and HEXB genes in a Human Embryonic Kidney 293 cell line stably expressing the µ-subunit. In association with GM2AP, HexM was shown to hydrolyze a fluorescent GM2 ganglioside derivative both in cellulo and in vitro. Gene transfer studies in both Tay-Sachs and Sandhoff mouse models demonstrated that HexM expression reduced brain GM2 ganglioside levels. PMID:26966698

Prenatal stress effects in a wild, long-lived primate: predictive adaptive responses in an unpredictable environment.

PubMed

Berghänel, Andreas; Heistermann, Michael; Schülke, Oliver; Ostner, Julia

2016-09-28

Prenatal maternal stress affects offspring phenotype in numerous species including humans, but it is debated whether these effects are evolutionarily adaptive. Relating stress to adverse conditions, current explanations invoke either short-term developmental constraints on offspring phenotype resulting in decelerated growth to avoid starvation, or long-term predictive adaptive responses (PARs) resulting in accelerated growth and reproduction in response to reduced life expectancies. Two PAR subtypes were proposed, acting either on predicted internal somatic states or predicted external environmental conditions, but because both affect phenotypes similarly, they are largely indistinguishable. Only external (not internal) PARs rely on high environmental stability particularly in long-lived species. We report on a crucial test case in a wild long-lived mammal, the Assamese macaque (Macaca assamensis), which evolved and lives in an unpredictable environment where external PARs are probably not advantageous. We quantified food availability, growth, motor skills, maternal caretaking style and maternal physiological stress from faecal glucocorticoid measures. Prenatal maternal stress was negatively correlated to prenatal food availability and led to accelerated offspring growth accompanied by decelerated motor skill acquisition and reduced immune function. These results support the 'internal PAR' theory, which stresses the role of stable adverse internal somatic states rather than stable external environments. © 2016 The Author(s).

Dynamic binding of replication protein a is required for DNA repair

PubMed Central

Chen, Ran; Subramanyam, Shyamal; Elcock, Adrian H.; Spies, Maria; Wold, Marc S.

2016-01-01

Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA–DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions. PMID:27131385

A disturbance-based ecosystem approach to maintaining and restoring freshwater habitats of evolutionarily significant units of anadromous salmonids in the Pacific Northwest.

Treesearch

G.H. Reeves; L.E. Benda; K.M. Burnett; P.A. Bisson; J.R. Sedell

1995-01-01

To preserve and recover evolutionarily significant units (ESUs) of anadromous salmonids Oncorhynchus spp. in the Pacific Northwest, long-term and short-term ecological processes that create and maintain freshwater habitats must be restored and protected. Aquatic ecosystems through- out the region are dynamic in space and time, and lack of...

Local Nash equilibrium in social networks.

PubMed

Zhang, Yichao; Aziz-Alaoui, M A; Bertelle, Cyrille; Guan, Jihong

2014-08-29

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Local Nash Equilibrium in Social Networks

PubMed Central

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-01-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures. PMID:25169150

Local Nash Equilibrium in Social Networks

NASA Astrophysics Data System (ADS)

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-08-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Stomatal regulation based on competition for water, stochastic rainfall, and xylem hydraulic vulnerability - a new theoretical model

NASA Astrophysics Data System (ADS)

Lu, Y.; Duursma, R.; Farrior, C.; Medlyn, B. E.

2016-12-01

Stomata control the exchange of soil water for atmospheric CO2, which is one of the most important resource trade-offs for plants. This trade-off has been studied a lot but not in the context of competition. Based on the theory of evolutionarily stable strategy, we search for the uninvadable (or the ESS) response of stomatal conductance to soil water content under stochastic rainfall, with which the dominant plant population should never be invaded by any rare mutants in the water competition due to a higher fitness. In this study, we define the fitness as the difference between the long-term average photosynthetic carbon gain and a carbon cost of stomatal opening. This cost has traditionally been considered an unknown constant. Here we extend this framework by assuming it as the energy required for xylem embolism refilling. With regard to the refilling process, we explore 2 questions 1) to what extent the embolized xylem vessels can be repaired via refilling; and 2) whether this refilling is immediate or has a time delay following the formation of xylem embolism. We compare various assumptions in a total of 5 scenarios and find that the ESS exists only if the xylem damage can be repaired completely. Then, with this ESS, we estimate annual vegetation photosynthesis and water consumption and compare them with empirical results. In conclusion, this study provides a different insight from the existing empirical and mechanistic models as well as the theoretical models based on the optimization theory. In addition, as the model result is a simple quantitative relation between stomatal conductance and soil water content, it can be easily incorporated into other vegetation function models.

Food web structure and the evolution of ecological communities

NASA Astrophysics Data System (ADS)

Quince, Christopher; Higgs, Paul G.; McKane, Alan J.

Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food web. The equations account for competition between species for the same resources, and for the diet choice of predators between alternative prey according to an evolutionarily stable strategy. The set of species present undergoes long-term evolution d ue to speciation and extinction events. We summarize results obtained on the macro-evolutionary dynamics of speciations and extinctions, and on the statistical properties of the food webs that are generated by the model. Simulations begin from small numbers of species and build up to larger webs with relatively constant species number on average. The rate of origination and extinction of species are relatively high, but remain roughly balanced throughout the simulations. When a 'parent' species undergoes sp eciation, the 'child' species usually adds to the same trophic level as the parent. The chance of the child species surviving is significantly higher if the parent is on the second or third trophic level than if it is on the first level, most likely due to a wider choice of possible prey for species on higher levels. Addition of a new species sometimes causes extinction of existing species. The parent species has a high probability of extinction because it has strong competition with the new species. Non-pa rental competitors of the new species also have a significantly higher extinction probability than average, as do prey of the new species. Predators of the new species are less likely than average to become extinct.

An ESS treatment of the pattern of female arrival at the mating site in the yellow dung fly scathophaga stercoraria (L.)

PubMed

Reuter; Ward; Blanckenhorn

1998-12-07

In most previous work on the yellow dung fly Scathophaga stercoraria (L.), as on other species, adaptive explanations have been sought for male behaviour whereas female behaviour has not been examined in similar detail. Here, the arrival of females at the mating site, fresh cattle droppings, is investigated. While almost all males are present shortly after pat deposition females arrive at a low, decreasing rate over an interval of about 5 hours. We propose that the distribution of female arrival times represents a mixed Evolutionarily Stable Strategy (ESS), formed by different trade-offs between costs and benefits of early and late arrival. Early arrival could be favoured by advantages due to better conditions for oviposition, faster egg development of reduced larval competition. Late arrival could be favoured by negative effects on females of male-male competition being weaker later after deposition. Computer simulations with distributions of arrival times deviating from the natural one were performed to "measure" the costs for females arriving at different times. These costs were compared with estimated benefits corresponding to the females' arrival times. This procedure revealed that females coming to the pat later in a population of females arriving shortly after deposition would be favoured. In a population arriving according to a uniform distribution, early females would have fitness advantages. Thus, evolution should lead to an intermediate distribution of arrival times, as in nature, i.e. female arrival behaviour is probably adaptive. The simulations also revealed that the intensity of sexual selection though male-male competition is highest with the natural pattern of female arrival. Therefore, natural selection generating this pattern amplifies the intensity of male-male interaction as a by-product. Copyright 1998 Academic Press

Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis.

PubMed

Belteton, Samuel A; Sawchuk, Megan G; Donohoe, Bryon S; Scarpella, Enrico; Szymanski, Daniel B

2018-01-01

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxin gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here, we used Arabidopsis ( Arabidopsis thaliana ) reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor long-lived microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls. © 2018 American Society of Plant Biologists. All Rights Reserved.

Targeting AMPK Signaling as a Neuroprotective Strategy in Parkinson's Disease.

PubMed

Curry, Daniel W; Stutz, Bernardo; Andrews, Zane B; Elsworth, John D

2018-03-26

Parkinson's disease (PD) is the second most common neurodegenerative disorder. It is characterized by the accumulation of intracellular α-synuclein aggregates and the degeneration of nigrostriatal dopaminergic neurons. While no treatment strategy has been proven to slow or halt the progression of the disease, there is mounting evidence from preclinical PD models that activation of 5'-AMP-activated protein kinase (AMPK) may have broad neuroprotective effects. Numerous dietary supplements and pharmaceuticals (e.g., metformin) that increase AMPK activity are available for use in humans, but clinical studies of their effects in PD patients are limited. AMPK is an evolutionarily conserved serine/threonine kinase that is activated by falling energy levels and functions to restore cellular energy balance. However, in response to certain cellular stressors, AMPK activation may exacerbate neuronal atrophy and cell death. This review describes the regulation and functions of AMPK, evaluates the controversies in the field, and assesses the potential of targeting AMPK signaling as a neuroprotective treatment for PD.

New strategy for drug discovery by large-scale association analysis of molecular networks of different species.

PubMed

Zhang, Bo; Fu, Yingxue; Huang, Chao; Zheng, Chunli; Wu, Ziyin; Zhang, Wenjuan; Yang, Xiaoyan; Gong, Fukai; Li, Yuerong; Chen, Xiaoyu; Gao, Shuo; Chen, Xuetong; Li, Yan; Lu, Aiping; Wang, Yonghua

2016-02-25

The development of modern omics technology has not significantly improved the efficiency of drug development. Rather precise and targeted drug discovery remains unsolved. Here a large-scale cross-species molecular network association (CSMNA) approach for targeted drug screening from natural sources is presented. The algorithm integrates molecular network omics data from humans and 267 plants and microbes, establishing the biological relationships between them and extracting evolutionarily convergent chemicals. This technique allows the researcher to assess targeted drugs for specific human diseases based on specific plant or microbe pathways. In a perspective validation, connections between the plant Halliwell-Asada (HA) cycle and the human Nrf2-ARE pathway were verified and the manner by which the HA cycle molecules act on the human Nrf2-ARE pathway as antioxidants was determined. This shows the potential applicability of this approach in drug discovery. The current method integrates disparate evolutionary species into chemico-biologically coherent circuits, suggesting a new cross-species omics analysis strategy for rational drug development.

Frogs Exploit Statistical Regularities in Noisy Acoustic Scenes to Solve Cocktail-Party-like Problems.

PubMed

Lee, Norman; Ward, Jessica L; Vélez, Alejandro; Micheyl, Christophe; Bee, Mark A

2017-03-06

Noise is a ubiquitous source of errors in all forms of communication [1]. Noise-induced errors in speech communication, for example, make it difficult for humans to converse in noisy social settings, a challenge aptly named the "cocktail party problem" [2]. Many nonhuman animals also communicate acoustically in noisy social groups and thus face biologically analogous problems [3]. However, we know little about how the perceptual systems of receivers are evolutionarily adapted to avoid the costs of noise-induced errors in communication. In this study of Cope's gray treefrog (Hyla chrysoscelis; Hylidae), we investigated whether receivers exploit a potential statistical regularity present in noisy acoustic scenes to reduce errors in signal recognition and discrimination. We developed an anatomical/physiological model of the peripheral auditory system to show that temporal correlation in amplitude fluctuations across the frequency spectrum ("comodulation") [4-6] is a feature of the noise generated by large breeding choruses of sexually advertising males. In four psychophysical experiments, we investigated whether females exploit comodulation in background noise to mitigate noise-induced errors in evolutionarily critical mate-choice decisions. Subjects experienced fewer errors in recognizing conspecific calls and in selecting the calls of high-quality mates in the presence of simulated chorus noise that was comodulated. These data show unequivocally, and for the first time, that exploiting statistical regularities present in noisy acoustic scenes is an important biological strategy for solving cocktail-party-like problems in nonhuman animal communication. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability

PubMed Central

Flourakis, Matthieu; Kula-Eversole, Elzbieta; Hutchison, Alan L.; Han, Tae Hee; Aranda, Kimberly; Moose, Devon L.; White, Kevin P.; Dinner, Aaron R.; Lear, Bridget C.; Ren, Dejian; Diekman, Casey O.; Raman, Indira M.; Allada, Ravi

2015-01-01

Summary Circadian clocks regulate membrane excitability in master pacemaker neurons to control daily rhythms of sleep and wake. Here we find that two distinctly timed electrical drives collaborate to impose rhythmicity on Drosophila clock neurons. In the morning, a voltage-independent sodium conductance via the NA/NALCN ion channel depolarizes these neurons. This current is driven by the rhythmic expression of NCA localization factor-1, linking the molecular clock to ion channel function. In the evening, basal potassium currents peak to silence clock neurons. Remarkably, daily antiphase cycles of sodium and potassium currents also drive mouse clock neuron rhythms. Thus, we reveal an evolutionarily ancient strategy for the neural mechanisms that govern daily sleep and wake. PMID:26276633

Target detection in insects: optical, neural and behavioral optimizations.

PubMed

Gonzalez-Bellido, Paloma T; Fabian, Samuel T; Nordström, Karin

2016-12-01

Motion vision provides important cues for many tasks. Flying insects, for example, may pursue small, fast moving targets for mating or feeding purposes, even when these are detected against self-generated optic flow. Since insects are small, with size-constrained eyes and brains, they have evolved to optimize their optical, neural and behavioral target visualization solutions. Indeed, even if evolutionarily distant insects display different pursuit strategies, target neuron physiology is strikingly similar. Furthermore, the coarse spatial resolution of the insect compound eye might actually be beneficial when it comes to detection of moving targets. In conclusion, tiny insects show higher than expected performance in target visualization tasks. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Intercellular interplay between Sirt1 signalling and cell metabolism in immune cell biology

PubMed Central

Chen, Xi; Lu, Yun; Zhang, Zhengguo; Wang, Jian; Yang, Hui; Liu, Guangwei

2015-01-01

Sirtuins are evolutionarily conserved class III histone deacetylases that have been the focus of intense scrutiny and interest since the discovery of Sir2 as a yeast longevity factor. Early reports demonstrated an important role of Sirt1 in aging and metabolism, but its critical regulatory role in the immune system has only been unveiled in recent years. In this review we discuss the latest advances in understanding the regulatory role of Sirt1 in immune responses as well as how Sirt1 translates metabolic cues to immune signals, which would bring new insights into both pathogenesis and potential therapeutic strategies of a variety of immune-related diseases, such as cancer, microbial infection, autoimmune diseases and transplantation. PMID:25890999

Spatial vs. non-spatial eco-evolutionary dynamics in a tumor growth model.

PubMed

You, Li; Brown, Joel S; Thuijsman, Frank; Cunningham, Jessica J; Gatenby, Robert A; Zhang, Jingsong; Staňková, Kateřina

2017-12-21

Metastatic prostate cancer is initially treated with androgen deprivation therapy (ADT). However, resistance typically develops in about 1 year - a clinical condition termed metastatic castrate-resistant prostate cancer (mCRPC). We develop and investigate a spatial game (agent based continuous space) of mCRPC that considers three distinct cancer cell types: (1) those dependent on exogenous testosterone (T + ), (2) those with increased CYP17A expression that produce testosterone and provide it to the environment as a public good (T P ), and (3) those independent of testosterone (T - ). The interactions within and between cancer cell types can be represented by a 3 × 3 matrix. Based on the known biology of this cancer there are 22 potential matrices that give roughly three major outcomes depending upon the absence (good prognosis), near absence or high frequency (poor prognosis) of T -  cells at the evolutionarily stable strategy (ESS). When just two cell types coexist the spatial game faithfully reproduces the ESS of the corresponding matrix game. With three cell types divergences occur, in some cases just two strategies coexist in the spatial game even as a non-spatial matrix game supports all three. Discrepancies between the spatial game and non-spatial ESS happen because different cell types become more or less clumped in the spatial game - leading to non-random assortative interactions between cell types. Three key spatial scales influence the distribution and abundance of cell types in the spatial game: i. Increasing the radius at which cells interact with each other can lead to higher clumping of each type, ii. Increasing the radius at which cells experience limits to population growth can cause densely packed tumor clusters in space, iii. Increasing the dispersal radius of daughter cells promotes increased mixing of cell types. To our knowledge the effects of these spatial scales on eco-evolutionary dynamics have not been explored in cancer models. The fact that cancer interactions are spatially explicit and that our spatial game of mCRPC provides in general different outcomes than the non-spatial game might suggest that non-spatial models are insufficient for capturing key elements of tumorigenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ascidians and the plasticity of the chordate developmental program.

PubMed

Lemaire, Patrick; Smith, William C; Nishida, Hiroki

2008-07-22

Little is known about the ancient chordates that gave rise to the first vertebrates, but the descendants of other invertebrate chordates extant at the time still flourish in the ocean. These invertebrates include the cephalochordates and tunicates, whose larvae share with vertebrate embryos a common body plan with a central notochord and a dorsal nerve cord. Tunicates are now thought to be the sister group of vertebrates. However, research based on several species of ascidians, a diverse and wide-spread class of tunicates, revealed that the molecular strategies underlying their development appear to diverge greatly from those found in vertebrates. Furthermore, the adult body plan of most tunicates, which arises following an extensive post-larval metamorphosis, shows little resemblance to the body plan of any other chordate. In this review, we compare the developmental strategies of ascidians and vertebrates and argue that the very divergence of these strategies reveals the surprising level of plasticity of the chordate developmental program and is a rich resource to identify core regulatory mechanisms that are evolutionarily conserved in chordates. Further, we propose that the comparative analysis of the architecture of ascidian and vertebrate gene regulatory networks may provide critical insight into the origin of the chordate body plan.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems.

PubMed

Szilágyi, András; Zachar, István; Scheuring, István; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

2017-11-27

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

PubMed Central

Szilágyi, András; Kun, Ádám; Könnyű, Balázs; Czárán, Tamás

2017-01-01

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future. PMID:29186916

Relatedness predicts multiple measures of investment in cooperative nest construction in sociable weavers

PubMed Central

Leighton, Gavin M.; Echeverri, Sebastian; Heinrich, Dirk; Kolberg, Holger

2015-01-01

Although communal goods are often critical to society, they are simultaneously susceptible to exploitation and are evolutionarily stable only if mechanisms exist to curtail exploitation. Mechanisms such as punishment and kin selection have been offered as general explanations for how communal resources can be maintained. Evidence for these mechanisms comes largely from humans and social insects, leaving their generality in question. To assess how communal resources are maintained, we observed cooperative nest construction in sociable weavers (Philetairus socius). The communal nest of sociable weavers provides thermal benefits for all individuals but requires continual maintenance. We observed cooperative nest construction and also recorded basic morphological characteristics. We also collected blood samples, performed next-generation sequencing, and isolated 2358 variable single nucleotide polymorphisms (SNPs) to estimate relatedness. We find that relatedness predicts investment in cooperative nest construction, while no other morphological characters significantly explain cooperative output. We argue that indirect benefits are a critical fitness component for maintaining the cooperative behavior that maintains the communal good. PMID:26726282

Parasites and deleterious mutations: interactions influencing the evolutionary maintenance of sex.

PubMed

Park, A W; Jokela, J; Michalakis, Y

2010-05-01

The restrictive assumptions associated with purely genetic and purely ecological mechanisms suggest that neither of the two forces, in isolation, can offer a general explanation for the evolutionary maintenance of sex. Consequently, attention has turned to pluralistic models (i.e. models that apply both ecological and genetic mechanisms). Existing research has shown that combining mutation accumulation and parasitism allows restrictive assumptions about genetic and parasite parameter values to be relaxed while still predicting the maintenance of sex. However, several empirical studies have shown that deleterious mutations and parasitism can reduce fitness to a greater extent than would be expected if the two acted independently. We show how interactions between these genetic and ecological forces can completely reverse predictions about the evolution of reproductive modes. Moreover, we demonstrate that synergistic interactions between infection and deleterious mutations can render sex evolutionarily stable even when there is antagonistic epistasis among deleterious mutations, thereby widening the conditions for the evolutionary maintenance of sex.

Chaperonin polymers in archaea: The cytoskeleton of prokaryotes?

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

Trent, J.D.; Kagawa, H.K.; Zaluzec, N.J.

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1more » mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.« less

ROCC, a conserved region in cohesin's Mcd1 subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation

PubMed Central

Eng, Thomas; Guacci, Vincent; Koshland, Doug

2014-01-01

Cohesin helps orchestrate higher-order chromosome structure, thereby promoting sister chromatid cohesion, chromosome condensation, DNA repair, and transcriptional regulation. To elucidate how cohesin facilitates these diverse processes, we mutagenized Mcd1p, the kleisin regulatory subunit of budding yeast cohesin. In the linker region of Mcd1p, we identified a novel evolutionarily conserved 10–amino acid cluster, termed the regulation of cohesion and condensation (ROCC) box. We show that ROCC promotes cohesion maintenance by protecting a second activity of cohesin that is distinct from its stable binding to chromosomes. The existence of this second activity is incompatible with the simple embrace mechanism of cohesion. In addition, we show that the ROCC box is required for the establishment of condensation. We provide evidence that ROCC controls cohesion maintenance and condensation establishment through differential functional interactions with Pds5p and Wpl1p. PMID:24966169

Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction

NASA Astrophysics Data System (ADS)

Tang, Le; Zhu, Songling; Mastriani, Emilio; Fang, Xin; Zhou, Yu-Jie; Li, Yong-Guo; Johnston, Randal N.; Guo, Zheng; Liu, Gui-Rong; Liu, Shu-Lin

2017-03-01

Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

PubMed

Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

DOE R&D Accomplishments Database

Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

1997-07-01

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

Cost-effectiveness of anatomical and functional test strategies for stable chest pain: public health perspective from a middle-income country.

PubMed

Bertoldi, Eduardo G; Stella, Steffen F; Rohde, Luis Eduardo P; Polanczyk, Carisi A

2017-05-04

The aim of this research is to evaluate the relative cost-effectiveness of functional and anatomical strategies for diagnosing stable coronary artery disease (CAD), using exercise (Ex)-ECG, stress echocardiogram (ECHO), single-photon emission CT (SPECT), coronary CT angiography (CTA) or stress cardiacmagnetic resonance (C-MRI). Decision-analytical model, comparing strategies of sequential tests for evaluating patients with possible stable angina in low, intermediate and high pretest probability of CAD, from the perspective of a developing nation's public healthcare system. Hypothetical cohort of patients with pretest probability of CAD between 20% and 70%. The primary outcome is cost per correct diagnosis of CAD. Proportion of false-positive or false-negative tests and number of unnecessary tests performed were also evaluated. Strategies using Ex-ECG as initial test were the least costly alternatives but generated more frequent false-positive initial tests and false-negative final diagnosis. Strategies based on CTA or ECHO as initial test were the most attractive and resulted in similar cost-effectiveness ratios (I$ 286 and I$ 305 per correct diagnosis, respectively). A strategy based on C-MRI was highly effective for diagnosing stable CAD, but its high cost resulted in unfavourable incremental cost-effectiveness (ICER) in moderate-risk and high-risk scenarios. Non-invasive strategies based on SPECT have been dominated. An anatomical diagnostic strategy based on CTA is a cost-effective option for CAD diagnosis. Functional strategies performed equally well when based on ECHO. C-MRI yielded acceptable ICER only at low pretest probability, and SPECT was not cost-effective in our analysis. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

[Progress in stable isotope labeled quantitative proteomics methods].

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Detecting and characterizing circular RNAs

PubMed Central

Jeck, William R.; Sharpless, Norman E.

2014-01-01

Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study has been difficult through traditional methods of RNA analysis. Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed comprehensive studies of circular RNA species. Recent studies have revealed thousands of endogenous circular RNAs (circRNAs) in mammalian cells, some of which are highly abundant and evolutionarily conserved. Evidence is emerging that some circRNAs might regulate microRNA (miRNA) function, and roles in transcriptional control have also been suggested. Therefore, study of this class of non-coding RNAs has potential implications for therapeutic and research applications. We believe the key future challenge to the field will be to understand the regulation and function of these unusual molecules. PMID:24811520

Temperature Induced Syllable Breaking Unveils Nonlinearly Interacting Timescales in Birdsong Motor Pathway

PubMed Central

Goldin, Matías A.; Alonso, Leandro M.; Alliende, Jorge A.; Goller, Franz; Mindlin, Gabriel B.

2013-01-01

The nature of telencephalic control over premotor and motor circuits is debated. Hypotheses range from complete usurping of downstream circuitry to highly interactive mechanisms of control. We show theoretically and experimentally, that telencephalic song motor control in canaries is consistent with a highly interactive strategy. As predicted from a theoretical model of respiratory control, mild cooling of a forebrain nucleus (HVC) led to song stretching, but further cooling caused progressive restructuring of song, consistent with the hypothesis that respiratory gestures are subharmonic responses to a timescale present in the output of HVC. This interaction between a life-sustaining motor function (respiration) and telencephalic song motor control suggests a more general mechanism of how nonlinear integration of evolutionarily new brain structures into existing circuitry gives rise to diverse, new behavior. PMID:23818988

Temperature induced syllable breaking unveils nonlinearly interacting timescales in birdsong motor pathway.

PubMed

Goldin, Matías A; Alonso, Leandro M; Alliende, Jorge A; Goller, Franz; Mindlin, Gabriel B

2013-01-01

The nature of telencephalic control over premotor and motor circuits is debated. Hypotheses range from complete usurping of downstream circuitry to highly interactive mechanisms of control. We show theoretically and experimentally, that telencephalic song motor control in canaries is consistent with a highly interactive strategy. As predicted from a theoretical model of respiratory control, mild cooling of a forebrain nucleus (HVC) led to song stretching, but further cooling caused progressive restructuring of song, consistent with the hypothesis that respiratory gestures are subharmonic responses to a timescale present in the output of HVC. This interaction between a life-sustaining motor function (respiration) and telencephalic song motor control suggests a more general mechanism of how nonlinear integration of evolutionarily new brain structures into existing circuitry gives rise to diverse, new behavior.

Notch signaling in lung diseases: focus on Notch1 and Notch3

PubMed Central

Zong, Dandan; Ouyang, Ruoyun; Li, Jinhua; Chen, Yan; Chen, Ping

2016-01-01

Notch signaling is an evolutionarily conserved cell–cell communication mechanism that plays a key role in lung homeostasis, injury and repair. The loss of regulation of Notch signaling, especially Notch1 and Notch3, has recently been linked to the pathogenesis of important lung diseases, in particular, chronic obstructive pulmonary disease (COPD), asthma, pulmonary fibrosis, pulmonary arterial hypertension (PAH), lung cancer and lung lesions in some congenital diseases. This review focuses on recent advances related to the mechanisms and the consequences of aberrant or absent Notch1/3 activity in the initiation and progression of lung diseases. Our increasing understanding of this signaling pathway offers great hope that manipulating Notch signaling may represent a promising alternative complementary therapeutic strategy in the future. PMID:27378579

Avoidance of fisheries-induced evolution: management implications for catch selectivity and limit reference points.

PubMed

Hutchings, Jeffrey A

2009-08-01

I examined how the fitness (r) associated with early- and late-maturing genotypes varies with fishing mortality (F) and age-/size-specific probability of capture. Life-history data on Newfoundland's northern Atlantic cod (Gadus morhua) allowed for the estimation of r for individuals maturing at 4 and 7 year in the absence of fishing. Catch selectivity data associated with four types of fishing gear (trap, gillnet, handline, otter trawl) were then incorporated to examine how r varied with gear type and with F. The resulting fitness functions were then used to estimate the F above which selection would favour early (4 year) rather than delayed (7 year) maturity. This evolutionarily-sensitive threshold, F evol, identifies a limit reference point somewhat similar to those used to define overfishing (e.g., F msy, F 0.1). Over-exploitation of northern cod resulted in fishing mortalities considerably greater than those required to effect evolutionary change. Selection for early maturity is reduced by the dome-shaped selectivities characteristic of fixed gears such as handlines (the greater the leptokurtosis, the lower the probability of a selection response) and enhanced by the knife-edged selectivities of bottom trawls. Strategies to minimize genetic change are consistent with traditional management objectives (e.g., yield maximization, population increase). Compliance with harvest control rules guided by evolutionarily-sensitive limit reference points, which may be achieved by adherence to traditional reference points such as F msy and F 0.1, should be sufficient to minimize the probability of fisheries-induced evolution for commercially exploited species.

Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules.

PubMed

Liu, Rui; Zhang, Shixi; Wei, Chao; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

2016-05-17

The unambiguous quantification of biomolecules is of great significance in fundamental biological research as well as practical clinical diagnosis. Due to the lack of a detectable moiety, the direct and highly sensitive quantification of biomolecules is often a "mission impossible". Consequently, tagging strategies to introduce detectable moieties for labeling target biomolecules were invented, which had a long and significant impact on studies of biomolecules in the past decades. For instance, immunoassays have been developed with radioisotope tagging by Yalow and Berson in the late 1950s. The later languishment of this technology can be almost exclusively ascribed to the use of radioactive isotopes, which led to the development of nonradioactive tagging strategy-based assays such as enzyme-linked immunosorbent assay, fluorescent immunoassay, and chemiluminescent and electrochemiluminescent immunoassay. Despite great success, these strategies suffered from drawbacks such as limited spectral window capacity for multiplex detection and inability to provide absolute quantification of biomolecules. After recalling the sequences of tagging strategies, an apparent question is why not use stable isotopes from the start? A reasonable explanation is the lack of reliable means for accurate and precise quantification of stable isotopes at that time. The situation has changed greatly at present, since several atomic mass spectrometric measures for metal stable isotopes have been developed. Among the newly developed techniques, inductively coupled plasma mass spectrometry is an ideal technique to determine metal stable isotope-tagged biomolecules, for its high sensitivity, wide dynamic linear range, and more importantly multiplex and absolute quantification ability. Since the first published report by our group, metal stable isotope tagging has become a revolutionary technique and gained great success in biomolecule quantification. An exciting research highlight in this area is the development and application of the mass cytometer, which fully exploited the multiplexing potential of metal stable isotope tagging. It realized the simultaneous detection of dozens of parameters in single cells, accurate immunophenotyping in cell populations, through modeling of intracellular signaling network and undoubted discrimination of function and connection of cell subsets. Metal stable isotope tagging has great potential applications in hematopoiesis, immunology, stem cells, cancer, and drug screening related research and opened a post-fluorescence era of cytometry. Herein, we review the development of biomolecule quantification using metal stable isotope tagging. Particularly, the power of multiplex and absolute quantification is demonstrated. We address the advantages, applicable situations, and limitations of metal stable isotope tagging strategies and propose suggestions for future developments. The transfer of enzymatic or fluorescent tagging to metal stable isotope tagging may occur in many aspects of biological and clinical practices in the near future, just as the revolution from radioactive isotope tagging to fluorescent tagging happened in the past.

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions

PubMed Central

Zu, Jian; Wang, Jinliang; Huang, Gang

2016-01-01

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey’s trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator’s trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions. PMID:27685540

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions.

Phylogenetic Analysis of Conservation Priorities for Aquatic Mammals and Their Terrestrial Relatives, with a Comparison of Methods

PubMed Central

May-Collado, Laura J.; Agnarsson, Ingi

2011-01-01

Background Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. Methodology/Principal Findings A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all ‘high priority’ species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. Conclusions/Significance These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct—and thus ‘biodiverse’—species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders. PMID:21799899

Evolving effective behaviours to interact with tag-based populations

NASA Astrophysics Data System (ADS)

Yucel, Osman; Crawford, Chad; Sen, Sandip

2015-07-01

Tags and other characteristics, externally perceptible features that are consistent among groups of animals or humans, can be used by others to determine appropriate response strategies in societies. This usage of tags can be extended to artificial environments, where agents can significantly reduce cognitive effort spent on appropriate strategy choice and behaviour selection by reusing strategies for interacting with new partners based on their tags. Strategy selection mechanisms developed based on this idea have successfully evolved stable cooperation in games such as the Prisoner's Dilemma game but relies upon payoff sharing and matching methods that limit the applicability of the tag framework. Our goal is to develop a general classification and behaviour selection approach based on the tag framework. We propose and evaluate alternative tag matching and adaptation schemes for a new, incoming individual to select appropriate behaviour against any population member of an existing, stable society. Our proposed approach allows agents to evolve both the optimal tag for the environment as well as appropriate strategies for existing agent groups. We show that these mechanisms will allow for robust selection of optimal strategies by agents entering a stable society and analyse the various environments where this approach is effective.

Thermoregulatory strategy may shape immune investment in Drosophila melanogaster.

PubMed

Kutch, Ian C; Sevgili, Hasan; Wittman, Tyler; Fedorka, Kenneth M

2014-10-15

As temperatures change, insects alter the amount of melanin in their cuticle to improve thermoregulation. However, melanin is also central to insect immunity, suggesting that thermoregulatory strategy may indirectly impact immune defense by altering the abundance of melanin pathway components (a hypothesis we refer to as thermoregulatory-dependent immune investment). This may be the case in the cricket Allonemobius socius, where warm environments (both seasonal and geographical) produced crickets with lighter cuticles and increased pathogen susceptibility. Unfortunately, the potential for thermoregulatory strategy to influence insect immunity has not been widely explored. Here we address the relationships between temperature, thermoregulatory strategy and immunity in the fruit fly Drosophila melanogaster. To this end, flies from two separate Canadian populations were reared in either a summer- or autumn-like environment. Shortly after adult eclosion, flies were moved to a common environment where their cuticle color and susceptibility to a bacterial pathogen (Pseudomonas aeruginosa) were measured. As with A. socius, individuals from summer-like environments exhibited lighter cuticles and increased pathogen susceptibility, suggesting that the thermoregulatory-immunity relationship is evolutionarily conserved across the hemimetabolous and holometabolous clades. If global temperatures continue to rise as expected, then thermoregulation might play an important role in host infection and mortality rates in systems that provide critical ecosystem services (e.g. pollination), or influence the prevalence of insect-vectored disease (e.g. malaria). © 2014. Published by The Company of Biologists Ltd.

Achieving nitritation in a continuous moving bed biofilm reactor at different temperatures through ratio control.

PubMed

Bian, Wei; Zhang, Shuyan; Zhang, Yanzhuo; Li, Wenjing; Kan, Ruizhe; Wang, Wenxiao; Zheng, Zhaoming; Li, Jun

2017-02-01

A ratio control strategy was implemented in a continuous moving bed biofilm reactor (MBBR) to investigate the response to different temperatures. The control strategy was designed to maintain a constant ratio between dissolved oxygen (DO) and total ammonia nitrogen (TAN) concentrations. The results revealed that a stable nitritation in a biofilm reactor could be achieved via ratio control, which compensated the negative influence of low temperatures by stronger oxygen-limiting conditions. Even with a temperature as low as 6°C, stable nitritation could be achieved when the controlling ratio did not exceed 0.17. Oxygen-limiting conditions in the biofilm reactor were determined by the DO/TAN concentrations ratio, instead of the mere DO concentration. This ratio control strategy allowed the achievement of stable nitritation without complete wash-out of NOB from the reactor. Through the ratio control strategy full nitritation of sidestream wastewater was allowed; however, for mainstream wastewater, only partial nitritation was recommended. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration.

PubMed

LeBlanc, André; Michaud, Sarah A; Percy, Andrew J; Hardie, Darryl B; Yang, Juncong; Sinclair, Nicholas J; Proudfoot, Jillaine I; Pistawka, Adam; Smith, Derek S; Borchers, Christoph H

2017-07-07

When quantifying endogenous plasma proteins for fundamental and biomedical research - as well as for clinical applications - precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of the best calibration strategies, since no blank matrix is available. Consequently, several alternative calibration strategies are employed by different laboratories. In this study, these methods were compared to a new approach using two different stable isotope-labeled standard (SIS) peptide isotopologues for each endogenous peptide to be quantified, enabling an external calibration curve as well as the quality control samples to be prepared in pooled human plasma without interference from endogenous peptides. This strategy improves the analytical performance of the assay and enables the accuracy of the assay to be monitored, which can also facilitate method development and validation.

A Novel Hybrid Iron Regulation Network Combines Features from Pathogenic and Nonpathogenic Yeasts.

PubMed

Gerwien, Franziska; Safyan, Abu; Wisgott, Stephanie; Hille, Fabrice; Kaemmer, Philipp; Linde, Jörg; Brunke, Sascha; Kasper, Lydia; Hube, Bernhard

2016-10-18

Iron is an essential micronutrient for both pathogens and their hosts, which restrict iron availability during infections in an effort to prevent microbial growth. Successful human pathogens like the yeast Candida glabrata have thus developed effective iron acquisition strategies. Their regulation has been investigated well for some pathogenic fungi and in the model organism Saccharomyces cerevisiae, which employs an evolutionarily derived system. Here, we show that C. glabrata uses a regulation network largely consisting of components of the S. cerevisiae regulon but also of elements of other pathogenic fungi. Specifically, similarly to baker's yeast, Aft1 is the main positive regulator under iron starvation conditions, while Cth2 degrades mRNAs encoding iron-requiring enzymes. However, unlike the case with S. cerevisiae, a Sef1 ortholog is required for full growth under iron limitation conditions, making C. glabrata an evolutionary intermediate to SEF1-dependent fungal pathogens. Therefore, C. glabrata has evolved an iron homeostasis system which seems to be unique within the pathogenic fungi. The fungus Candida glabrata represents an evolutionarily close relative of the well-studied and benign baker's yeast and model organism Saccharomyces cerevisiae On the other hand, C. glabrata is an important opportunistic human pathogen causing both superficial and systemic infections. The ability to acquire trace metals, in particular, iron, and to tightly regulate this process during infection is considered an important virulence attribute of a variety of pathogens. Importantly, S. cerevisiae uses a highly derivative regulatory system distinct from those of other fungi. Until now, the regulatory mechanism of iron homeostasis in C. glabrata has been mostly unknown. Our study revealed a hybrid iron regulation network that is unique to C. glabrata and is placed at an evolutionary midpoint between those of S. cerevisiae and related fungal pathogens. We thereby show that, in the host, even a successful human pathogen can rely largely on a strategy normally found in nonpathogenic fungi from a terrestrial environment. Copyright © 2016 Gerwien et al.

Genetic variability of the stable fly assessed on a global scale using amplified fragment length polymorphism

USDA-ARS?s Scientific Manuscript database

The stable fly, Stomoxys calcitrans (L) (Diptera: Muscidae), is a blood-feeding, economically important pest of animals and humans worldwide. Improved management strategies are essential and their development would benefit from studies on genetic diversity of stable flies. Such research, especially ...

To brood or not to brood: Are marine invertebrates that protect their offspring more resilient to ocean acidification?

NASA Astrophysics Data System (ADS)

Lucey, Noelle Marie; Lombardi, Chiara; Demarchi, Lucia; Schulze, Anja; Gambi, Maria Cristina; Calosi, Piero

2015-07-01

Anthropogenic atmospheric carbon dioxide (CO2) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought to have largely deleterious effects on marine invertebrates, primarily impacting early life stages and consequently, their recruitment and species’ survival. Most research in this field has been limited to short-term, single-species and single-life stage studies, making it difficult to determine which taxa will be evolutionarily successful under OA conditions. We circumvent these limitations by relating the dominance and distribution of the known polychaete worm species living in a naturally acidic seawater vent system to their life history strategies. These data are coupled with breeding experiments, showing all dominant species in this natural system exhibit parental care. Our results provide evidence supporting the idea that long-term survival of marine species in acidic conditions is related to life history strategies where eggs are kept in protected maternal environments (brooders) or where larvae have no free swimming phases (direct developers). Our findings are the first to formally validate the hypothesis that species with life history strategies linked to parental care are more protected in an acidifying ocean compared to their relatives employing broadcast spawning and pelagic larval development.

G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structures in vitro and are unwound by the Pfh1 DNA helicase

PubMed Central

Wallgren, Marcus; Mohammad, Jani B.; Yan, Kok-Phen; Pourbozorgi-Langroudi, Parham; Ebrahimi, Mahsa; Sabouri, Nasim

2016-01-01

Certain guanine-rich sequences have an inherent propensity to form G-quadruplex (G4) structures. G4 structures are e.g. involved in telomere protection and gene regulation. However, they also constitute obstacles during replication if they remain unresolved. To overcome these threats to genome integrity, organisms harbor specialized G4 unwinding helicases. In Schizosaccharomyces pombe, one such candidate helicase is Pfh1, an evolutionarily conserved Pif1 homolog. Here, we addressed whether putative G4 sequences in S. pombe can adopt G4 structures and, if so, whether Pfh1 can resolve them. We tested two G4 sequences, derived from S. pombe ribosomal and telomeric DNA regions, and demonstrated that they form inter- and intramolecular G4 structures, respectively. Also, Pfh1 was enriched in vivo at the ribosomal G4 DNA and telomeric sites. The nuclear isoform of Pfh1 (nPfh1) unwound both types of structure, and although the G4-stabilizing compound Phen-DC3 significantly enhanced their stability, nPfh1 still resolved them efficiently. However, stable G4 structures significantly inhibited adenosine triphosphate hydrolysis by nPfh1. Because ribosomal and telomeric DNA contain putative G4 regions conserved from yeasts to humans, our studies support the important role of G4 structure formation in these regions and provide further evidence for a conserved role for Pif1 helicases in resolving G4 structures. PMID:27185885

Stable and efficient nitrogen-containing-carbon based electrocatalysts for reactions in energy conversion systems.

PubMed

Wang, Sicong; Teng, Zhenyuan; Wang, Chengyin; Wang, Guoxiu

2018-05-17

High activity and stability are crucial for practical electrocatalysts used for reactions in fuel cells, metal-air batteries and water electrolysis including ORR, HER, OER and oxidation reactions of formic acid and alcohols. N-C based electrocatalysts have shown promising prospects for catalyzing these reactions, however, there is no systematic review for strategies toward engineering active and stable N-C based electrocatalysts reported by far. Herein, a comprehensive comparison of recently reported N-C based electrocatalysts regarding both electrocatalytic activity and long-term stability is presented. In the first part of this review, relationships between electrocatalytic reactions and element selections for modifying N-C based materials are discussed. Afterwards, synthesis methods for N-C based electrocatalysts are summarized, and synthetic strategies for highly stable N-C based electrocatalysts are presented. Multiple tables containing data on crucial parameters for both electrocatalytic activity and stability are displayed in this review. Finally, constructing M-Nx moieties is proposed as the most promising engineering strategy for stable N-C based electrocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The timing of life history events in the presence of soft disturbances.

PubMed

Bertacchi, Daniela; Zucca, Fabio; Ambrosini, Roberto

2016-01-21

We study a model for the evolutionarily stable strategy (ESS) used by biological populations for choosing the time of life-history events, such as arrival from migration and breeding. In our model we account for both intra-species competition (early individuals have a competitive advantage) and a disturbance which strikes at a random time, killing a fraction 1-p of the population. Disturbances include spells of bad weather, such as freezing or heavily raining days. It has been shown by Iwasa and Levin (1995) that when the disturbance is so strong that it kills any individual present when it strikes (hard disturbance, p=0), then the ESS is a mixed strategy (individuals choose their arrival date in an interval of possible dates, according to a certain probability distribution). In this case, individuals wait for a certain time and afterwards start arriving (or breeding) every day. In this paper we explore a biologically more realistic situation whereby the disturbance kills only a fraction of the individuals (soft disturbance, p>0). We also remove some technical assumptions which Iwasa and Levin made on the distribution of the disturbance. We prove that the ESS is still a mixed choice of times, however with respect to the case of hard disturbance, a new phenomenon arises: whenever the disturbance is soft, if the competition is sufficiently strong, the waiting time disappears and a fraction of the population arrives at the earliest day possible, while the rest will arrive throughout the whole period during which the disturbance may occur. This means that under strong competition, the payoff of early arrival balances the increased risk of being killed by the disturbance. We study the behaviour of the ESS and of the average fitness of the population, depending on the parameters involved. We also investigate how the population may be affected by climate change: namely the occurrence of more extreme weather events, which may kill a larger fraction of the population, and time shifts of the distribution of the disturbance. We show how the ESS and the average fitness change under the new climate and discuss which is the impact of the new climate on a population that still follows the old strategy. In particular, we show that, at least under some conditions, extreme weather events imply a temporary decrease of the average fitness of the population due to an increased mortality. In addition, if the population adapts to the new climate, the population may have a larger fitness. Copyright © 2015 Elsevier Ltd. All rights reserved.

microRNA Therapeutics in Cancer - An Emerging Concept.

PubMed

Shah, Maitri Y; Ferrajoli, Alessandra; Sood, Anil K; Lopez-Berestein, Gabriel; Calin, George A

2016-10-01

MicroRNAs (miRNAs) are an evolutionarily conserved class of small, regulatory non-coding RNAs that negatively regulate protein coding gene and other non-coding transcripts expression. miRNAs have been established as master regulators of cellular processes, and they play a vital role in tumor initiation, progression and metastasis. Further, widespread deregulation of microRNAs have been reported in several cancers, with several microRNAs playing oncogenic and tumor suppressive roles. Based on these, miRNAs have emerged as promising therapeutic tools for cancer management. In this review, we have focused on the roles of miRNAs in tumorigenesis, the miRNA-based therapeutic strategies currently being evaluated for use in cancer, and the advantages and current challenges to their use in the clinic. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors[OPEN

PubMed Central

Venturelli, Sascha; Belz, Regina G.; Kämper, Andreas; Berger, Alexander; von Horn, Kyra; Wegner, André; Böcker, Alexander; Zabulon, Gérald; Barneche, Fredy; Lauer, Ulrich M.; Bitzer, Michael

2015-01-01

To secure their access to water, light, and nutrients, many plant species have developed allelopathic strategies to suppress competitors. To this end, they release into the rhizosphere phytotoxic substances that inhibit the germination and growth of neighbors. Despite the importance of allelopathy in shaping natural plant communities and for agricultural production, the underlying molecular mechanisms are largely unknown. Here, we report that allelochemicals derived from the common class of cyclic hydroxamic acid root exudates directly affect the chromatin-modifying machinery in Arabidopsis thaliana. These allelochemicals inhibit histone deacetylases both in vitro and in vivo and exert their activity through locus-specific alterations of histone acetylation and associated gene expression. Our multilevel analysis collectively shows how plant-plant interactions interfere with a fundamental cellular process, histone acetylation, by targeting an evolutionarily highly conserved class of enzymes. PMID:26530086

Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors

PubMed Central

Lakatos, Lóránt; Csorba, Tibor; Pantaleo, Vitantonio; Chapman, Elisabeth J; Carrington, James C; Liu, Yu-Ping; Dolja, Valerian V; Calvino, Lourdes Fernández; López-Moya, Juan José; Burgyán, József

2006-01-01

RNA silencing is an evolutionarily conserved system that functions as an antiviral mechanism in higher plants and insects. To counteract RNA silencing, viruses express silencing suppressors that interfere with both siRNA- and microRNA-guided silencing pathways. We used comparative in vitro and in vivo approaches to analyse the molecular mechanism of suppression by three well-studied silencing suppressors. We found that silencing suppressors p19, p21 and HC-Pro each inhibit the intermediate step of RNA silencing via binding to siRNAs, although the molecular features required for duplex siRNA binding differ among the three proteins. None of the suppressors affected the activity of preassembled RISC complexes. In contrast, each suppressor uniformly inhibited the siRNA-initiated RISC assembly pathway by preventing RNA silencing initiator complex formation. PMID:16724105

Thinking Evolutionarily About Obesity

PubMed Central

Genné-Bacon, Elizabeth A.

2014-01-01

Obesity, diabetes, and metabolic syndrome are growing worldwide health concerns, yet their causes are not fully understood. Research into the etiology of the obesity epidemic is highly influenced by our understanding of the evolutionary roots of metabolic control. For half a century, the thrifty gene hypothesis, which argues that obesity is an evolutionary adaptation for surviving periods of famine, has dominated the thinking on this topic. Obesity researchers are often not aware that there is, in fact, limited evidence to support the thrifty gene hypothesis and that alternative hypotheses have been suggested. This review presents evidence for and against the thrifty gene hypothesis and introduces readers to additional hypotheses for the evolutionary origins of the obesity epidemic. Because these alternate hypotheses imply significantly different strategies for research and clinical management of obesity, their consideration is critical to halting the spread of this epidemic. PMID:24910556

Advances in stable isotope assisted labeling strategies with information science.

PubMed

Kigawa, Takanori

2017-08-15

Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets. Various combinatorial selective labeling schemes have been developed as more sophisticated labeling strategies. In these strategies, amino acids are represented by combinations of SI labeled samples, rather than simply assigning one amino acid to one SI labeled sample as in the case of conventional amino acid-selective labeling. These strategies have proven to be useful for NMR analyses of difficult proteins, such as those in large complex systems, in living cells, attached or integrated into membranes, or with poor solubility. In this review, recent advances in stable isotope assisted labeling strategies will be discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Mechanisms and evolution of deceptive pollination in orchids.

PubMed

Jersáková, Jana; Johnson, Steven D; Kindlmann, Pavel

2006-05-01

The orchid family is renowned for its enormous diversity of pollination mechanisms and unusually high occurrence of non-rewarding flowers compared to other plant families. The mechanisms of deception in orchids include generalized food deception, food-deceptive floral mimicry, brood-site imitation, shelter imitation, pseudoantagonism, rendezvous attraction and sexual deception. Generalized food deception is the most common mechanism (reported in 38 genera) followed by sexual deception (18 genera). Floral deception in orchids has been intensively studied since Darwin, but the evolution of non-rewarding flowers still presents a major puzzle for evolutionary biology. The two principal hypotheses as to how deception could increase fitness in plants are (i) reallocation of resources associated with reward production to flowering and seed production, and (ii) higher levels of cross-pollination due to pollinators visiting fewer flowers on non-rewarding plants, resulting in more outcrossed progeny and more efficient pollen export. Biologists have also tried to explain why deception is overrepresented in the orchid family. These explanations include: (i) efficient removal and deposition of pollinaria from orchid flowers in a single pollinator visit, thus obviating the need for rewards to entice multiple visits from pollinators; (ii) efficient transport of orchid pollen, thus requiring less reward-induced pollinator constancy; (iii) low-density populations in many orchids, thus limiting the learning of associations of floral phenotypes and rewards by pollinators; (iv) packaging of pollen in pollinaria with limited carry-over from flower to flower, thus increasing the risks of geitonogamous self-pollination when pollinators visit many flowers on rewarding plants. All of these general and orchid-specific hypotheses are difficult to reconcile with the well-established pattern for rewardlessness to result in low pollinator visitation rates and consequently low levels of fruit production. Arguments that deception evolves because rewards are costly are particularly problematic in that small amounts of nectar are unlikely to have a significant effect on the energy budget of orchids, and because reproduction in orchids is often severely pollen-, rather than resource-limited. Several recent experimental studies have shown that deception promotes cross-pollination, but it remains unknown whether actual outcrossing rates are generally higher in deceptive orchids. Our review of the literature shows that there is currently no evidence that deceptive orchids carry higher levels of genetic load (an indirect measure of outcrossing rate) than their rewarding counterparts. Cross-pollination does, however, result in dramatic increases in seed quality in almost all orchids and has the potential to increase pollen export (by reducing pollen discounting). We suggest that floral deception is particularly beneficial, because of its promotion of outcrossing, when pollinators are abundant, but that when pollinators are consistently rare, selection may favour a nectar reward or a shift to autopollination. Given that nectar-rewardlessness is likely to have been the ancestral condition in orchids and yet is evolutionarily labile, more attention will need to be given to explanations as to why deception constitutes an 'evolutionarily stable strategy'.

An In Situ One-Pot Synthetic Approach towards Multivariate Zirconium MOFs.

PubMed

Sun, Yujia; Sun, Lixian; Feng, Dawei; Zhou, Hong-Cai

2016-05-23

Chemically highly stable MOFs incorporating multiple functionalities are of great interest for applications under harsh environments. Herein, we presented a facile one-pot synthetic strategy to incorporate multiple functionalities into stable Zr-MOFs from mixed ligands of different geometry and connectivity. Via our strategy, tetratopic tetrakis(4-carboxyphenyl)porphyrin (TCPP) ligands were successfully integrated into UiO-66 while maintaining the crystal structure, morphology, and ultrahigh chemical stability of UiO-66. The amount of incorporated TCPP is controllable. Through various combinations of BDC derivatives and TCPP, 49 MOFs with multiple functionalities were obtained. Among them, MOFs modified with FeTCPPCl were demonstrated to be catalytically active for the oxidation of ABTS. We anticipate our strategy to provide a facile route to introduce multiple functionalities into stable Zr-MOFs for a wide variety of potential applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vestibular cerebellum of thick-toed geckos (Chondrodactylus turnery GRAY, 1864) and C57/BL6N mice after the long-term space flight on the biosatellite BION-M1.

PubMed

Alexandra, Proshchina; Anastasia, Kharlamova; Valeriy, Barabanov; Victoria, Gulimova; Sergey, Saveliev

2017-01-01

The aim of this study was to estimate the effects of long-term space flights on neuronal and glial cells of the vestibular cerebellum of C57/BL6N mice and thick-toed geckos (Chondrodactylus turnery GRAY, 1864). The cerebella from 26 mice and 13 geckos were used in this study. Ten mice and five geckos were flown aboard the BION-M1 biosatellite. The other animals were used as controls. We used immunohistochemical techniques and classical histological method to reveal cell types in the vestibular cerebellum. Nonspecific pathomorphological changes in the Purkinje cells (such as chromatolysis, vacuolization and hyperchromatosis) were observed in the flight groups. However, these changes are reversible and were also found in some neurons in the control groups. In addition, as the vestibular cerebellum is an evolutionarily stable structure, thick-toed geckos may be a useful model for space flight studies on the vertebrate cerebellum. Copyright © 2016 Elsevier B.V. All rights reserved.

Managing neurobehavioral capability when social expediency trumps biological imperatives

PubMed Central

Spaeth, Andrea M.; Goel, Namni; Dinges, David F.

2013-01-01

Sleep, which is evolutionarily conserved across species, is a biological imperative that cannot be ignored or replaced. However, the percentage of habitually sleep-restricted adults has increased in recent decades. Extended work hours and commutes, shift work schedules, and television viewing are particularly potent social factors that influence sleep duration. Chronic partial sleep restriction, a product of these social expediencies, leads to the accumulation of sleep debt over time and consequently increases sleep propensity, decreases alertness, and impairs critical aspects of cognitive functioning. Significant interindividual variability in the neurobehavioral responses to sleep restriction exists—this variability is stable and phenotypic—suggesting a genetic basis. Identifying vulnerability to sleep loss is essential as many adults cannot accurately judge their level of impairment in response to sleep restriction. Indeed, the consequences of impaired performance and the lack of insight due to sleep loss can be catastrophic. In order to cope with the effects of social expediencies on biological imperatives, identification of biological (including genetic) and behavioral markers of sleep loss vulnerability as well as development of technological approaches for fatigue management are critical. PMID:22877676

Regulatory functions of SnRK1 in stress-responsive gene expression and in plant growth and development.

PubMed

Cho, Young-Hee; Hong, Jung-Woo; Kim, Eun-Chul; Yoo, Sang-Dong

2012-04-01

Sucrose-nonfermentation1-related protein kinase1 (SnRK1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. Efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. To overcome these limitations and study SnRK1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable expression in transgenic plants. We found that both rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) SnRK1 activities critically influence stress-inducible gene expression and the induction of stress tolerance. Genetic, molecular, and chromatin immunoprecipitation analyses further revealed that the nuclear SnRK1 modulated target gene transcription in a submergence-dependent manner. From early seedling development through late senescence, SnRK1 activities appeared to modulate developmental processes in the plants. Our findings offer insight into the regulatory functions of plant SnRK1 in stress-responsive gene regulation and in plant growth and development throughout the life cycle.

Complex interactions amongst N-cadherin, DLAR, and Liprin-α regulate Drosophila photoreceptor axon targeting

PubMed Central

Prakash, Saurabh; Maclendon, Helen; Dubreuil, Catherine I.; Ghose, Aurnab; Hwa, Jennifer; Dennehy, Kelly A.; Tomalty, Katharine M.H.; Clark, Kelsey; Van Vactor, David; Clandinin, Thomas R.

2009-01-01

The formation of stable adhesive contacts between pre- and post-synaptic neurons represents the initial step in synapse assembly. The cell adhesion molecule N-cadherin, the receptor tyrosine phosphatase DLAR, and the scaffolding molecule Liprin-α play critical, evolutionarily conserved roles in this process. However, how these proteins signal to the growth cone, and are themselves regulated, remains poorly understood. Using Drosophila photoreceptors (R cells) as a model, we evaluate genetic and physical interactions among these three proteins. We demonstrate that DLAR function in this context is independent of phosphatase activity, but requires interactions mediated by its intracellular domain. Genetic studies reveal both positive and, surprisingly, inhibitory interactions amongst all three genes. These observations are corroborated by biochemical studies demonstrating that DLAR physically associates via its phosphatase domain with N-cadherin in Drosophila embryos. Together, these data demonstrate that N-cadherin, DLAR, and Liprin-α function in a complex to regulate adhesive interactions between pre- and post-synaptic cells, and provide a novel mechanism for controlling the activity of liprin-α in the developing growth cone. PMID:19766621

Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation

PubMed Central

Zhang, Zhengjian; Boskovic, Zarko; Hussain, Mahmud M; Hu, Wenxin; Inouye, Carla; Kim, Han-Je; Abole, A Katherine; Doud, Mary K; Lewis, Timothy A; Koehler, Angela N; Schreiber, Stuart L; Tjian, Robert

2015-01-01

Intrinsically disordered proteins/regions (IDPs/IDRs) are proteins or peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. In this study, we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions. DOI: http://dx.doi.org/10.7554/eLife.07777.001 PMID:26314865

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

NASA Astrophysics Data System (ADS)

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-12-01

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics.

PubMed

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-12-22

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantification.

PubMed

Asara, John M; Zhang, Xiang; Zheng, Bin; Christofk, Heather H; Wu, Ning; Cantley, Lewis C

2006-01-01

Most proteomics approaches for relative quantification of protein expression use a combination of stable-isotope labeling and mass spectrometry. Traditionally, researchers have used difference gel electrophoresis (DIGE) from stained 1D and 2D gels for relative quantification. While differences in protein staining intensity can often be visualized, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. A method is presented for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using In-gel Stable-Isotope Labeling (ISIL). Proteins extracted from any source (tissue, cell line, immunoprecipitate, etc.), treated under two experimental conditions, are resolved in separate lanes by gel electrophoresis. The regions of interest (visualized by staining) are reacted separately with light versus heavy isotope-labeled reagents, and the gel slices are then mixed and digested with proteases. The resulting peptides are then analyzed by LC-MS to determine relative abundance of light/heavy isotope pairs and analyzed by LC-MS/MS for identification of sequence and modifications. The strategy compares well with other relative quantification strategies, and in silico calculations reveal its effectiveness as a global relative quantification strategy. An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification.

Well-conditioning global-local analysis using stable generalized/extended finite element method for linear elastic fracture mechanics

NASA Astrophysics Data System (ADS)

Malekan, Mohammad; Barros, Felicio Bruzzi

2016-11-01

Using the locally-enriched strategy to enrich a small/local part of the problem by generalized/extended finite element method (G/XFEM) leads to non-optimal convergence rate and ill-conditioning system of equations due to presence of blending elements. The local enrichment can be chosen from polynomial, singular, branch or numerical types. The so-called stable version of G/XFEM method provides a well-conditioning approach when only singular functions are used in the blending elements. This paper combines numeric enrichment functions obtained from global-local G/XFEM method with the polynomial enrichment along with a well-conditioning approach, stable G/XFEM, in order to show the robustness and effectiveness of the approach. In global-local G/XFEM, the enrichment functions are constructed numerically from the solution of a local problem. Furthermore, several enrichment strategies are adopted along with the global-local enrichment. The results obtained with these enrichments strategies are discussed in detail, considering convergence rate in strain energy, growth rate of condition number, and computational processing. Numerical experiments show that using geometrical enrichment along with stable G/XFEM for global-local strategy improves the convergence rate and the conditioning of the problem. In addition, results shows that using polynomial enrichment for global problem simultaneously with global-local enrichments lead to ill-conditioned system matrices and bad convergence rate.

Evolutionarily diverse SYP1 Qa-SNAREs jointly sustain pollen tube growth in Arabidopsis.

PubMed

Slane, Daniel; Reichardt, Ilka; El Kasmi, Farid; Bayer, Martin; Jürgens, Gerd

2017-11-01

Intracellular membrane fusion is effected by SNARE proteins that reside on adjacent membranes and form bridging trans-SNARE complexes. Qa-SNARE members of the Arabidopsis SYP1 family are involved in membrane fusion at the plasma membrane or during cell plate formation. Three SYP1 family members have been classified as pollen-specific as inferred from gene expression profiling studies, and two of them, SYP124 and SYP125, are confined to angiosperms. The SYP124 gene appears genetically unstable, whereas its sister gene SYP125 shows essentially no variation among Arabidopsis accessions. The third pollen-specific member SYP131 is sister to SYP132, which appears evolutionarily conserved in the plant lineage. Although evolutionarily diverse, the three SYP1 proteins are functionally overlapping in that only the triple mutant syp124 syp125 syp131 shows a specific and severe male gametophytic defect. While pollen development and germination appear normal, pollen tube growth is arrested during passage through the style. Our results suggest that angiosperm pollen tubes employ a combination of ancient and modern Qa-SNARE proteins to sustain their growth-promoting membrane dynamics during the reproductive process. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Mammalian monogamy is not controlled by a single gene

PubMed Central

Fink, Sabine; Excoffier, Laurent; Heckel, Gerald

2006-01-01

Complex social behavior in Microtus voles and other mammals has been postulated to be under the direct genetic control of a single locus: the arginine vasopressin 1a receptor (avpr1a) gene. Using a phylogenetic approach, we show that a repetitive element in the promoter region of avpr1a, which reportedly causes social monogamy, is actually widespread in nonmonogamous Microtus and other rodents. There was no evidence for intraspecific polymorphism in regard to the presence or absence of the repetitive element. Among 25 rodent species studied, the element was absent in only two closely related nonmonogamous species, indicating that this absence is certainly the result of an evolutionarily recent loss. Our analyses further demonstrate that the repetitive structures upstream of the avpr1a gene in humans and primates, which have been associated with social bonding, are evolutionarily distinct from those in rodents. Our evolutionary approach reveals that monogamy in rodents is not controlled by a single polymorphism in the promoter region of the avpr1a gene. We thus resolve the contradiction between the claims for an evolutionarily conserved genetic programming of social behavior in mammals and the vast evidence for highly complex and flexible mating systems. PMID:16832060

Imperfect information facilitates the evolution of reciprocity.

PubMed

Kurokawa, Shun

2016-06-01

The existence of cooperation demands explanation since cooperation is costly to the actor. Reciprocity has long been regarded as a potential explanatory mechanism for the existence of cooperation. Reciprocity is a mechanism wherein a cooperator responds to an opponent's behavior by switching his/her own behavior. Hence, a possible problematic case relevant to the theory of reciprocity evolution arises when the mechanism is such that the information regarding an opponent's behavior is imperfect. Although it has been confirmed also by previous theoretical studies that imperfect information interferes with the evolution of reciprocity, this argument is based on the assumption that there are no mistakes in behavior. And, a previous study presumed that it might be expected that when such mistakes occur, reciprocity can more readily evolve in the case of imperfect information than in the case of perfect information. The reason why the previous study considers so is that in the former case, reciprocators can miss defections incurred by other reciprocators' mistakes due to imperfect information, allowing cooperation to persist when such reciprocators meet. However, contrary to this expectation, the previous study has shown that even when mistakes occur, imperfect information interferes with the evolution of reciprocity. Nevertheless, the previous study assumed that payoffs are linear (i.e., that the effect of behavior is additive and there are no synergetic effects). In this study, we revisited the same problem but removed the assumption that payoffs are linear. We used evolutionarily stable strategy analysis to compare the condition for reciprocity to evolve when mistakes occur and information is imperfect with the condition for reciprocity to evolve when mistakes occur and information is perfect. Our study revealed that when payoffs are not linear, imperfect information can facilitate the evolution of reciprocity when mistakes occur; while when payoffs are linear, imperfect information disturbs the evolution of reciprocity even when mistakes occur. Imperfect information can encourage the evolution of cooperation. Copyright © 2016 Elsevier Inc. All rights reserved.

Conservative versus invasive stable ischemic heart disease management strategies: what do we plan to learn from the ISCHEMIA trial?

PubMed

Cheng-Torres, Kathleen A; Desai, Karan P; Sidhu, Mandeep S; Maron, David J; Boden, William E

2016-01-01

Over the past decade, landmark randomized clinical trials comparing initial management strategies in stable ischemic heart disease (SIHD) have demonstrated no significant reduction in 'hard' end points (all-cause mortality, cardiac death or myocardial infarction) with one strategy versus another. The main advantage derived from early revascularization is improved short-term quality of life. Nonetheless, questions remain regarding how best to manage SIHD patients, such as whether a high-risk subgroup can be identified that may experience a survival or myocardial infarction benefit from early revascularization, and if not, when should diagnostic catheterization and revascularization be performed. The International Study of Comparative Health Effectiveness with Medical and Invasive Approaches trial is designed to address these questions by randomizing SIHD patients with at least moderate ischemia to an initial conservative strategy of optimal medical therapy or an initial invasive strategy of optimal medical therapy plus cardiac catheterization and revascularization.

Hydrophobization and bioconjugation for enhanced siRNA delivery and targeting

PubMed Central

De Paula, Daniel; Bentley, M. Vitória L.B.; Mahato, Ram I.

2007-01-01

RNA interference (RNAi) is an evolutionarily conserved process by which double-stranded small interfering RNA (siRNA) induces sequence-specific, post-transcriptional gene silencing. Unlike other mRNA targeting strategies, RNAi takes advantage of the physiological gene silencing machinery. The potential use of siRNA as therapeutic agents has attracted great attention as a novel approach for treating severe and chronic diseases. RNAi can be achieved by either delivery of chemically synthesized siRNAs or endogenous expression of small hairpin RNA, siRNA, and microRNA (miRNA). However, the relatively high dose of siRNA required for gene silencing limits its therapeutic applications. This review discusses several strategies to improve therapeutic efficacy as well as to abrogate off-target effects and immunostimulation caused by siRNAs. There is an in-depth discussion on various issues related to the (1) mechanisms of RNAi, (2) methods of siRNA production, (3) barriers to RNAi-based therapies, (4) biodistribution, (5) design of siRNA molecules, (6) chemical modification and bioconjugation, (7) complex formation with lipids and polymers, (8) encapsulation into lipid particles, and (9) target specificity for enhanced therapeutic effectiveness. PMID:17329355

Evolving Strategies for Cancer and Autoimmunity: Back to the Future

PubMed Central

Lane, Peter J. L.; McConnell, Fiona M.; Anderson, Graham; Nawaf, Maher G.; Gaspal, Fabrina M.; Withers, David R.

2014-01-01

Although current thinking has focused on genetic variation between individuals and environmental influences as underpinning susceptibility to both autoimmunity and cancer, an alternative view is that human susceptibility to these diseases is a consequence of the way the immune system evolved. It is important to remember that the immunological genes that we inherit and the systems that they control were shaped by the drive for reproductive success rather than for individual survival. It is our view that human susceptibility to autoimmunity and cancer is the evolutionarily acceptable side effect of the immune adaptations that evolved in early placental mammals to accommodate a fundamental change in reproductive strategy. Studies of immune function in mammals show that high affinity antibodies and CD4 memory, along with its regulation, co-evolved with placentation. By dissection of the immunologically active genes and proteins that evolved to regulate this step change in the mammalian immune system, clues have emerged that may reveal ways of de-tuning both effector and regulatory arms of the immune system to abrogate autoimmune responses whilst preserving protection against infection. Paradoxically, it appears that such a detuned and deregulated immune system is much better equipped to mount anti-tumor immune responses against cancers. PMID:24782861

Structural symmetry in evolutionary games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-10-06

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. © 2015 The Author(s).

Structural symmetry in evolutionary games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be ‘evolutionarily equivalent’ in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term ‘homogeneous’ should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry. PMID:26423436

Psychopathy and instrumental aggression: Evolutionary, neurobiological, and legal perspectives.

PubMed

Glenn, Andrea L; Raine, Adrian

2009-01-01

In the study of aggression, psychopathy represents a disorder that is of particular interest because it often involves aggression which is premeditated, emotionless, and instrumental in nature; this is especially true for more serious types of offenses. Such instrumental aggression is aimed at achieving a goal (e.g., to obtain resources such as money, or to gain status). Unlike the primarily reactive aggression observed in other disorders, psychopaths appear to engage in aggressive acts for the purpose of benefiting themselves. This is especially interesting in light of arguments that psychopathy may represent an alternative life-history strategy that is evolutionarily adaptive; behaviors such as aggression, risk-taking, manipulation, and promiscuous sexual behavior observed in psychopathy may be means by which psychopaths gain advantage over others. Recent neurobiological research supports the idea that abnormalities in brain regions key to emotion and morality may allow psychopaths to pursue such a strategy-psychopaths may not experience the social emotions such as empathy, guilt, and remorse that typically discourage instrumentally aggressive acts, and may even experience pleasure when committing these acts. Findings from brain imaging studies of psychopaths may have important implications for the law.

Understanding spatio-temporal strategies of adult zebrafish exploration in the open field test.

PubMed

Stewart, Adam Michael; Gaikwad, Siddharth; Kyzar, Evan; Kalueff, Allan V

2012-04-27

Zebrafish (Danio rerio) are emerging as a useful model organism for neuroscience research. Mounting evidence suggests that various traditional rodent paradigms may be adapted for testing zebrafish behavior. The open field test is a popular rodent test of novelty exploration, recently applied to zebrafish research. To better understand fish novelty behavior, we exposed adult zebrafish to two different open field arenas for 30 min, assessing the amount and temporal patterning of their exploration. While (similar to rodents) zebrafish scale their locomotory activity depending on the size of the tank, the temporal patterning of their activity was independent of arena size. These observations strikingly parallel similar rodent behaviors, suggesting that spatio-temporal strategies of animal exploration may be evolutionarily conserved across vertebrate species. In addition, we found interesting oscillations in zebrafish exploration, with the per-minute distribution of their horizontal activity demonstrating sinusoidal-like patterns. While such patterning is not reported for rodents and other higher vertebrates, a nonlinear regression analysis confirmed the oscillation patterning of all assessed zebrafish behavioral endpoints in both open field arenas, revealing a potentially important aspect of novelty exploration in lower vertebrates. Copyright © 2012 Elsevier B.V. All rights reserved.

Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics

PubMed Central

Vu Manh, Thien-Phong; Elhmouzi-Younes, Jamila; Urien, Céline; Ruscanu, Suzana; Jouneau, Luc; Bourge, Mickaël; Moroldo, Marco; Foucras, Gilles; Salmon, Henri; Marty, Hélène; Quéré, Pascale; Bertho, Nicolas; Boudinot, Pierre; Dalod, Marc; Schwartz-Cornil, Isabelle

2015-01-01

Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey. PMID:26150816

YAP and the Hippo pathway in pediatric cancer.

PubMed

Ahmed, Atif A; Mohamed, Abdalla D; Gener, Melissa; Li, Weijie; Taboada, Eugenio

2017-01-01

The Hippo pathway is an important signaling pathway that controls cell proliferation and apoptosis. It is evolutionarily conserved in mammals and is stimulated by cell-cell contact, inhibiting cell proliferation in response to increased cell density. During early embryonic development, the Hippo signaling pathway regulates organ development and size, and its functions result in the coordinated balance between proliferation, apoptosis, and differentiation. Its principal effectors, YAP and TAZ, regulate signaling by the embryonic stem cells and determine cell fate and histogenesis. Dysfunction of this pathway contributes to cancer development in adults and children. Emerging studies have shed light on the upregulation of Hippo pathway members in several pediatric cancers and may offer prognostic information on rhabdomyosarcoma, osteosarcoma, Wilms tumor, neuroblastoma, medulloblastoma, and other brain gliomas. We review the results of such published studies and highlight the potential clinical application of this pathway in pediatric oncologic and pathologic studies. These studies support targeting this pathway as a novel treatment strategy.

Nematode and ciliate nasal infection in captive archey's frogs (Leiopelma archeyi).

PubMed

Shaw, Stephanie; Speare, Richard; Lynn, Denis H; Yeates, Gregor; Zhao, Zeng; Berger, Lee; Jakob-Hoff, Richard

2011-09-01

Archey's frogs (Leiopelma archeyi) are first on the list of evolutionarily distinct and globally endangered (EDGE) amphibians. Captive breeding is an important strategy for protection of the species, but programs are hampered by a lack of information on diseases present in wild and captive populations. Two novel nematodes (Koerneria sp. and Rhabditis sp.) were found separately in four captive Archey's frogs showing clinical signs of hemorrhagic purulent nasal discharge and weight loss. One of these frogs also had a novel protozoal infection (Tetrahymena) in the nasal cavity. Koerneria, Rhabditis, and Tetrahymena have not previously been reported in amphibians in New Zealand. One frog was treated successfully with oral moxidectin at 0.4 mg/kg for the nematode infection and topical metronidazole at 10 mg/kg for the protozoal infection. The clinical signs abated only after both infections were cleared. The second frog died before treatment could be established. The third and fourth frogs were found dead.

The Hippo pathway in hepatocellular carcinoma: Non-coding RNAs in action.

PubMed

Shi, Xuan; Zhu, Hai-Rong; Liu, Tao-Tao; Shen, Xi-Zhong; Zhu, Ji-Min

2017-08-01

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the third leading cause of cancer-related death worldwide. However, current strategies curing HCC are far from satisfaction. The Hippo pathway is an evolutionarily conserved tumor suppressive pathway that plays crucial roles in organ size control and tissue homeostasis. Its dysregulation is commonly observed in various types of cancer including HCC. Recently, the prominent role of non-coding RNAs in the Hippo pathway during normal development and neoplastic progression is also emerging in liver. Thus, further investigation into the regulatory network between non-coding RNAs and the Hippo pathway and their connections with HCC may provide new therapeutic avenues towards developing an effective preventative or perhaps curative treatment for HCC. Herein we summarize the role of non-coding RNAs in the Hippo pathway, with an emphasis on their contribution to carcinogenesis, diagnosis, treatment and prognosis of HCC. Copyright © 2017 Elsevier B.V. All rights reserved.

Oxidative stress-induced autophagy: Role in pulmonary toxicity

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

Malaviya, Rama; Laskin, Jeffrey D.; Laskin, Debra L., E-mail: laskin@eohsi.rutgers.edu

2014-03-01

Autophagy is an evolutionarily conserved catabolic process important in regulating the turnover of essential proteins and in elimination of damaged organelles and protein aggregates. Autophagy is observed in the lung in response to oxidative stress generated as a consequence of exposure to environmental toxicants. Whether autophagy plays role in promoting cell survival or cytotoxicity is unclear. In this article recent findings on oxidative stress-induced autophagy in the lung are reviewed; potential mechanisms initiating autophagy are also discussed. A better understanding of autophagy and its role in pulmonary toxicity may lead to the development of new strategies to treat lung injurymore » associated with oxidative stress. - Highlights: • Exposure to pulmonary toxicants is associated with oxidative stress. • Oxidative stress is known to induce autophagy. • Autophagy is upregulated in the lung following exposure to pulmonary toxicants. • Autophagy may be protective or pathogenic.« less

Ketone body metabolism and cardiovascular disease

PubMed Central

Cotter, David G.; Schugar, Rebecca C.

2013-01-01

Ketone bodies are metabolized through evolutionarily conserved pathways that support bioenergetic homeostasis, particularly in brain, heart, and skeletal muscle when carbohydrates are in short supply. The metabolism of ketone bodies interfaces with the tricarboxylic acid cycle, β-oxidation of fatty acids, de novo lipogenesis, sterol biosynthesis, glucose metabolism, the mitochondrial electron transport chain, hormonal signaling, intracellular signal transduction pathways, and the microbiome. Here we review the mechanisms through which ketone bodies are metabolized and how their signals are transmitted. We focus on the roles this metabolic pathway may play in cardiovascular disease states, the bioenergetic benefits of myocardial ketone body oxidation, and prospective interactions among ketone body metabolism, obesity, metabolic syndrome, and atherosclerosis. Ketone body metabolism is noninvasively quantifiable in humans and is responsive to nutritional interventions. Therefore, further investigation of this pathway in disease models and in humans may ultimately yield tailored diagnostic strategies and therapies for specific pathological states. PMID:23396451

Niche metabolism in parasitic protozoa

PubMed Central

Ginger, Michael L

2005-01-01

Complete or partial genome sequences have recently become available for several medically and evolutionarily important parasitic protozoa. Through the application of bioinformatics complete metabolic repertoires for these parasites can be predicted. For experimentally intractable parasites insight provided by metabolic maps generated in silico has been startling. At its more extreme end, such bioinformatics reckoning facilitated the discovery in some parasites of mitochondria remodelled beyond previous recognition, and the identification of a non-photosynthetic chloroplast relic in malarial parasites. However, for experimentally tractable parasites, mapping of the general metabolic terrain is only a first step in understanding how the parasite modulates its streamlined, yet still often puzzlingly complex, metabolism in order to complete life cycles within host, vector, or environment. This review provides a comparative overview and discussion of metabolic strategies used by several different parasitic protozoa in order to subvert and survive host defences, and illustrates how genomic data contribute to the elucidation of parasite metabolism. PMID:16553311

Equilibria, prudent compromises, and the "waiting" game.

PubMed

Sim, Kwang Mong

2005-08-01

While evaluation of many e-negotiation agents are carried out through empirical studies, this work supplements and complements existing literature by analyzing the problem of designing market-driven agents (MDAs) in terms of equilibrium points and stable strategies. MDAs are negotiation agents designed to make prudent compromises taking into account factors such as time preference, outside option, and rivalry. This work shows that 1) in a given market situation, an MDA negotiates optimally because it makes minimally sufficient concession, and 2) by modeling negotiation of MDAs as a game gamma of incomplete information, it is shown that the strategies adopted by MDAs are stable. In a bilateral negotiation, it is proven that the strategy pair of two MDAs forms a sequential equilibrium for gamma. In a multilateral negotiation, it is shown that the strategy profile of MDAs forms a market equilibrium for gamma.

The optimal imaging strategy for patients with stable chest pain: a cost-effectiveness analysis.

PubMed

Genders, Tessa S S; Petersen, Steffen E; Pugliese, Francesca; Dastidar, Amardeep G; Fleischmann, Kirsten E; Nieman, Koen; Hunink, M G Myriam

2015-04-07

The optimal imaging strategy for patients with stable chest pain is uncertain. To determine the cost-effectiveness of different imaging strategies for patients with stable chest pain. Microsimulation state-transition model. Published literature. 60-year-old patients with a low to intermediate probability of coronary artery disease (CAD). Lifetime. The United States, the United Kingdom, and the Netherlands. Coronary computed tomography (CT) angiography, cardiac stress magnetic resonance imaging, stress single-photon emission CT, and stress echocardiography. Lifetime costs, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios. The strategy that maximized QALYs and was cost-effective in the United States and the Netherlands began with coronary CT angiography, continued with cardiac stress imaging if angiography found at least 50% stenosis in at least 1 coronary artery, and ended with catheter-based coronary angiography if stress imaging induced ischemia of any severity. For U.K. men, the preferred strategy was optimal medical therapy without catheter-based coronary angiography if coronary CT angiography found only moderate CAD or stress imaging induced only mild ischemia. In these strategies, stress echocardiography was consistently more effective and less expensive than other stress imaging tests. For U.K. women, the optimal strategy was stress echocardiography followed by catheter-based coronary angiography if echocardiography induced mild or moderate ischemia. Results were sensitive to changes in the probability of CAD and assumptions about false-positive results. All cardiac stress imaging tests were assumed to be available. Exercise electrocardiography was included only in a sensitivity analysis. Differences in QALYs among strategies were small. Coronary CT angiography is a cost-effective triage test for 60-year-old patients who have nonacute chest pain and a low to intermediate probability of CAD. Erasmus University Medical Center.

Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

PubMed Central

2011-01-01

Background Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge Suberites domuncula, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme. Results We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues. Conclusions This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis. PMID:21457554

Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model.

PubMed

Martins, José; Pinto, Alberto

2017-04-01

We use the reinfection SIRI epidemiological model to analyze the impact of education programs and vaccine scares on individuals decisions to vaccinate or not. The presence of the reinfection provokes the novelty of the existence of three Nash equilibria for the same level of the morbidity relative risk instead of a single Nash equilibrium as occurs in the SIR model studied by Bauch and Earn (PNAS 101:13391-13394, 2004). The existence of three Nash equilibria, with two of them being evolutionary stable, introduces two scenarios with relevant and opposite features for the same level of the morbidity relative risk: the low-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a low probability; and the high-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a high probability. We introduce the evolutionary vaccination dynamics for the SIRI model and we prove that it is bistable. The bistability of the evolutionary dynamics indicates that the damage provoked by false scares on the vaccination perceived morbidity risks can be much higher and much more persistent than in the SIR model. Furthermore, the vaccination education programs to be efficient they need to implement a mechanism to suddenly increase the vaccination coverage level.

An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice.

PubMed

Chen, Jun; Gao, He; Zheng, Xiao-Ming; Jin, Mingna; Weng, Jian-Feng; Ma, Jin; Ren, Yulong; Zhou, Kunneng; Wang, Qi; Wang, Jie; Wang, Jiu-Lin; Zhang, Xin; Cheng, Zhijun; Wu, Chuanyin; Wang, Haiyang; Wan, Jian-Min

2015-08-01

Plant breeding relies on creation of novel allelic combinations for desired traits. Identification and utilization of beneficial alleles, rare alleles and evolutionarily conserved genes in the germplasm (referred to as 'hidden' genes) provide an effective approach to achieve this goal. Here we show that a chemically induced null mutation in an evolutionarily conserved gene, FUWA, alters multiple important agronomic traits in rice, including panicle architecture, grain shape and grain weight. FUWA encodes an NHL domain-containing protein, with preferential expression in the root meristem, shoot apical meristem and inflorescences, where it restricts excessive cell division. Sequence analysis revealed that FUWA has undergone a bottleneck effect, and become fixed in landraces and modern cultivars during domestication and breeding. We further confirm a highly conserved role of FUWA homologs in determining panicle architecture and grain development in rice, maize and sorghum through genetic transformation. Strikingly, knockdown of the FUWA transcription level by RNA interference results in an erect panicle and increased grain size in both indica and japonica genetic backgrounds. This study illustrates an approach to create new germplasm with improved agronomic traits for crop breeding by tapping into evolutionary conserved genes. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts

PubMed Central

Polačik, Matej; Smith, Carl; Honza, Marcel; Reichard, Martin

2018-01-01

Obligate brood parasites manipulate other species into raising their offspring. Avian and insect brood parasitic systems demonstrate how interacting species engage in reciprocal coevolutionary arms races through behavioral and morphological adaptations and counteradaptations. Mouthbrooding cichlid fishes are renowned for their remarkable evolutionary radiations and complex behaviors. In Lake Tanganyika, mouthbrooding cichlids are exploited by the only obligate nonavian vertebrate brood parasite, the cuckoo catfish Synodontis multipunctatus. We show that coevolutionary history and individual learning both have a major impact on the success of cuckoo catfish parasitism between coevolved sympatric and evolutionarily naïve allopatric cichlid species. The rate of cuckoo catfish parasitism in coevolved Tanganyikan hosts was 3 to 11 times lower than in evolutionarily naïve cichlids. Moreover, using experimental infections, we demonstrate that parasite egg rejection in sympatric hosts was much higher, leading to seven times greater parasite survival in evolutionarily naïve than sympatric hosts. However, a high rejection frequency of parasitic catfish eggs by coevolved sympatric hosts came at a cost of increased rejection of their own eggs. A significant cost of catfish parasitism was universal, except for coevolved sympatric cichlid species with previous experience of catfish parasitism, demonstrating that learning and individual experience both contribute to a successful host response. PMID:29732407

The evolutionarily conserved interaction between LC3 and p62 selectively mediates autophagy-dependent degradation of mutant huntingtin.

PubMed

Tung, Ying-Tsen; Hsu, Wen-Ming; Lee, Hsinyu; Huang, Wei-Pang; Liao, Yung-Feng

2010-07-01

Mammalian p62/sequestosome-1 protein binds to both LC3, the mammalian homologue of yeast Atg8, and polyubiquitinated cargo proteins destined to undergo autophagy-mediated degradation. We previously identified a cargo receptor-binding domain in Atg8 that is essential for its interaction with the cargo receptor Atg19 in selective autophagic processes in yeast. We, thus, sought to determine whether this interaction is evolutionally conserved from yeast to mammals. Using an amino acid replacement approach, we demonstrate that cells expressing mutant LC3 (LC3-K30D, LC3-K51A, or LC3-L53A) all exhibit defective lipidation of LC3, a disrupted LC3-p62 interaction, and impaired autophagic degradation of p62, suggesting that the p62-binding site of LC3 is localized within an evolutionarily conserved domain. Importantly, whereas cells expressing these LC3 mutants exhibited similar overall autophagic activity comparable to that of cells expressing wild-type LC3, autophagy-mediated clearance of the aggregation-prone mutant Huntingtin was defective in the mutant-expressing cells. Together, these results suggest that p62 directly binds to the evolutionarily conserved cargo receptor-binding domain of Atg8/LC3 and selectively mediates the clearance of mutant Huntingtin.

[Amphioxus ortholog of ECSIT, an evolutionarily conserved adaptor in the Toll and BMP signaling pathways].

PubMed

Lin, Y H; Zhang, W; Li, J W; Zhang, H W; Chen, D Y

2017-01-01

In vertebrates, evolutionarily conserved signaling intermediate in the Toll pathway (ECSIT) interacts with the TNF-receptor associated factor 6 (TRAF6) to regulate the processing of MEKK1, activate NF-κB, and also control BMP target genes. However, the role of ECSIT in invertebrates remains largely unexplored. We performed comparative investigations of the expression, gene structure, and phylogeny of ECSIT, Toll-like receptor (TLR), and Smad4 in the cephalochordate Branchiostoma belcheri. Phylogenetic analysis indicated that, in amphioxus, ECSIT, TLR, and Smad4 form independent clusters at the base of Chordate   clusters. Interestingly, overall gene structures were comparable to those in vertebrate orthologs. Transcripts of AmphiECSIT were detectable at the mid-neural stage, and continued to be expressed in the epithelium of the pharyngeal region at later stages. In adult animals, strong expression was observed in the nerve cord, endostyle, epithelial cells of the gut and wheel organ, genital membrane of the testis, and coelom and lymphoid cavities, what is highly similar to AmphiTLR and AmphiSmad4 expression patterns during development and in adult organisms. Our data suggests that ECSIT is evolutionarily conserved. Its amphioxus ortholog functions during embryonic development and as part of the innate immune system and may be involved in TLR/BMP signaling.

Evolutionarily Conserved Epitopes on Human Immunodeficiency Virus Type 1 (HIV-1) and Feline Immunodeficiency Virus Reverse Transcriptases Detected by HIV-1-Infected Subjects

PubMed Central

Sanou, Missa P.; Roff, Shannon R.; Mennella, Antony; Sleasman, John W.; Rathore, Mobeen H.; Levy, Jay A.

2013-01-01

Anti-human immunodeficiency virus (HIV) cytotoxic T lymphocyte (CTL)-associated epitopes, evolutionarily conserved on both HIV type 1 (HIV-1) and feline immunodeficiency virus (FIV) reverse transcriptases (RT), were identified using gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and carboxyfluorescein diacetate succinimide ester (CFSE) proliferation assays followed by CTL-associated cytotoxin analysis. The peripheral blood mononuclear cells (PBMC) or T cells from HIV-1-seropositive (HIV+) subjects were stimulated with overlapping RT peptide pools. The PBMC from the HIV+ subjects had more robust IFN-γ responses to the HIV-1 peptide pools than to the FIV peptide pools, except for peptide-pool F3. In contrast, much higher and more frequent CD8+ T-cell proliferation responses were observed with the FIV peptide pools than with the HIV peptide pools. HIV-1-seronegative subjects had no proliferation or IFN-γ responses to the HIV and FIV peptide pools. A total of 24% (40 of 166) of the IFN-γ responses to HIV pools and 43% (23 of 53) of the CD8+ T-cell proliferation responses also correlated to responses to their counterpart FIV pools. Thus, more evolutionarily conserved functional epitopes were identified by T-cell proliferation than by IFN-γ responses. In the HIV+ subjects, peptide-pool F3, but not the HIV H3 counterpart, induced the most IFN-γ and proliferation responses. These reactions to peptide-pool F3 were highly reproducible and persisted over the 1 to 2 years of testing. All five individual peptides and epitopes of peptide-pool F3 induced IFN-γ and/or proliferation responses in addition to inducing CTL-associated cytotoxin responses (perforin, granzyme A, granzyme B). The epitopes inducing polyfunctional T-cell activities were highly conserved among human, simian, feline, and ungulate lentiviruses, which indicated that these epitopes are evolutionarily conserved. These results suggest that FIV peptides could be used in an HIV-1 vaccine. PMID:23824804

Dietary vitamin K guidance: an effective strategy for stable control of oral anticoagulation?

USDA-ARS?s Scientific Manuscript database

Numerous factors have been identified as risk factors for instability of oral anticoagulation, including variability in vitamin K intake. However few studies have directly tested the feasibility of manipulating dietary vitamin K to achieve stable oral anticoagulation. Recent findings from a rando...

A hierarchy of strategies heroin-using mothers employ to reduce harm to their children.

PubMed

Richter, K P; Bammer, G

2000-12-01

The present paper explores strategies that drug-using women employ to protect their children from drug-related harm. Twenty-two mothers were recruited through word-of-mouth, field recruitment, and flyers. Semi-structured interviews were used to collect mother's views on parenting and heroin use. Analysis was conducted using a standard qualitative software package. A hierarchy of seven strategies was identified: (1) stop using; (2) go into treatment; (3) maintain a stable small habit; (4) shield children from drug-related activities; (5) keep the home environment stable, safe, and secure; (6) stay out of gaol; and, if the children's needs still cannot be met, (7) place them with a trusted caregiver and maintain as active a parental role as possible. These strategies, derived innovatively from mothers' experiences, provide progressive goals for treatment and can also serve as measures of success. In addition, they may determine how well children fare in drug-affected families.

Risky Business: An Analysis of Orange County's Investment Strategy.

ERIC Educational Resources Information Center

Augustine, John H.; Fairclough, Scott

1996-01-01

The investment strategy of Orange County (California), which led to insolvency of its investment pool, is analyzed and lessons applicable to institutions of higher education are examined. Focus is on two elements: leveraged investment strategy that depended on stable or declining interest rates, and a liquidity crisis. It is concluded that…

Intelligence and homosexuality.

PubMed

Kanazawa, Satoshi

2012-09-01

The origin of preferences and values is an unresolved theoretical problem in behavioural sciences. The Savanna-IQ Interaction Hypothesis, derived from the Savanna Principle and a theory of the evolution of general intelligence, suggests that more intelligent individuals are more likely to acquire and espouse evolutionarily novel preferences and values than less intelligent individuals, but general intelligence has no effect on the acquisition and espousal of evolutionarily familiar preferences and values. Ethnographies of traditional societies suggest that exclusively homosexual behaviour was probably rare in the ancestral environment, so the Hypothesis would predict that more intelligent individuals are more likely to identify themselves as homosexual and engage in homosexual behaviour. Analyses of three large, nationally representative samples (two of which are prospectively longitudinal) from two different nations confirm the prediction.

[Seasonal changes of steroid levels in blood plasma of three Phodopus species (Mammalia, Cricetinae)].

PubMed

Feoktistova, N Iu; Kropotkina, M V; Naĭĭdenko, S V

2010-01-01

Seasonal change of the base plasma level of testosterone and cortisol in males and progesterone, estradiol, and cortisol levels in females were analyzed in three Phodopus species: Ph. campbelli (Campbell's dwarf hamster), Ph. sungorus (Russian dwarf hamster), and Ph. roborovskii (Roborovski's dwarf hamster). Our results showed a significant difference in the seasonal plasma level of testosterone and cortisol in males and cortisol in females of all Phodopus species, though the rhythms of breeding activity were similar. The results are discussed in the context of adaptive differences between hormonal patterns of evolutionarily young species (Campbell's dwarf hamster and Russian dwarf hamster) and the evolutionarily old Roborovski's dwarf hamster, the phylogenic position of which is currently under discussion.

Dynamic Portfolio Strategy Using Clustering Approach

PubMed Central

Lu, Ya-Nan; Li, Sai-Ping; Jiang, Xiong-Fei; Zhong, Li-Xin; Qiu, Tian

2017-01-01

The problem of portfolio optimization is one of the most important issues in asset management. We here propose a new dynamic portfolio strategy based on the time-varying structures of MST networks in Chinese stock markets, where the market condition is further considered when using the optimal portfolios for investment. A portfolio strategy comprises two stages: First, select the portfolios by choosing central and peripheral stocks in the selection horizon using five topological parameters, namely degree, betweenness centrality, distance on degree criterion, distance on correlation criterion and distance on distance criterion. Second, use the portfolios for investment in the investment horizon. The optimal portfolio is chosen by comparing central and peripheral portfolios under different combinations of market conditions in the selection and investment horizons. Market conditions in our paper are identified by the ratios of the number of trading days with rising index to the total number of trading days, or the sum of the amplitudes of the trading days with rising index to the sum of the amplitudes of the total trading days. We find that central portfolios outperform peripheral portfolios when the market is under a drawup condition, or when the market is stable or drawup in the selection horizon and is under a stable condition in the investment horizon. We also find that peripheral portfolios gain more than central portfolios when the market is stable in the selection horizon and is drawdown in the investment horizon. Empirical tests are carried out based on the optimal portfolio strategy. Among all possible optimal portfolio strategies based on different parameters to select portfolios and different criteria to identify market conditions, 65% of our optimal portfolio strategies outperform the random strategy for the Shanghai A-Share market while the proportion is 70% for the Shenzhen A-Share market. PMID:28129333

Dynamic Portfolio Strategy Using Clustering Approach.

PubMed

Ren, Fei; Lu, Ya-Nan; Li, Sai-Ping; Jiang, Xiong-Fei; Zhong, Li-Xin; Qiu, Tian

2017-01-01

The problem of portfolio optimization is one of the most important issues in asset management. We here propose a new dynamic portfolio strategy based on the time-varying structures of MST networks in Chinese stock markets, where the market condition is further considered when using the optimal portfolios for investment. A portfolio strategy comprises two stages: First, select the portfolios by choosing central and peripheral stocks in the selection horizon using five topological parameters, namely degree, betweenness centrality, distance on degree criterion, distance on correlation criterion and distance on distance criterion. Second, use the portfolios for investment in the investment horizon. The optimal portfolio is chosen by comparing central and peripheral portfolios under different combinations of market conditions in the selection and investment horizons. Market conditions in our paper are identified by the ratios of the number of trading days with rising index to the total number of trading days, or the sum of the amplitudes of the trading days with rising index to the sum of the amplitudes of the total trading days. We find that central portfolios outperform peripheral portfolios when the market is under a drawup condition, or when the market is stable or drawup in the selection horizon and is under a stable condition in the investment horizon. We also find that peripheral portfolios gain more than central portfolios when the market is stable in the selection horizon and is drawdown in the investment horizon. Empirical tests are carried out based on the optimal portfolio strategy. Among all possible optimal portfolio strategies based on different parameters to select portfolios and different criteria to identify market conditions, 65% of our optimal portfolio strategies outperform the random strategy for the Shanghai A-Share market while the proportion is 70% for the Shenzhen A-Share market.

Microbial competition in porous environments can select against rapid biofilm growth

PubMed Central

Coyte, Katharine Z.; Tabuteau, Hervé; Gaffney, Eamonn A.; Durham, William M.

2017-01-01

Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow–biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live. PMID:28007984

Reciprocal immune benefit based on complementary production of antibiotics by the leech Hirudo verbana and its gut symbiont Aeromonas veronii.

PubMed

Tasiemski, Aurélie; Massol, François; Cuvillier-Hot, Virginie; Boidin-Wichlacz, Céline; Roger, Emmanuel; Rodet, Franck; Fournier, Isabelle; Thomas, Frédéric; Salzet, Michel

2015-12-04

The medicinal leech has established a long-term mutualistic association with Aeromonas veronii, a versatile bacterium which can also display free-living waterborne and fish- or human-pathogenic lifestyles. Here, we investigated the role of antibiotics in the dynamics of interaction between the leech and its gut symbiont Aeromonas. By combining biochemical and molecular approaches, we isolated and identified for the first time the antimicrobial peptides (AMPs) produced by the leech digestive tract and by its symbiont Aeromonas. Immunohistochemistry data and PCR analyses evidenced that leech AMP genes are induced in the gut epithelial cells when Aeromonas load is low (starved animals), while repressed when Aeromonas abundance is the highest (post blood feeding). The asynchronous production of AMPs by both partners suggests that these antibiotic substances (i) provide them with reciprocal protection against invasive bacteria and (ii) contribute to the unusual simplicity of the gut microflora of the leech. This immune benefit substantially reinforces the evidence of an evolutionarily stable association between H. verbana and A. veronii. Altogether these data may provide insights into the processes making the association with an Aeromonas species in the digestive tract either deleterious or beneficial.

Learning dynamics explains human behaviour in prisoner's dilemma on networks.

PubMed

Cimini, Giulio; Sánchez, Angel

2014-05-06

Cooperative behaviour lies at the very basis of human societies, yet its evolutionary origin remains a key unsolved puzzle. Whereas reciprocity or conditional cooperation is one of the most prominent mechanisms proposed to explain the emergence of cooperation in social dilemmas, recent experimental findings on networked Prisoner's Dilemma games suggest that conditional cooperation also depends on the previous action of the player-namely on the 'mood' in which the player is currently in. Roughly, a majority of people behave as conditional cooperators if they cooperated in the past, whereas they ignore the context and free ride with high probability if they did not. However, the ultimate origin of this behaviour represents a conundrum itself. Here, we aim specifically to provide an evolutionary explanation of moody conditional cooperation (MCC). To this end, we perform an extensive analysis of different evolutionary dynamics for players' behavioural traits-ranging from standard processes used in game theory based on pay-off comparison to others that include non-economic or social factors. Our results show that only a dynamic built upon reinforcement learning is able to give rise to evolutionarily stable MCC, and at the end to reproduce the human behaviours observed in the experiments.

Selection on skewed characters and the paradox of stasis

PubMed Central

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

2018-01-01

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 modelling 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 samples size. 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. PMID:28921508

Evolution of optimal Hill coefficients in nonlinear public goods games.

PubMed

Archetti, Marco; Scheuring, István

2016-10-07

In evolutionary game theory, the effect of public goods like diffusible molecules has been modelled using linear, concave, sigmoid and step functions. The observation that biological systems are often sigmoid input-output functions, as described by the Hill equation, suggests that a sigmoid function is more realistic. The Michaelis-Menten model of enzyme kinetics, however, predicts a concave function, and while mechanistic explanations of sigmoid kinetics exist, we lack an adaptive explanation: what is the evolutionary advantage of a sigmoid benefit function? We analyse public goods games in which the shape of the benefit function can evolve, in order to determine the optimal and evolutionarily stable Hill coefficients. We find that, while the dynamics depends on whether output is controlled at the level of the individual or the population, intermediate or high Hill coefficients often evolve, leading to sigmoid input-output functions that for some parameters are so steep to resemble a step function (an on-off switch). Our results suggest that, even when the shape of the benefit function is unknown, biological public goods should be modelled using a sigmoid or step function rather than a linear or concave function. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contingent movement and cooperation evolve under generalized reciprocity

PubMed Central

Hamilton, Ian M; Taborsky, Michael

2005-01-01

How cooperation and altruism among non-relatives can persist in the face of cheating remains a key puzzle in evolutionary biology. Although mechanisms such as direct and indirect reciprocity and limited movement have been put forward to explain such cooperation, they cannot explain cooperation among unfamiliar, highly mobile individuals. Here we show that cooperation may be evolutionarily stable if decisions taken to cooperate and to change group membership are both dependent on anonymous social experience (generalized reciprocity). We find that a win–stay, lose–shift rule (where shifting is either moving away from the group or changing tactics within the group after receiving defection) evolves in evolutionary simulations when group leaving is moderately costly (i.e. the current payoff to being alone is low, but still higher than that in a mutually defecting group, and new groups are rarely encountered). This leads to the establishment of widespread cooperation in the population. If the costs of group leaving are reduced, a similar group-leaving rule evolves in association with cooperation in pairs and exploitation of larger anonymous groups. We emphasize that mechanisms of assortment within populations are often behavioural decisions and should not be considered independently of the evolution of cooperation. PMID:16191638

Improved Compressive Sensing of Natural Scenes Using Localized Random Sampling

PubMed Central

Barranca, Victor J.; Kovačič, Gregor; Zhou, Douglas; Cai, David

2016-01-01

Compressive sensing (CS) theory demonstrates that by using uniformly-random sampling, rather than uniformly-spaced sampling, higher quality image reconstructions are often achievable. Considering that the structure of sampling protocols has such a profound impact on the quality of image reconstructions, we formulate a new sampling scheme motivated by physiological receptive field structure, localized random sampling, which yields significantly improved CS image reconstructions. For each set of localized image measurements, our sampling method first randomly selects an image pixel and then measures its nearby pixels with probability depending on their distance from the initially selected pixel. We compare the uniformly-random and localized random sampling methods over a large space of sampling parameters, and show that, for the optimal parameter choices, higher quality image reconstructions can be consistently obtained by using localized random sampling. In addition, we argue that the localized random CS optimal parameter choice is stable with respect to diverse natural images, and scales with the number of samples used for reconstruction. We expect that the localized random sampling protocol helps to explain the evolutionarily advantageous nature of receptive field structure in visual systems and suggests several future research areas in CS theory and its application to brain imaging. PMID:27555464

MISTIC2: comprehensive server to study coevolution in protein families.

PubMed

Colell, Eloy A; Iserte, Javier A; Simonetti, Franco L; Marino-Buslje, Cristina

2018-06-14

Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for structurally or functionally important sites. MISTIC is a server designed to assist users to calculate covariation in protein families and provide them with an interactive tool to visualize the results. Here, we present MISTIC2, an update to the previous server, that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA). The results visualization framework has been reworked for improved performance, compatibility and user experience. It includes a circos representation of the information contained in the alignment, an interactive covariation network, a 3D structure viewer and a sequence logo. Others components provide additional information such as residue annotations, a roc curve for assessing contact prediction, data tables and different ways of filtering the data and exporting figures. Comparison of different methods is easily done and scores combination is also possible. A newly implemented web service allows users to access MISTIC2 programmatically using an API to calculate covariation and retrieve results. MISTIC2 is available at: https://mistic2.leloir.org.ar.

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

PubMed Central

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-01-01

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains. PMID:26691589

Sexual conflict over parental investment in repeated bouts: negotiation reduces overall care.

PubMed

Lessells, C M; McNamara, John M

2012-04-22

Understanding the evolution of parental care is complicated by the occurrence of evolutionary conflicts of interest within the family, variation in the quality and state of family members, and repeated bouts of investment in a family of offspring. As a result, family members are expected to negotiate over care. We present a model for the resolution of sexual conflict in which parents negotiate over repeated bouts of care. Negotiation is mediated by parents deciding at the start of each bout how much care to give on the basis of the state (mass) of offspring, which reflects the amount of care previously received. The evolutionarily stable pattern of care depends on whether the parents care together for the whole family, or each cares alone for part of the divided family. When they care together, they provide less care in the first bout, more in the last bout, and less care overall, resulting in lower parental and offspring fitness. Our results emphasize that negotiation over parental care may occur as a means of avoiding exploitation owing to sexual conflict, even in the absence of variation in the quality of either sex of parent, and lead to a reduction in fitness.

Increased calcium absorption from synthetic stable amorphous calcium carbonate: Double-blind randomized crossover clinical trial in post-menopausal women

USDA-ARS?s Scientific Manuscript database

Calcium supplementation is a widely recognized strategy for achieving adequate calcium intake. We designed this blinded, randomized, crossover interventional trial to compare the bioavailability of a new stable synthetic amorphous calcium carbonate (ACC) with that of crystalline calcium carbonate (C...

Novel approaches using Push-Pull strategy for stable fly control

USDA-ARS?s Scientific Manuscript database

The stable fly, Stomoxys calcitrans, has been considered as the most important insect pest of cattle in the United States. The negative impacts of biting result in significant weight loss and milk production, which attribute to huge economic losses in cattle industry. The control of this pest heavil...

Sustaining high-energy orbits of bi-stable energy harvesters by attractor selection

NASA Astrophysics Data System (ADS)

Udani, Janav P.; Arrieta, Andres F.

2017-11-01

Nonlinear energy harvesters have the potential to efficiently convert energy over a wide frequency range; however, difficulties in attaining and sustaining high-energy oscillations restrict their applicability in practical scenarios. In this letter, we propose an actuation methodology to switch the state of bi-stable harvesters from the low-energy intra-well configuration to the coexisting high-energy inter-well configuration by controlled phase shift perturbations. The strategy is designed to introduce a change in the system state without creating distinct metastable attractors by exploiting the basins of attraction of the coexisting stable attractors. Experimental results indicate that the proposed switching strategy yields a significant improvement in energy transduction capabilities, is highly economical, enabling the rapid recovery of energy spent in the disturbance, and can be practically implemented with widely used low-strain piezoelectric transducers.

Evolution with Reinforcement Learning in Negotiation

PubMed Central

Zou, Yi; Zhan, Wenjie; Shao, Yuan

2014-01-01

Adaptive behavior depends less on the details of the negotiation process and makes more robust predictions in the long term as compared to in the short term. However, the extant literature on population dynamics for behavior adjustment has only examined the current situation. To offset this limitation, we propose a synergy of evolutionary algorithm and reinforcement learning to investigate long-term collective performance and strategy evolution. The model adopts reinforcement learning with a tradeoff between historical and current information to make decisions when the strategies of agents evolve through repeated interactions. The results demonstrate that the strategies in populations converge to stable states, and the agents gradually form steady negotiation habits. Agents that adopt reinforcement learning perform better in payoff, fairness, and stableness than their counterparts using classic evolutionary algorithm. PMID:25048108

Evolution with reinforcement learning in negotiation.

PubMed

Zou, Yi; Zhan, Wenjie; Shao, Yuan

2014-01-01

Adaptive behavior depends less on the details of the negotiation process and makes more robust predictions in the long term as compared to in the short term. However, the extant literature on population dynamics for behavior adjustment has only examined the current situation. To offset this limitation, we propose a synergy of evolutionary algorithm and reinforcement learning to investigate long-term collective performance and strategy evolution. The model adopts reinforcement learning with a tradeoff between historical and current information to make decisions when the strategies of agents evolve through repeated interactions. The results demonstrate that the strategies in populations converge to stable states, and the agents gradually form steady negotiation habits. Agents that adopt reinforcement learning perform better in payoff, fairness, and stableness than their counterparts using classic evolutionary algorithm.

Selection of energy source and evolutionary stable strategies for power plants under financial intervention of government

NASA Astrophysics Data System (ADS)

Hafezalkotob, Ashkan; Mahmoudi, Reza

2017-09-01

Currently, many socially responsible governments adopt economic incentives and deterrents to manage environmental impacts of electricity suppliers. Considering the Stackelberg leadership of the government, the government's role in the competition of power plants in an electricity market is investigated. A one-population evolutionary game model of power plants is developed to study how their production strategy depends on tariffs levied by the government. We establish that a unique evolutionary stable strategy (ESS) for the population exists. Numerical examples demonstrate that revenue maximization and environment protection policies of the government significantly affect the production ESS of competitive power plants. The results reveal that the government can introduce a green energy source as an ESS of the competitive power plants by imposing appropriate tariffs.

Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity.

PubMed

Edwards, David P; Gilroy, James J; Thomas, Gavin H; Uribe, Claudia A Medina; Haugaasen, Torbjørn

2015-09-21

The conversion of natural habitats to farmland is a major driver of the global extinction crisis. Two strategies are promoted to mitigate the impacts of agricultural expansion on biodiversity: land sharing integrates wildlife-friendly habitats within farmland landscapes, and land sparing intensifies farming to allow the offset of natural reserves. A key question is which strategy would protect the most phylogenetic diversity--the total evolutionary history shared across all species within a community. Conserving phylogenetic diversity decreases the chance of losing unique phenotypic and ecological traits and provides benefits for ecosystem function and stability. Focusing on birds in the threatened Chocó-Andes hotspot of endemism, we tested the relative benefits of each strategy for retaining phylogenetic diversity in tropical cloud forest landscapes threatened by cattle pastures. Using landscape simulations, we find that land sharing would protect lower community-level phylogenetic diversity than land sparing and that with increasing distance from forest (from 500 to >1,500 m), land sharing is increasingly inferior to land sparing. Isolation from forest also leads to the loss of more evolutionarily distinct species from communities within land-sharing landscapes, which can be avoided with effective land sparing. Land-sharing policies that promote the integration of small-scale wildlife-friendly habitats might be of limited benefit without the simultaneous protection of larger blocks of natural habitat, which is most likely to be achieved via land-sparing measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Expression and characterization of an antifreeze protein from the perennial rye grass, Lolium perenne.

PubMed

Lauersen, Kyle J; Brown, Alan; Middleton, Adam; Davies, Peter L; Walker, Virginia K

2011-06-01

Antifreeze proteins (AFP) are an evolutionarily diverse class of stress response products best known in certain metazoans that adopt a freeze-avoidance survival strategy. The perennial ryegrass, Lolium perenne (Lp), cannot avoid winter temperatures below the crystallization point and is thought to use its LpAFP in a freeze-tolerant strategy. In order to examine properties of LpAFP in relation to L. perenne's life history, cDNA cloning, recombinant protein characterization, ice-binding activities, gene copy number, and expression responses to low temperature were examined. Transcripts, encoded by only a few gene copies, appeared to increase in abundance after diploid plants were transferred to 4°C for 1-2 days, and in parallel with the ice recrystallization inhibition activities. Circular dichroism spectra of recombinant LpAFP showed three clear folding transition temperatures including one between 10 and 15°C, suggesting to us that folding modifications of the secreted AFP could allow the targeted degradation of the protein in planta when temperatures increase. Although LpAFP showed low thermal hysteresis activity and partitioning into ice, it was similar to AFPs from freeze-avoiding organisms in other respects. Therefore, the type of low temperature resistance strategy adopted by a particular species may not depend on the type of AFP. The independence of AFP sequence and life-history has practical implications for the development of genetically-modified crops with enhanced freeze tolerance. Copyright © 2011 Elsevier Inc. All rights reserved.

''Illusion of control'' in Time-Horizon Minority and Parrondo Games

NASA Astrophysics Data System (ADS)

Satinover, J. B.; Sornette, D.

2007-12-01

Human beings like to believe they are in control of their destiny. This ubiquitous trait seems to increase motivation and persistence, and is probably evolutionarily adaptive [J.D. Taylor, S.E. Brown, Psych. Bull. 103, 193 (1988); A. Bandura, Self-efficacy: the exercise of control (WH Freeman, New York, 1997)]. But how good really is our ability to control? How successful is our track record in these areas? There is little understanding of when and under what circumstances we may over-estimate [E. Langer, J. Pers. Soc. Psych. 7, 185 (1975)] or even lose our ability to control and optimize outcomes, especially when they are the result of aggregations of individual optimization processes. Here, we demonstrate analytically using the theory of Markov Chains and by numerical simulations in two classes of games, the Time-Horizon Minority Game [M.L. Hart, P. Jefferies, N.F. Johnson, Phys. A 311, 275 (2002)] and the Parrondo Game [J.M.R. Parrondo, G.P. Harmer, D. Abbott, Phys. Rev. Lett. 85, 5226 (2000); J.M.R. Parrondo, How to cheat a bad mathematician (ISI, Italy, 1996)], that agents who optimize their strategy based on past information may actually perform worse than non-optimizing agents. In other words, low-entropy (more informative) strategies under-perform high-entropy (or random) strategies. This provides a precise definition of the “illusion of control” in certain set-ups a priori defined to emphasize the importance of optimization.

Versatile Synthesis of Stable, Functional Polypeptides via Reaction with Epoxides.

PubMed

Gharakhanian, Eric G; Deming, Timothy J

2015-06-08

Methodology was developed for efficient alkylation of methionine residues using epoxides as a general strategy to introduce a wide range of functional groups onto polypeptides. Use of a spacer between epoxide and functional groups further allowed addition of sterically demanding functionalities. Contrary to other methods to alkylate methionine residues, epoxide alkylations allow the reactions to be conducted in wet protic media and give sulfonium products that are stable against dealkylation. These functionalizations are notable since they are chemoselective, utilize stable and readily available epoxides, and allow facile incorporation of an unprecedented range of functional groups onto simple polypeptides using stable linkages.

Learning Strategies Assessed by Journal Writing: Prediction of Learning Outcomes by Quantity, Quality, and Combinations of Learning Strategies

ERIC Educational Resources Information Center

Glogger, Inga; Schwonke, Rolf; Holzapfel, Lars; Nuckles, Matthias; Renkl, Alexander

2012-01-01

Recently, there have been efforts to rethink assessment. Instead of informing about (relatively stable) learner characteristics, assessment should assist instruction by looking at the learning process, facilitating feedback about what students' next step in learning could be. Similarly, new forms of strategy assessment aim at capturing…

Mind the gap... in intelligence: re-examining the relationship between inequality and health.

PubMed

Kanazawa, Satoshi

2006-11-01

Wilkinson contends that economic inequality reduces the health and life expectancy of the whole population but his argument does not make sense within its own evolutionary framework. Recent evolutionary psychological theory suggests that the human brain, adapted to the ancestral environment, has difficulty comprehending and dealing with entities and situations that did not exist in the ancestral environment and that general intelligence evolved as a domain-specific adaptation to solve evolutionarily novel problems. Since most dangers to health in the contemporary society are evolutionarily novel, it follows that more intelligent individuals are better able to recognize and deal with such dangers and live longer. Consistent with the theory, the macro-level analyses show that income inequality and economic development have no effect on life expectancy at birth, infant mortality and age-specific mortality net of average intelligence quotient (IQ) in 126 countries. They also show that an average IQ has a very large and significant effect on population health but not in the evolutionarily familiar sub-Saharan Africa. At the micro level, the General Social Survey data show that, while both income and intelligence have independent positive effects on self-reported health, intelligence has a stronger effect than income. The data collectively suggest that individuals in wealthier and more egalitarian societies live longer and stay healthier, not because they are wealthier or more egalitarian but because they are more intelligent.

The relative roles of cultural drift and acoustic adaptation in shaping syllable repertoires of island bird populations change with time since colonization.

PubMed

Potvin, Dominique A; Clegg, Sonya M

2015-02-01

In birds, song divergence often precedes and facilitates divergence of other traits. We assessed the relative roles of cultural drift, innovation, and acoustic adaptation in divergence of island bird dialects, using silvereyes (Zosterops lateralis). In recently colonized populations, syllable diversity was not significantly lower than source populations, shared syllables between populations decreased with increasing number of founder events, and dialect variation displayed contributions from both habitat features and drift. The breadth of multivariate space occupied by recently colonized Z. l. lateralis populations was comparable to evolutionarily old forms that have diverged over thousands to hundreds of thousands of years. In evolutionarily old subspecies, syllable diversity was comparable to the mainland and the amount of variation in syllable composition explained by habitat features increased by two- to threefold compared to recently colonized populations. Together these results suggest that cultural drift influences syllable repertoires in recently colonized populations, but innovation likely counters syllable loss from colonization. In evolutionarily older populations, the influence of acoustic adaptation increases, possibly favoring a high diversity of syllables. These results suggest that the relative importance of cultural drift and acoustic adaptation changes with time since colonization in island bird populations, highlighting the value of considering multiple mechanisms and timescale of divergence when investigating island song divergence. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria

PubMed Central

2013-01-01

Background As one of the most dominant bacterial groups on Earth, cyanobacteria play a pivotal role in the global carbon cycling and the Earth atmosphere composition. Understanding their molecular responses to environmental perturbations has important scientific and environmental values. Since important biological processes or networks are often evolutionarily conserved, the cross-species transcriptional network analysis offers a useful strategy to decipher conserved and species-specific transcriptional mechanisms that cells utilize to deal with various biotic and abiotic disturbances, and it will eventually lead to a better understanding of associated adaptation and regulatory networks. Results In this study, the Weighted Gene Co-expression Network Analysis (WGCNA) approach was used to establish transcriptional networks for four important cyanobacteria species under metal stress, including iron depletion and high copper conditions. Cross-species network comparison led to discovery of several core response modules and genes possibly essential to metal stress, as well as species-specific hub genes for metal stresses in different cyanobacteria species, shedding light on survival strategies of cyanobacteria responding to different environmental perturbations. Conclusions The WGCNA analysis demonstrated that the application of cross-species transcriptional network analysis will lead to novel insights to molecular response to environmental changes which will otherwise not be achieved by analyzing data from a single species. PMID:23421563

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

PubMed Central

Leininger, Elizabeth C.; Kelley, Darcy B.

2013-01-01

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated  Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors. PMID:23407829

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution

PubMed Central

Price, Christopher T. D.; Richards, Ashley M.; Von Dwingelo, Juanita E.; Samara, Hala A.; Kwaik, Yousef Abu

2013-01-01

Summary Legionella pneumophila, the causative agent of Legionnaires’ disease, invades and proliferates within a diverse range of free-living amoeba in the environment but upon transmission to humans the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. L. pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. PMID:24112119

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls.

PubMed

Leininger, Elizabeth C; Kelley, Darcy B

2013-04-07

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors.

SLEEPLESS is a bi-functional regulator of excitability and cholinergic synaptic transmission

PubMed Central

Wu, Meilin; Robinson, James E.; Joiner, William J.

2014-01-01

Summary Background Although sleep is conserved throughout evolution, the molecular basis of its control is still largely a mystery. We previously showed that the quiver/sleepless (qvr/sss) gene encodes a membrane-tethered protein that is required for normal sleep in Drosophila. SLEEPLESS (SSS) protein functions, at least in part, by upregulating the levels and open probability of Shaker (Sh) potassium channels to suppress neuronal excitability and enable sleep. Consistent with this proposed mechanism, loss-of-function mutations in Sh phenocopy qvr/sss null mutants. However, sleep is more genetically modifiable in Sh than in qvr/sss mutants, suggesting that sss may regulate additional molecules to influence sleep. Results Here we show that SSS also antagonizes nicotinic acetylcholine receptors (nAChRs) to reduce synaptic transmission and promote sleep. Mimicking this antagonism with the nAChR inhibitor mecamylamine or by RNAi knockdown of specific nAChR subunits is sufficient to restore sleep to qvr/sss mutants. Regulation of nAChR activity by SSS occurs post-transcriptionally since the levels of nAChR mRNAs are unchanged in qvr/sss mutants. Regulation of nAChR activity by SSS may in fact be direct, since SSS forms a stable complex with and antagonizes fly nAChR function in transfected cells. Intriguingly, lynx1, a mammalian homolog of SSS, can partially restore normal sleep to qvr/sss mutants, and lynx1 can form stable complexes with Shaker-type channels and nAChRs. Conclusions Together, our data point to an evolutionarily conserved, bi-functional role for SSS and its homologs in controlling excitability and synaptic transmission in fundamental processes of the nervous system such as sleep. PMID:24613312

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

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

Casjens S. R.; Dunn J.; Mongodin, E. F.

2012-03-14

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so aremore » informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33-40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi {approx}900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short {le}20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant.« less

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

PubMed Central

Casjens, Sherwood R.; Mongodin, Emmanuel F.; Qiu, Wei-Gang; Luft, Benjamin J.; Schutzer, Steven E.; Gilcrease, Eddie B.; Huang, Wai Mun; Vujadinovic, Marija; Aron, John K.; Vargas, Levy C.; Freeman, Sam; Radune, Diana; Weidman, Janice F.; Dimitrov, George I.; Khouri, Hoda M.; Sosa, Julia E.; Halpin, Rebecca A.; Dunn, John J.; Fraser, Claire M.

2012-01-01

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant. PMID:22432010

Evolutionary Determinants of Morphological Polymorphism in Colonial Animals.

PubMed

Simpson, Carl; Jackson, Jeremy B C; Herrera-Cubilla, Amalia

2017-07-01

Colonial animals commonly exhibit morphologically polymorphic modular units that are phenotypically distinct and specialize in specific functional tasks. But how and why these polymorphic modules have evolved is poorly understood. Across colonial invertebrates, there is wide variation in the degree of polymorphism, from none in colonial ascidians to extreme polymorphism in siphonophores, such as the Portuguese man-of-war. Bryozoa are a phylum of exclusively colonial invertebrates that uniquely exhibit almost the entire range of polymorphism, from monomorphic species to others that rival siphonophores in their polymorphic complexity. Previous approaches to understanding the evolution of polymorphism have been based on analyses of (1) the functional role of polymorphs or (2) presumed evolutionary costs and benefits based on evolutionary theory that postulates polymorphism should be evolutionarily sustainable only in more stable environments because polymorphism commonly leads to the loss of feeding and sexual competence. Here we use bryozoans from opposite shores of the Isthmus of Panama to revisit the environmental hypothesis by comparison of faunas from distinct oceanographic provinces that differ greatly in environmental variability, and we then examine the correlations between the extent of polymorphism in relation to patterns of ecological succession and variation in life histories. We find no support for the environmental hypothesis. Distributions of the incidence of polymorphism in the oceanographically unstable Eastern Pacific are indistinguishable from those in the more stable Caribbean. In contrast, the temporal position of species in a successional sequence is collinear with the degree of polymorphism because species with fewer types of polymorphs are competitively replaced by species with higher numbers of polymorphs on the same substrata. Competitively dominant species also exhibit patterns of growth that increase their competitive ability. The association between degrees of polymorphism and variations in life histories is fundamental to understanding of the macroevolution of polymorphism.

Ecological perspectives on synthetic biology: insights from microbial population biology

PubMed Central

Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

2015-01-01

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID:25767468

Essential roles for lines in mediating leg and antennal proximodistal patterning and generating a stable Notch signaling interface at segment borders.

PubMed

Greenberg, Lina; Hatini, Victor

2009-06-01

The Drosophila leg imaginal disc provides a paradigm with which to understand the fundamental developmental mechanisms that generate an intricate appendage structure. Leg formation depends on the subdivision of the leg proximodistal (PD) axis into broad domains by the leg gap genes. The leg gap genes act combinatorially to initiate the expression of the Notch ligands Delta (Dl) and Serrate (Ser) in a segmental pattern. Dl and Ser induce the expression of a set of transcriptional regulators along the segment border, which mediate leg segment growth and joint morphogenesis. Here we show that Lines accumulates in nuclei in the presumptive tarsus and the inter-joints of proximal leg segments and governs the formation of these structures by destabilizing the nuclear protein Bowl. Across the presumptive tarsus, lines modulates the opposing expression landscapes of the leg gap gene dachshund (dac) and the tarsal PD genes, bric-a-brac 2 (bab), apterous (ap) and BarH1 (Bar). In this manner, lines inhibits proximal tarsal fates and promotes medial and distal tarsal fates. Across proximal leg segments, lines antagonizes bowl to promote Dl expression by relief-of-repression. In turn, Dl signals asymmetrically to stabilize Bowl in adjacent distal cells. Bowl, then, acts cell-autonomously, together with one or more redundant factors, to repress Dl expression. Together, lines and bowl act as a binary switch to generate a stable Notch signaling interface between Dl-expressing cells and adjacent distal cell. lines plays analogous roles in developing antennae, which are serially homologous to legs, suggesting evolutionarily conserved roles for lines in ventral appendage formation.

History of Peer Victimization and Children's Response to School Bullying

ERIC Educational Resources Information Center

Elledge, L. Christian; Cavell, Timothy A.; Ogle, Nick T.; Malcolm, Kenya T.; Newgent, Rebecca A.; Faith, Melissa A.

2010-01-01

We examined the degree to which children with and without a history of stable peer victimization differentially endorse strategies for dealing with school bullies. Participants were 323 children, 58 of whom met criteria for chronic peer victimization. Children with a history of stable peer victimization differed from comparison children in how…

Nuclear autophagy: An evolutionarily conserved mechanism of nuclear degradation in the cytoplasm.

PubMed

Luo, Majing; Zhao, Xueya; Song, Ying; Cheng, Hanhua; Zhou, Rongjia

2016-11-01

Macroautophagy/autophagy is a catabolic process that is essential for cellular homeostasis. Studies on autophagic degradation of cytoplasmic components have generated interest in nuclear autophagy. Although its mechanisms and roles have remained elusive, tremendous progress has been made toward understanding nuclear autophagy. Nuclear autophagy is evolutionarily conserved in eukaryotes that may target various nuclear components through a series of processes, including nuclear sensing, nuclear export, autophagic substrate encapsulation and autophagic degradation in the cytoplasm. However, the molecular processes and regulatory mechanisms involved in nuclear autophagy remain largely unknown. Numerous studies have highlighted the importance of nuclear autophagy in physiological and pathological processes such as cancer. This review focuses on current advances in nuclear autophagy and provides a summary of its research history and landmark discoveries to offer new perspectives.

Protein chainmail variants in dsDNA viruses

PubMed Central

Zhou, Z. Hong; Chiou, Joshua

2017-01-01

First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β sheet in the axial (A) domain, spine helix in the peripheral (P) domain, and an extended (E) loop. HK97 capsid consists of covalently-linked copies of just one HK97-like fold protein and represents the most effective strategy to form highly stable chainmail needed for dsDNA genome encapsidation. Recently, near-atomic resolution structures enabled by cryo electron microscopy (cryoEM) have revealed a range of other, more complex variants of this strategy for constructing dsDNA viruses. The first strategy, exemplified by P22-like phages, is the attachment of an insertional (I) domain to the core 5-stranded β sheet of the HK97-like fold. The atomic models of the Bordetella phage BPP-1 showcases an alternative topology of the classic HK97 topology of the HK97-like fold, as well as the second strategy for constructing stable capsids, where an auxiliary jellyroll protein dimer serves to cement the non-covalent chainmail formed by capsid protein subunits. The third strategy, found in lambda-like phages, uses auxiliary protein trimers to stabilize the underlying non-covalent chainmail near the 3-fold axis. Herpesviruses represent highly complex viruses that use a combination of these strategies, resulting in four-level hierarchical organization including a non-covalent chainmail formed by the HK97-like fold domain found in the floor region. A thorough understanding of these structures should help unlock the enigma of the emergence and evolution of dsDNA viruses and inform bioengineering efforts based on these viruses. PMID:29177192

Long-Term Weight Maintenance Strategies Are Experienced as a Burden by Persons Who Have Lost Weight Compared to Persons with a lifetime Normal, Stable Weight.

PubMed

Kruseman, Maaike; Schmutz, Noémi; Carrard, Isabelle

2017-01-01

To assess dietary intake, eating patterns, physical activity and eating behaviors, and to explore strategies and perceptions of the experience of weight maintenance in weight loss maintainers (weight loss maintenance (WLM) ≥ 10% weight loss maintained for ≥1 year) and in matched controls with a lifetime stable normal weight. Volunteers (32) were recruited by a snowball procedure in this cross-sectional, mixed-methods study. Diet, physical activity, and eating behaviors were assessed with validated questionnaires. Strategies and experiences were investigated during interviews. Descriptive coding, thematic analysis (qualitative data) as well as descriptive analysis and t-tests (quantitative data) were performed. Both groups had similar energy and macronutrient consumption. Those in the WLM group reported higher levels of exercise and scored higher on several dimensions of eating disorders. Four themes - 'food choices,' 'quantities and portion control,' 'physical activity', and 'burden' - emerged from the qualitative data. Both groups used similar weight maintenance strategies, but those in the WLM group experienced a higher burden, expressing effortful control which contrasted with the control group's confidence in their internal cues. Our results show an additional burden related with maintaining weight loss compared to keeping a stable normal weight. They provide evidence to devise interventions that will address the difficulty of regulating intake. © 2017 The Author(s) Published by S. Karger GmbH, Freiburg.

Haplotype-Based Association Analysis via Variance-Components Score Test

PubMed Central

Tzeng, Jung-Ying ; Zhang, Daowen 

2007-01-01

Haplotypes provide a more informative format of polymorphisms for genetic association analysis than do individual single-nucleotide polymorphisms. However, the practical efficacy of haplotype-based association analysis is challenged by a trade-off between the benefits of modeling abundant variation and the cost of the extra degrees of freedom. To reduce the degrees of freedom, several strategies have been considered in the literature. They include (1) clustering evolutionarily close haplotypes, (2) modeling the level of haplotype sharing, and (3) smoothing haplotype effects by introducing a correlation structure for haplotype effects and studying the variance components (VC) for association. Although the first two strategies enjoy a fair extent of power gain, empirical evidence showed that VC methods may exhibit only similar or less power than the standard haplotype regression method, even in cases of many haplotypes. In this study, we report possible reasons that cause the underpowered phenomenon and show how the power of the VC strategy can be improved. We construct a score test based on the restricted maximum likelihood or the marginal likelihood function of the VC and identify its nontypical limiting distribution. Through simulation, we demonstrate the validity of the test and investigate the power performance of the VC approach and that of the standard haplotype regression approach. With suitable choices for the correlation structure, the proposed method can be directly applied to unphased genotypic data. Our method is applicable to a wide-ranging class of models and is computationally efficient and easy to implement. The broad coverage and the fast and easy implementation of this method make the VC strategy an effective tool for haplotype analysis, even in modern genomewide association studies. PMID:17924336

Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions.

PubMed

Lo, Te-Wen; Pickle, Catherine S; Lin, Steven; Ralston, Edward J; Gurling, Mark; Schartner, Caitlin M; Bian, Qian; Doudna, Jennifer A; Meyer, Barbara J

2013-10-01

Exploitation of custom-designed nucleases to induce DNA double-strand breaks (DSBs) at genomic locations of choice has transformed our ability to edit genomes, regardless of their complexity. DSBs can trigger either error-prone repair pathways that induce random mutations at the break sites or precise homology-directed repair pathways that generate specific insertions or deletions guided by exogenously supplied DNA. Prior editing strategies using site-specific nucleases to modify the Caenorhabditis elegans genome achieved only the heritable disruption of endogenous loci through random mutagenesis by error-prone repair. Here we report highly effective strategies using TALE nucleases and RNA-guided CRISPR/Cas9 nucleases to induce error-prone repair and homology-directed repair to create heritable, precise insertion, deletion, or substitution of specific DNA sequences at targeted endogenous loci. Our robust strategies are effective across nematode species diverged by 300 million years, including necromenic nematodes (Pristionchus pacificus), male/female species (Caenorhabditis species 9), and hermaphroditic species (C. elegans). Thus, genome-editing tools now exist to transform nonmodel nematode species into genetically tractable model organisms. We demonstrate the utility of our broadly applicable genome-editing strategies by creating reagents generally useful to the nematode community and reagents specifically designed to explore the mechanism and evolution of X chromosome dosage compensation. By developing an efficient pipeline involving germline injection of nuclease mRNAs and single-stranded DNA templates, we engineered precise, heritable nucleotide changes both close to and far from DSBs to gain or lose genetic function, to tag proteins made from endogenous genes, and to excise entire loci through targeted FLP-FRT recombination.

DJ-1 links muscle ROS production with metabolic reprogramming and systemic energy homeostasis in mice.

PubMed

Shi, Sally Yu; Lu, Shun-Yan; Sivasubramaniyam, Tharini; Revelo, Xavier S; Cai, Erica P; Luk, Cynthia T; Schroer, Stephanie A; Patel, Prital; Kim, Raymond H; Bombardier, Eric; Quadrilatero, Joe; Tupling, A Russell; Mak, Tak W; Winer, Daniel A; Woo, Minna

2015-06-16

Reactive oxygen species (ROS) have been linked to a wide variety of pathologies, including obesity and diabetes, but ROS also act as endogenous signalling molecules, regulating numerous biological processes. DJ-1 is one of the most evolutionarily conserved proteins across species, and mutations in DJ-1 have been linked to some cases of Parkinson's disease. Here we show that DJ-1 maintains cellular metabolic homeostasis via modulating ROS levels in murine skeletal muscles, revealing a role of DJ-1 in maintaining efficient fuel utilization. We demonstrate that, in the absence of DJ-1, ROS uncouple mitochondrial respiration and activate AMP-activated protein kinase, which triggers Warburg-like metabolic reprogramming in muscle cells. Accordingly, DJ-1 knockout mice exhibit higher energy expenditure and are protected from obesity, insulin resistance and diabetes in the setting of fuel surplus. Our data suggest that promoting mitochondrial uncoupling may be a potential strategy for the treatment of obesity-associated metabolic disorders.

HIV-1 Nef interferes with host cell motility by deregulation of Cofilin.

PubMed

Stolp, Bettina; Reichman-Fried, Michal; Abraham, Libin; Pan, Xiaoyu; Giese, Simone I; Hannemann, Sebastian; Goulimari, Polyxeni; Raz, Erez; Grosse, Robert; Fackler, Oliver T

2009-08-20

HIV-1 Nef is a key factor in AIDS pathogenesis. Here, we report that Nef potently inhibits motility of fibroblasts and chemotaxis of HIV-1-infected primary human T lymphocytes toward the chemokines SDF-1alpha, CCL-19, and CCL-21 ex vivo. Furthermore, Nef inhibits guided motility of zebrafish primordial germ cells toward endogenous SDF-1a in vivo. These migration defects result from Nef-mediated inhibition of the actin remodeling normally triggered by migratory stimuli. Nef strongly induces phosphorylation of cofilin, inactivating this evolutionarily conserved actin-depolymerizing factor that promotes cell motility when unphosphorylated. Nef-dependent cofilin deregulation requires association of Nef with the cellular kinase Pak2. Disruption of Nef-Pak2 association restores the cofilin phosphorylation levels and actin remodeling that facilitate cell motility. We conclude that HIV-1 Nef alters Pak2 function, which directly or indirectly inactivates cofilin, thereby restricting migration of infected T lymphocytes as part of a strategy to optimize immune evasion and HIV-1 replication.

YAP and the Hippo pathway in pediatric cancer

PubMed Central

Mohamed, Abdalla D.; Gener, Melissa; Li, Weijie; Taboada, Eugenio

2017-01-01

ABSTRACT The Hippo pathway is an important signaling pathway that controls cell proliferation and apoptosis. It is evolutionarily conserved in mammals and is stimulated by cell–cell contact, inhibiting cell proliferation in response to increased cell density. During early embryonic development, the Hippo signaling pathway regulates organ development and size, and its functions result in the coordinated balance between proliferation, apoptosis, and differentiation. Its principal effectors, YAP and TAZ, regulate signaling by the embryonic stem cells and determine cell fate and histogenesis. Dysfunction of this pathway contributes to cancer development in adults and children. Emerging studies have shed light on the upregulation of Hippo pathway members in several pediatric cancers and may offer prognostic information on rhabdomyosarcoma, osteosarcoma, Wilms tumor, neuroblastoma, medulloblastoma, and other brain gliomas. We review the results of such published studies and highlight the potential clinical application of this pathway in pediatric oncologic and pathologic studies. These studies support targeting this pathway as a novel treatment strategy. PMID:28616573

Nutrition modulation of human aging: The calorie restriction paradigm.

PubMed

Das, Sai Krupa; Balasubramanian, Priya; Weerasekara, Yasoma K

2017-11-05

Globally, the aging population is growing rapidly, creating an urgent need to attenuate age-related health conditions, including metabolic disease and disability. A promising strategy for healthy aging based on consistently positive results from studies with a variety of species, including non-human primates (NHP), is calorie restriction (CR), or the restriction of energy intake while maintaining intake of essential nutrients. The burgeoning evidence for this approach in humans is reviewed and the major study to date to address this question, CALERIE (Comprehensive Assessment of the Long-term Effects of Reducing Intake of Energy), is described. CALERIE findings indicate the feasibility of CR in non-obese humans, confirm observations in NHP, and are consistent with improvements in disease risk reduction and potential anti-aging effects. Finally, the mechanisms of CR in humans are reviewed which sums up the fact that evolutionarily conserved mechanisms mediate the anti-aging effects of CR. Overall, the prospect for further research in both NHP and humans is highly encouraging. Copyright © 2017 Elsevier B.V. All rights reserved.

Paired related homeobox 1 is associated with the invasive properties of glioblastoma cells.

PubMed

Sugiyama, Mai; Hasegawa, Hitoki; Ito, Satoko; Sugiyama, Kazuya; Maeda, Masao; Aoki, Kosuke; Wakabayashi, Toshihiko; Hamaguchi, Michinari; Natsume, Atsushi; Senga, Takeshi

2015-03-01

Glioblastoma is a highly proliferative and invasive tumor. Despite extensive efforts to develop treatments for glioblastoma, the currently available therapies have only limited effects. To develop novel strategies for glioblastoma treatment, it is crucial to elucidate the molecular mechanisms that promote the invasive properties of glioblastoma. In the present study, we showed that the paired related homeobox 1 (PRRX1) is associated with glioblastoma cell invasion. The depletion of PRRX1 suppressed the invasion and neurosphere formation of glioblastoma cells. Conversely, the exogenous expression of PRRX1 promoted invasion. The Notch signaling pathway, which is an evolutionarily conserved pathway that is essential for developmental processes, plays an important role in the tumorigenesis of glioblastoma. The expression of PRRX1 induced the activation of Notch signaling, and the inhibition of Notch signaling suppressed PRRX1-mediated cell invasion. Our results indicate that activation of Notch signaling by PRRX1 is associated with the promotion of glioblastoma cell invasion.

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

Li, Peng; Rivera-Cancel, Giomar; Kinch, Lisa N.

Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure ofmore » VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.« less

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

Li, Peng; Rivera-Cancel, Giomar; Kinch, Lisa N.

Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered thatVibrio parahaemolyticusVtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure of VtrA/VtrC withmore » bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.« less

A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods

NASA Astrophysics Data System (ADS)

Novinec, Marko; Korenč, Matevž; Caflisch, Amedeo; Ranganathan, Rama; Lenarčič, Brigita; Baici, Antonio

2014-02-01

Allosteric modifiers have the potential to fine-tune enzyme activity. Therefore, targeting allosteric sites is gaining increasing recognition as a strategy in drug design. Here we report the use of computational methods for the discovery of the first small-molecule allosteric inhibitor of the collagenolytic cysteine peptidase cathepsin K, a major target for the treatment of osteoporosis. The molecule NSC13345 is identified by high-throughput docking of compound libraries to surface sites on the peptidase that are connected to the active site by an evolutionarily conserved network of residues (protein sector). The crystal structure of the complex shows that NSC13345 binds to a novel allosteric site on cathepsin K. The compound acts as a hyperbolic mixed modifier in the presence of a synthetic substrate, it completely inhibits collagen degradation and has good selectivity for cathepsin K over related enzymes. Altogether, these properties qualify our methodology and NSC13345 as promising candidates for allosteric drug design.

TEAD1 mediates the oncogenic activities of Hippo-YAP1 signaling in osteosarcoma.

PubMed

Chai, Jiwei; Xu, Shijie; Guo, Fengbo

2017-06-24

Hippo signaling pathway is an evolutionarily conserved developmental network that governs the downstream transcriptional co-activators, YAP and TAZ, which bind to and activate the output of TEADs that responsible for cell proliferation, apoptosis, and stem cell self renewal. Emerging evidence has shown the tumor suppressor properties of Hippo signaling. However, limited knowledge is available concerning the downstream transcription factors of Hippo pathway in osteosarcoma (OS). In this study, we demonstrated that TEAD1 was the major transcription factor of Hippo signaling pathway in OS. Genetic silencing of TEAD1 suppressed multiple malignant phenotypes of OS cells including cell proliferation, apoptosis resistance, and invasive potential. Mechanistically, we showed that TEAD1 largely exerted its transcriptional control of its functional targets, PTGS2 and CYR61. Collectively, this work identifies the YAP1/TEAD1 complex as the representative dysregulated profile of Hippo signaling in OS and provides proof-of-principle that targeting TEAD1 may be a therapeutic strategy of osteosarcoma. Copyright © 2017. Published by Elsevier Inc.

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

PubMed

Liscovitch-Brauer, Noa; Alon, Shahar; Porath, Hagit T; Elstein, Boaz; Unger, Ron; Ziv, Tamar; Admon, Arie; Levanon, Erez Y; Rosenthal, Joshua J C; Eisenberg, Eli

2017-04-06

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses

PubMed Central

Köberlin, Marielle S.; Snijder, Berend; Heinz, Leonhard X.; Baumann, Christoph L.; Fauster, Astrid; Vladimer, Gregory I.; Gavin, Anne-Claude; Superti-Furga, Giulio

2015-01-01

Summary Lipid composition affects the biophysical properties of membranes that provide a platform for receptor-mediated cellular signaling. To study the regulatory role of membrane lipid composition, we combined genetic perturbations of sphingolipid metabolism with the quantification of diverse steps in Toll-like receptor (TLR) signaling and mass spectrometry-based lipidomics. Membrane lipid composition was broadly affected by these perturbations, revealing a circular network of coregulated sphingolipids and glycerophospholipids. This evolutionarily conserved network architecture simultaneously reflected membrane lipid metabolism, subcellular localization, and adaptation mechanisms. Integration of the diverse TLR-induced inflammatory phenotypes with changes in lipid abundance assigned distinct functional roles to individual lipid species organized across the network. This functional annotation accurately predicted the inflammatory response of cells derived from patients suffering from lipid storage disorders, based solely on their altered membrane lipid composition. The analytical strategy described here empowers the understanding of higher-level organization of membrane lipid function in diverse biological systems. PMID:26095250

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2

PubMed Central

Jain, Devanshi; Puno, M Rhyan; Meydan, Cem; Lailler, Nathalie; Mason, Christopher E; Lima, Christopher D; Anderson, Kathryn V

2018-01-01

Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, ‘ketu’, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis. PMID:29360036

Numerical and analytical approaches to an advection-diffusion problem at small Reynolds number and large Péclet number

NASA Astrophysics Data System (ADS)

Fuller, Nathaniel J.; Licata, Nicholas A.

2018-05-01

Obtaining a detailed understanding of the physical interactions between a cell and its environment often requires information about the flow of fluid surrounding the cell. Cells must be able to effectively absorb and discard material in order to survive. Strategies for nutrient acquisition and toxin disposal, which have been evolutionarily selected for their efficacy, should reflect knowledge of the physics underlying this mass transport problem. Motivated by these considerations, in this paper we discuss the results from an undergraduate research project on the advection-diffusion equation at small Reynolds number and large Péclet number. In particular, we consider the problem of mass transport for a Stokesian spherical swimmer. We approach the problem numerically and analytically through a rescaling of the concentration boundary layer. A biophysically motivated first-passage problem for the absorption of material by the swimming cell demonstrates quantitative agreement between the numerical and analytical approaches. We conclude by discussing the connections between our results and the design of smart toxin disposal systems.

Comparative Aspects of BRAF Mutations in Canine Cancers

PubMed Central

Mochizuki, Hiroyuki; Breen, Matthew

2015-01-01

Activating mutations of the BRAF gene lead to constitutive activation of the MAPK pathway. The characterization and discovery of BRAF mutations in a variety of human cancers has led to the development of specific inhibitors targeting the BRAF/MAPK pathway and dramatically changed clinical outcomes in BRAF-mutant melanoma patients. Recent discovery of BRAF mutation in canine cancers underscores the importance of MAPK pathway activation as an oncogenic molecular alteration evolutionarily conserved between species. A comparative approach using the domestic dog as a spontaneous cancer model will provide new insights into the dysregulation of BRAF/MAPK pathway in carcinogenesis and facilitate in vivo studies to evaluate therapeutic strategies targeting this pathway’s molecules for cancer therapy. The BRAF mutation in canine cancers may also represent a molecular marker and therapeutic target in veterinary oncology. This review article summarizes the current knowledge on BRAF mutations in human and canine cancers and discusses the potential applications of this abnormality in veterinary oncology. PMID:29061943

The Plasmodium selenoproteome

PubMed Central

Lobanov, Alexey V.; Delgado, Cesar; Rahlfs, Stefan; Novoselov, Sergey V.; Kryukov, Gregory V.; Gromer, Stephan; Hatfield, Dolph L.; Becker, Katja; Gladyshev, Vadim N.

2006-01-01

The use of selenocysteine (Sec) as the 21st amino acid in the genetic code has been described in all three major domains of life. However, within eukaryotes, selenoproteins are only known in animals and algae. In this study, we characterized selenoproteomes and Sec insertion systems in protozoan Apicomplexa parasites. We found that among these organisms, Plasmodium and Toxoplasma utilized Sec, whereas Cryptosporidium did not. However, Plasmodium had no homologs of known selenoproteins. By searching computationally for evolutionarily conserved selenocysteine insertion sequence (SECIS) elements, which are RNA structures involved in Sec insertion, we identified four unique Plasmodium falciparum selenoprotein genes. These selenoproteins were incorrectly annotated in PlasmoDB, were conserved in other Plasmodia and had no detectable homologs in other species. We provide evidence that two Plasmodium SECIS elements supported Sec insertion into parasite and endogenous selenoproteins when they were expressed in mammalian cells, demonstrating that the Plasmodium SECIS elements are functional and indicating conservation of Sec insertion between Apicomplexa and animals. Dependence of the plasmodial parasites on selenium suggests possible strategies for antimalarial drug development. PMID:16428245

Bistability and State Transition of a Delay Differential Equation Model of Neutrophil Dynamics

NASA Astrophysics Data System (ADS)

Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

This paper studies the existence of bistable states and control strategies to induce state transitions of a delay differential equation model of neutrophil dynamics. We seek the conditions that a stable steady state and an oscillatory state coexist in the neutrophil dynamical system. Physiologically, stable steady state represents the healthy state, while oscillatory state is usually associated with diseases such as cyclical neutropenia. We study the control strategies to induce the transitions from the disease state to the healthy state by introducing temporal perturbations to system parameters. This study is valuable in designing clinical protocols for the treatment of cyclical neutropenia.

Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

NASA Astrophysics Data System (ADS)

Huizhong, Dong; Hongli, Song

An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

Gaze Strategies in Skateboard Trick Jumps: Spatiotemporal Constraints in Complex Locomotion.

PubMed

Klostermann, André; Küng, Philip

2017-03-01

This study aimed to further the knowledge on gaze behavior in locomotion by studying gaze strategies in skateboard jumps of different difficulty that had to be performed either with or without an obstacle. Nine experienced skateboarders performed "Ollie" and "Kickflip" jumps either over an obstacle or over a plane surface. The stable gaze at 5 different areas of interest was calculated regarding its relative duration as well as its temporal order. During the approach phase, an interaction between area of interest and obstacle condition, F(3, 24) = 12.91, p <  .05, η p 2  = .62, was found with longer stable-gaze locations at the takeoff area in attempts with an obstacle (p <  .05, η p 2  = .47). In contrast, in attempts over a plane surface, longer stable-gaze locations at the skateboard were revealed (p <  .05, η p 2  = .73). Regarding the trick difficulty factor, the skateboarders descriptively showed longer stable-gaze locations at the skateboard for the "Kickflip" than for the "Ollie" in the no-obstacle condition only (p>.05, d = 0.74). Finally, during the jump phase, neither obstacle condition nor trick difficulty affected gaze behavior differentially. This study underlines the functional adaptability of the visuomotor system to changing demands in highly dynamic situations. As a function of certain constraints, different gaze strategies were observed that can be considered as highly relevant for successfully performing skateboard jumps.

A Late Stage Strategy for the Functionalization of Triazolium-based NHC catalysts.

PubMed

Ozboya, Kerem E; Rovis, Tomislav

A strategy for the diversification of triazolium-based catalysts is presented. This method is based on the reduction to the triazoline, which serves as a suitable and stable substrate for Pd-mediated cross-coupling, followed by trityl cation mediated reoxidation to the triazolium.

Male secondary sexual structures and the systematics of the Thereus oppia species group (Lepidoptera, Lycaenidae, Eumaeini)

PubMed Central

Robbins, Robert K.; Heredia, María Dolores; Busby, Robert C.

2015-01-01

Abstract The Thereus oppia species group includes species with and without a scent pad, which is a histologically and morphologically characterized male secondary sexual structure on the dorsal surface of the forewing. To assess the hypothesis that these structures are lost evolutionarily, but not regained (Dollo’s Law), the taxonomy of this species group is revised. Thereus lomalarga sp. n., and Thereus brocki sp. n., are described. Diagnostic traits, especially male secondary structures, within the Thereus oppia species group are illustrated. Distributional and biological information is summarized for each species. Three species have been reared, and the caterpillars eat Loranthaceae. An inferred phylogeny is consistent with the hypothesis that scent pads in the Thereus oppia species group have been lost evolutionarily twice (in allopatry), and not re-gained. PMID:26448715

Harsh, Firm, and Permissive Parenting in Low-Income Families.

ERIC Educational Resources Information Center

Shumow, Lee; Vandell, Deborah Lowe; Posner, Jill K.

1998-01-01

Parents' reports of their child-rearing expectations and intentions were measured for 184 low-income urban families when children were in the third and fifth grades. Parenting strategies were stable over time. Parenting strategies were related to measures of adjustment at school, behavior problems in the home, academic achievement, and…

Spatial Strategies in the Description of Complex Configurations

ERIC Educational Resources Information Center

Tenbrink, Thora; Coventry, Kenny R.; Andonova, Elena

2011-01-01

How people describe complex arrangements of objects in a small-scale setting has not been sufficiently investigated to predict when discourse strategies shift versus remain stable. In a study involving 100 native German participants, we investigated speakers' choices of perspective, as well as location and orientation information, when describing…

Strategy as simple rules.

PubMed

Eisenhardt, K M; Sull, D N

2001-01-01

The success of Yahoo!, eBay, Enron, and other companies that have become adept at morphing to meet the demands of changing markets can't be explained using traditional thinking about competitive strategy. These companies have succeeded by pursuing constantly evolving strategies in market spaces that were considered unattractive according to traditional measures. In this article--the third in an HBR series by Kathleen Eisenhardt and Donald Sull on strategy in the new economy--the authors ask, what are the sources of competitive advantage in high-velocity markets? The secret, they say, is strategy as simple rules. The companies know that the greatest opportunities for competitive advantage lie in market confusion, but they recognize the need for a few crucial strategic processes and a few simple rules. In traditional strategy, advantage comes from exploiting resources or stable market positions. In strategy as simple rules, advantage comes from successfully seizing fleeting opportunities. Key strategic processes, such as product innovation, partnering, or spinout creation, place the company where the flow of opportunities is greatest. Simple rules then provide the guidelines within which managers can pursue such opportunities. Simple rules, which grow out of experience, fall into five broad categories: how- to rules, boundary conditions, priority rules, timing rules, and exit rules. Companies with simple-rules strategies must follow the rules religiously and avoid the temptation to change them too frequently. A consistent strategy helps managers sort through opportunities and gain short-term advantage by exploiting the attractive ones. In stable markets, managers rely on complicated strategies built on detailed predictions of the future. But when business is complicated, strategy should be simple.

Housing and sexual health among street-involved youth.

PubMed

Kumar, Maya M; Nisenbaum, Rosane; Barozzino, Tony; Sgro, Michael; Bonifacio, Herbert J; Maguire, Jonathon L

2015-10-01

Street-involved youth (SIY) carry a disproportionate burden of sexually transmitted diseases (STD). Studies among adults suggest that improving housing stability may be an effective primary prevention strategy for improving sexual health. Housing options available to SIY offer varying degrees of stability and adult supervision. This study investigated whether housing options offering more stability and adult supervision are associated with fewer STD and related risk behaviors among SIY. A cross-sectional study was performed using public health survey and laboratory data collected from Toronto SIY in 2010. Three exposure categories were defined a priori based on housing situation: (1) stable and supervised housing, (2) stable and unsupervised housing, and (3) unstable and unsupervised housing. Multivariate logistic regression was used to test the association between housing category and current or recent STD. Secondary analyses were performed using the following secondary outcomes: blood-borne infection, recent binge-drinking, and recent high-risk sexual behavior. The final analysis included 184 SIY. Of these, 28.8 % had a current or recent STD. Housing situation was stable and supervised for 12.5 %, stable and unsupervised for 46.2 %, and unstable and unsupervised for 41.3 %. Compared to stable and supervised housing, there was no significant association between current or recent STD among stable and unsupervised housing or unstable and unsupervised housing. There was no significant association between housing category and risk of blood-borne infection, binge-drinking, or high-risk sexual behavior. Although we did not demonstrate a significant association between stable and supervised housing and lower STD risk, our incorporation of both housing stability and adult supervision into a priori defined exposure groups may inform future studies of housing-related prevention strategies among SIY. Multi-modal interventions beyond housing alone may also be required to prevent sexual morbidity among these vulnerable youth.

Ad hoc vs. Non-ad hoc Percutaneous Coronary Intervention Strategies in Patients With Stable Coronary Artery Disease.

PubMed

Toyota, Toshiaki; Morimoto, Takeshi; Shiomi, Hiroki; Ando, Kenji; Ono, Koh; Shizuta, Satoshi; Kato, Takao; Saito, Naritatsu; Furukawa, Yutaka; Nakagawa, Yoshihisa; Horie, Minoru; Kimura, Takeshi

2017-03-24

Few studies have evaluated the prevalence and clinical outcomes of ad hoc percutaneous coronary intervention (PCI), performing diagnostic coronary angiography and PCI in the same session, in stable coronary artery disease (CAD) patients.Methods and Results:From the CREDO-Kyoto PCI/CABG registry cohort-2, 6,943 patients were analyzed as having stable CAD and undergoing first PCI. Ad hoc PCI and non-ad hoc PCI were performed in 1,722 (24.8%) and 5,221 (75.1%) patients, respectively. The cumulative 5-year incidence and adjusted risk for all-cause death were not significantly different between the 2 groups (15% vs. 15%, P=0.53; hazard ratio: 1.15, 95% confidence interval: 0.98-1.35, P=0.08). Ad hoc PCI relative to non-ad hoc PCI was associated with neutral risk for myocardial infarction, any coronary revascularization, and bleeding, but was associated with a trend towards lower risk for stroke (hazard ratio: 0.78, 95% confidence interval: 0.60-1.02, P=0.06). Ad hoc PCI in stable CAD patients was associated with at least comparable 5-year clinical outcomes as with non-ad hoc PCI. Considering patients' preference and the cost-saving, the ad hoc PCI strategy might be a safe and attractive option for patients with stable CAD, although the prevalence of ad hoc PCI was low in the current study population.

Phylogenetic lineages in Entomophthoromycota

USDA-ARS?s Scientific Manuscript database

Entomophthoromycota Humber is one of five major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular st...

SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms

PubMed Central

Muyle, Aline; Käfer, Jos; Zemp, Niklaus; Mousset, Sylvain; Picard, Franck; Marais, Gabriel AB

2016-01-01

We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20–35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available. PMID:27492231

Spacecraft Guidance Strategies for Proximity Maneuvering and Close Approach with a Tumbling Object

DTIC Science & Technology

2010-03-01

R., and Junkins, J. L. (1984), ‘Optimal Open-Loop and Stable Feedback Control of Rigid Spacecraft Attitude Maneuvers ,’ The Journal of the... SPACECRAFT GUIDANCE STRATEGIES FOR PROXIMITY MANEUVERING AND CLOSE APPROACH WITH A TUMBLING OBJECT by George A. Boyarko March 2010...Dissertation 4. TITLE AND SUBTITLE: Spacecraft Guidance Strategies for Proximity Maneuvering and Close Approach with a Tumbling Object 6. AUTHOR

Dynamics and control of twisting bi-stable structures

NASA Astrophysics Data System (ADS)

Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

2018-02-01

Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states of the bi-stable twisting I-beam structures. The obtained optimal piezoelectric actuator positioning is not necessarily intuitive and when used with the proposed dynamic actuation strategy serve as a blueprint for the actuation of such multi-stable compliant structures to produce fast and large deflections with highly embeddable actuators. This class of structures has potential applications in aerospace systems and soft/compliant robotics.

Structural and biophysical properties of h-FANCI ARM repeat protein.

PubMed

Siddiqui, Mohd Quadir; Choudhary, Rajan Kumar; Thapa, Pankaj; Kulkarni, Neha; Rajpurohit, Yogendra S; Misra, Hari S; Gadewal, Nikhil; Kumar, Satish; Hasan, Syed K; Varma, Ashok K

2017-11-01

Fanconi anemia complementation groups - I (FANCI) protein facilitates DNA ICL (Inter-Cross-link) repair and plays a crucial role in genomic integrity. FANCI is a 1328 amino acids protein which contains armadillo (ARM) repeats and EDGE motif at the C-terminus. ARM repeats are functionally diverse and evolutionarily conserved domain that plays a pivotal role in protein-protein and protein-DNA interactions. Considering the importance of ARM repeats, we have explored comprehensive in silico and in vitro approach to examine folding pattern. Size exclusion chromatography, dynamic light scattering (DLS) and glutaraldehyde crosslinking studies suggest that FANCI ARM repeat exist as monomer as well as in oligomeric forms. Circular dichroism (CD) and fluorescence spectroscopy results demonstrate that protein has predominantly α- helices and well-folded tertiary structure. DNA binding was analysed using electrophoretic mobility shift assay by autoradiography. Temperature-dependent CD, Fluorescence spectroscopy and DLS studies concluded that protein unfolds and start forming oligomer from 30°C. The existence of stable portion within FANCI ARM repeat was examined using limited proteolysis and mass spectrometry. The normal mode analysis, molecular dynamics and principal component analysis demonstrated that helix-turn-helix (HTH) motif present in ARM repeat is highly dynamic and has anti-correlated motion. Furthermore, FANCI ARM repeat has HTH structural motif which binds to double-stranded DNA.

Identification of Putative Mek1 Substrates during Meiosis in Saccharomyces cerevisiae Using Quantitative Phosphoproteomics

PubMed Central

Suhandynata, Raymond T.; Wan, Lihong; Zhou, Huilin; Hollingsworth, Nancy M.

2016-01-01

Meiotic recombination plays a key role in sexual reproduction as it generates crossovers that, in combination with sister chromatid cohesion, physically connect homologous chromosomes, thereby promoting their proper segregation at the first meiotic division. Meiotic recombination is initiated by programmed double strand breaks (DSBs) catalyzed by the evolutionarily conserved, topoisomerase-like protein Spo11. Repair of these DSBs is highly regulated to create crossovers between homologs that are distributed throughout the genome. This repair requires the presence of the mitotic recombinase, Rad51, as well as the strand exchange activity of the meiosis-specific recombinase, Dmc1. A key regulator of meiotic DSB repair in Saccharomyces cerevisiae is the meiosis-specific kinase Mek1, which promotes interhomolog strand invasion and is required for the meiotic recombination checkpoint and the crossover/noncrossover decision. Understanding how Mek1 regulates meiotic recombination requires the identification of its substrates. Towards that end, an unbiased phosphoproteomic approach utilizing Stable Isotope Labeling by Amino Acids in Cells (SILAC) was utilized to generate a list of potential Mek1 substrates, as well as proteins containing consensus phosphorylation sites for cyclin-dependent kinase, the checkpoint kinases, Mec1/Tel1, and the polo-like kinase, Cdc5. These experiments represent the first global phosphoproteomic dataset for proteins in meiotic budding yeast. PMID:27214570

Cold temperature preference in bacterially infected Drosophila melanogaster improves survival but is remarkably suboptimal.

PubMed

Fedorka, Kenneth M; Kutch, Ian C; Collins, Louisa; Musto, Edward

Altering one's temperature preference (e.g. behavioral fever or behavioral chill) is a common immune defense among ectotherms that is likely to be evolutionarily conserved. However, the temperature chosen by an infected host may not be optimal for pathogen defense, causing preference to be inefficient. Here we examined the efficiency of temperature preference in Drosophila melanogaster infected with an LD 50 of the gram negative bacteria Pseudomonas aeruginosa. To this end, we estimated the host's uninfected and infected temperature preferences as well as their optimal survival temperature. We found that flies decreased their preference from 26.3°C to 25.2°C when infected, and this preference was stable over 48h. Furthermore, the decrease in temperature preference was associated with an increased chance of surviving the infection. Nevertheless, the infected temperature preference did not coincide with the optimum temperature for infection survival, which lies at or below 21.4°C. These data suggest that the behavioral response to P. aeruginosa infection is considerably inefficient, and the mechanisms that may account for this pattern are discussed. Future studies of infected temperature preferences should document its efficiency, as this understudied aspect of behavioral immunity can provide important insight into preference evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Parental effects alter the adaptive value of an adult behavioural trait.

PubMed

Kilner, Rebecca M; Boncoraglio, Giuseppe; Henshaw, Jonathan M; Jarrett, Benjamin J M; De Gasperin, Ornela; Attisano, Alfredo; Kokko, Hanna

2015-09-22

The parents' phenotype, or the environment they create for their young, can have long-lasting effects on their offspring, with profound evolutionary consequences. Yet, virtually no work has considered how such parental effects might change the adaptive value of behavioural traits expressed by offspring upon reaching adulthood. To address this problem, we combined experiments on burying beetles (Nicrophorus vespilloides) with theoretical modelling and focussed on one adult behavioural trait in particular: the supply of parental care. We manipulated the early-life environment and measured the fitness payoffs associated with the supply of parental care when larvae reached maturity. We found that (1) adults that received low levels of care as larvae were less successful at raising larger broods and suffered greater mortality as a result: they were low-quality parents. Furthermore, (2) high-quality males that raised offspring with low-quality females subsequently suffered greater mortality than brothers of equivalent quality, which reared larvae with higher quality females. Our analyses identify three general ways in which parental effects can change the adaptive value of an adult behavioural trait: by influencing the associated fitness benefits and costs; by consequently changing the evolutionary outcome of social interactions; and by modifying the evolutionarily stable expression of behavioural traits that are themselves parental effects.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions.

PubMed

Graham, Carly F; Eberts, Rebecca L; Morgan, Thomas D; Boreham, Douglas R; Lance, Stacey L; Manzon, Richard G; Martino, Jessica A; Rogers, Sean M; Wilson, Joanna Y; Somers, Christopher M

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship

PubMed Central

Schluter, Jonas; Schoech, Armin P.; Foster, Kevin R.; Mitri, Sara

2016-01-01

Bacteria regulate many phenotypes via quorum sensing systems. Quorum sensing is typically thought to evolve because the regulated cooperative phenotypes are only beneficial at certain cell densities. However, quorum sensing systems are also threatened by non-cooperative “cheaters” that may exploit quorum-sensing regulated cooperation, which begs the question of how quorum sensing systems are maintained in nature. Here we study the evolution of quorum sensing using an individual-based model that captures the natural ecology and population structuring of microbial communities. We first recapitulate the two existing observations on quorum sensing evolution: density-dependent benefits favor quorum sensing but competition and cheating will destabilize it. We then model quorum sensing in a dense community like a biofilm, which reveals a novel benefit to quorum sensing that is intrinsically evolutionarily stable. In these communities, competing microbial genotypes gradually segregate over time leading to positive correlation between density and genetic similarity between neighboring cells (relatedness). This enables quorum sensing to track genetic relatedness and ensures that costly cooperative traits are only activated once a cell is safely surrounded by clonemates. We hypothesize that under similar natural conditions, the benefits of quorum sensing will not result from an assessment of density but from the ability to infer kinship. PMID:27120081

Evolution of pathogen virulence across space during an epidemic

USGS Publications Warehouse

Osnas, Erik; Hurtado, Paul J.; Dobson, Andrew P.

2015-01-01

We explore pathogen virulence evolution during the spatial expansion of an infectious disease epidemic in the presence of a novel host movement trade-off, using a simple, spatially explicit mathematical model. This work is motivated by empirical observations of the Mycoplasma gallisepticum invasion into North American house finch (Haemorhous mexicanus) populations; however, our results likely have important applications to other emerging infectious diseases in mobile hosts. We assume that infection reduces host movement and survival and that across pathogen strains the severity of these reductions increases with pathogen infectiousness. Assuming these trade-offs between pathogen virulence (host mortality), pathogen transmission, and host movement, we find that pathogen virulence levels near the epidemic front (that maximize wave speed) are lower than those that have a short-term growth rate advantage or that ultimately prevail (i.e., are evolutionarily stable) near the epicenter and where infection becomes endemic (i.e., that maximize the pathogen basic reproductive ratio). We predict that, under these trade-offs, less virulent pathogen strains will dominate the periphery of an epidemic and that more virulent strains will increase in frequency after invasion where disease is endemic. These results have important implications for observing and interpreting spatiotemporal epidemic data and may help explain transient virulence dynamics of emerging infectious diseases.

Insights in connecting phenotypes in bacteria to coevolutionary information

NASA Astrophysics Data System (ADS)

Cheng, Ryan; Morcos, Faruck; Hayes, Ryan; Helm, Rodney; Levine, Herbert; Onuchic, Jose

It has long been known that protein sequences are far from random. These sequences have been evolutionarily selected to maintain their ability to fold into stable, three-dimensional folded structures as well as their ability to form macromolecular assemblies, perform catalytic functions, etc. For these reasons, there exist quantifiable mutational patterns in the collection of sequence data for a protein family arising from the need to maintain favorable residue-residue interactions to facilitate folding as well as cellular function. Here, we focus on studying the correlated mutational patterns that give rise to interaction specificity in bacterial two-component signaling (TCS) systems. TCS proteins have evolved to be able to preferentially bind and transfer a phosphate group to their signaling partner while avoiding phosphotransfer with non-partners. We infer a Potts model Hamiltonian governing the correlated mutational patterns that are observed in the sequence data of TCS partners and apply this model to recently published in vivo mutational data. Our findings further support the notion that statistical models built from sequence data can be used to predict bacterial phenotypes as well as engineer interaction specificity between non-partner TCS proteins. This research has been supported by the NSF INSPIRE Award (MCB-1241332) and by the CTBP sponsored by the NSF (Grant PHY- 1427654).

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Evolutionarily stable size of a megagametophyte: evolution of tiny megagametophytes of angiosperms from large ones of gymnosperms.

PubMed

Sakai, Satoki

2013-02-01

To examine the factors favoring large megagametophytes of gymnosperms and tiny ones of angiosperms, a game model for seed production was developed in which megagametophytes growing in the same female parent compete for resources provided by the parent. In the model, megagametophytes may continue to grow until seed completion or may cease to grow at a certain time and regrow at pollination or fertilization. Autonomous abortion of unpollinated or unfertilized megagametophytes may occur either at pollination or fertilization. Those megagametophytes absorb a certain amount of resources before abortion, due to constraints in the signal process, in addition to the resources absorbed before pollination or fertilization. It was found that both growth habits can be the ESS: megagametophytes continue to grow without cessation and monopolize resources, such as gymnosperms, or cease to grow until fertilization to reduce the loss of resources due to autonomous abortion, such as angiosperms. The former and the latter are the ESS if the time interval between pollination and fertilization is long and short, respectively. Thus, the fertilization interval may be a critical factor selecting for large megagametophytes of gymnosperms or tiny ones of angiosperms. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor

PubMed Central

Anandhakumar, Jayamani; Moustafa, Yara W.; Chowdhary, Surabhi; Kainth, Amoldeep S.

2016-01-01

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the “anchor away” (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. PMID:27185874

Evolutionarily stable disequilibrium: endless dynamics of evolution in a stationary population.

PubMed

Takeuchi, Nobuto; Kaneko, Kunihiko; Hogeweg, Paulien

2016-05-11

Evolution is often conceived as changes in the properties of a population over generations. Does this notion exhaust the possible dynamics of evolution? Life is hierarchically organized, and evolution can operate at multiple levels with conflicting tendencies. Using a minimal model of such conflicting multilevel evolution, we demonstrate the possibility of a novel mode of evolution that challenges the above notion: individuals ceaselessly modify their genetically inherited phenotype and fitness along their lines of descent, without involving apparent changes in the properties of the population. The model assumes a population of primitive cells (protocells, for short), each containing a population of replicating catalytic molecules. Protocells are selected towards maximizing the catalytic activity of internal molecules, whereas molecules tend to evolve towards minimizing it in order to maximize their relative fitness within a protocell. These conflicting evolutionary tendencies at different levels and genetic drift drive the lineages of protocells to oscillate endlessly between high and low intracellular catalytic activity, i.e. high and low fitness, along their lines of descent. This oscillation, however, occurs independently in different lineages, so that the population as a whole appears stationary. Therefore, ongoing evolution can be hidden behind an apparently stationary population owing to conflicting multilevel evolution. © 2016 The Authors.

The evolution of plant virus transmission pathways.

PubMed

Hamelin, Frédéric M; Allen, Linda J S; Prendeville, Holly R; Hajimorad, M Reza; Jeger, Michael J

2016-05-07

The evolution of plant virus transmission pathways is studied through transmission via seed, pollen, or a vector. We address the questions: under what circumstances does vector transmission make pollen transmission redundant? Can evolution lead to the coexistence of multiple virus transmission pathways? We restrict the analysis to an annual plant population in which reproduction through seed is obligatory. A semi-discrete model with pollen, seed, and vector transmission is formulated to investigate these questions. We assume vector and pollen transmission rates are frequency-dependent and density-dependent, respectively. An ecological stability analysis is performed for the semi-discrete model and used to inform an evolutionary study of trade-offs between pollen and seed versus vector transmission. Evolutionary dynamics critically depend on the shape of the trade-off functions. Assuming a trade-off between pollen and vector transmission, evolution either leads to an evolutionarily stable mix of pollen and vector transmission (concave trade-off) or there is evolutionary bi-stability (convex trade-off); the presence of pollen transmission may prevent evolution of vector transmission. Considering a trade-off between seed and vector transmission, evolutionary branching and the subsequent coexistence of pollen-borne and vector-borne strains is possible. This study contributes to the theory behind the diversity of plant-virus transmission patterns observed in nature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of dominance in sporophytic self-incompatibility systems: I. Genetic load and coevolution of levels of dominance in pollen and pistil.

PubMed

Llaurens, Violaine; Billiard, Sylvain; Castric, Vincent; Vekemans, Xavier

2009-09-01

Recent theoretical advances have suggested that various forms of balancing selection may promote the evolution of dominance through an increase of the proportion of heterozygote genotypes. We test whether dominance can evolve in the sporophytic self-incompatibility (SSI) system in plants. SSI prevents mating between individuals expressing identical SI phenotypes by recognition of pollen by pistils, which avoids selfing and inbreeding depression. SI phenotypes depend on a complex network of dominance relationships between alleles at the self-incompatibility locus (S-locus). Empirical studies suggest that these relationships are not random, but the exact evolutionary processes shaping these relationships remain unclear. We investigate the expected patterns of dominance under the hypothesis that dominance is a direct target of natural selection. We follow the fate of a mutant allele at the S-locus whose dominance relationships are changed but whose specificity remains unaltered. We show that strict codominance is not evolutionarily stable in SSI, and that inbreeding depression due to deleterious mutations linked or unlinked to the S-locus exerts strong constraints on changes in relative levels of dominance in pollen and pistil. Our results provide a general adaptive explanation for most patterns of dominance relationships empirically observed in natural plant populations.

Trade-off between learning and exploitation: the Pareto-optimal versus evolutionarily stable learning schedule in cumulative cultural evolution.

PubMed

Wakano, Joe Yuichiro; Miura, Chiaki

2014-02-01

Inheritance of culture is achieved by social learning and improvement is achieved by individual learning. To realize cumulative cultural evolution, social and individual learning should be performed in this order in one's life. However, it is not clear whether such a learning schedule can evolve by the maximization of individual fitness. Here we study optimal allocation of lifetime to learning and exploitation in a two-stage life history model under a constant environment. We show that the learning schedule by which high cultural level is achieved through cumulative cultural evolution is unlikely to evolve as a result of the maximization of individual fitness, if there exists a trade-off between the time spent in learning and the time spent in exploiting the knowledge that has been learned in earlier stages of one's life. Collapse of a fully developed culture is predicted by a game-theoretical analysis where individuals behave selfishly, e.g., less learning and more exploiting. The present study suggests that such factors as group selection, the ability of learning-while-working ("on the job training"), or environmental fluctuation might be important in the realization of rapid and cumulative cultural evolution that is observed in humans. Copyright © 2013 Elsevier Inc. All rights reserved.

Reefs happen

USGS Publications Warehouse

Kinzie, R. A.; Buddemeier, R.W.

1996-01-01

Corals and coral reefs confront us with a variety of paradoxes in terms of their responses to global change. The species appear evolutionarily long-lived and stable, and combinations of organisms recur and persist at levels ranging from endosymbiosis to palaeocommunity structure. The fact that these organisms and communities occupy a seemingly precarious environment near the common interface of land, sea, and air suggests that they possess powerful adaptive and acclimative mechanisms, and the special characteristics associated with their range of reproductive options, their modular (colonial) form, and their symbiotic associations provide multiple pathways for adaptation. At the same time, they are widely considered to be vulnerable to anthropogenic stresses, and to show signs of deterioration on a global scale. Interest in corals is further enhanced by their unique position with regard to the carbon cycle, with inorganic and organic carbon metabolisms that are of comparable magnitudes. The durable limestone structures they create modify the shallow-water environment, and their mineral skeletons preserve in their isotopic, chemical, and structural characteristics records of past environmental conditions. Whether as survivors, recorders, or victims, their relationship to global change is fascinating and instructive. This paper provides a general background and context for the specific papers that make up this topical issue of Global Change Biology. ?? 1996 Blackwell Science Ltd.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions

PubMed Central

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; Boreham, Douglas R.; Lance, Stacey L.; Manzon, Richard G.; Martino, Jessica A.; Rogers, Sean M.; Wilson, Joanna Y.; Somers, Christopher M.

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment. PMID:26807722

A facile strategy for enzyme immobilization with highly stable hierarchically porous metal-organic frameworks.

PubMed

Liu, Xiao; Qi, Wei; Wang, Yuefei; Su, Rongxin; He, Zhimin

2017-11-16

Metal-organic frameworks (MOFs) have drawn extensive research interest as candidates for enzyme immobilization owing to their tunable porosity, high surface area, and excellent chemical/thermal stability. Herein, we report a facile and universal strategy for enzyme immobilization using highly stable hierarchically porous metal-organic frameworks (HP-MOFs). The HP-MOFs were stable over a wide pH range (pH = 2-11 for HP-DUT-5) and met the catalysis conditions of most enzymes. The as-prepared hierarchical micro/mesoporous MOFs with mesoporous defects showed a superior adsorption capacity towards enzymes. The maximum adsorption capacity of HP-DUT-5 for glucose oxidase (GOx) and uricase was 208 mg g -1 and 225 mg g -1 , respectively. Furthermore, we constructed two multi-enzyme biosensors for glucose and uric acid (UA) by immobilizing GOx and uricase with horseradish peroxidase (HRP) on HP-DUT-5, respectively. These sensors were efficiently applied in the colorimetric detection of glucose and UA and showed good sensitivity, selectivity, and recyclability.

Adaptive Topographies and Equilibrium Selection in an Evolutionary Game

PubMed Central

Osinga, Hinke M.; Marshall, James A. R.

2015-01-01

It has long been known in the field of population genetics that adaptive topographies, in which population equilibria maximise mean population fitness for a trait regardless of its genetic bases, do not exist. Whether one chooses to model selection acting on a single locus or multiple loci does matter. In evolutionary game theory, analysis of a simple and general game involving distinct roles for the two players has shown that whether strategies are modelled using a single ‘locus’ or one ‘locus’ for each role, the stable population equilibria are unchanged and correspond to the fitness-maximising evolutionary stable strategies of the game. This is curious given the aforementioned population genetical results on the importance of the genetic bases of traits. Here we present a dynamical systems analysis of the game with roles detailing how, while the stable equilibria in this game are unchanged by the number of ‘loci’ modelled, equilibrium selection may differ under the two modelling approaches. PMID:25706762

Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments

PubMed Central

New, Aaron M.; Cerulus, Bram; Govers, Sander K.; Perez-Samper, Gemma; Zhu, Bo; Boogmans, Sarah; Xavier, Joao B.; Verstrepen, Kevin J.

2014-01-01

Organisms respond to environmental changes by adapting the expression of key genes. However, such transcriptional reprogramming requires time and energy, and may also leave the organism ill-adapted when the original environment returns. Here, we study the dynamics of transcriptional reprogramming and fitness in the model eukaryote Saccharomyces cerevisiae in response to changing carbon environments. Population and single-cell analyses reveal that some wild yeast strains rapidly and uniformly adapt gene expression and growth to changing carbon sources, whereas other strains respond more slowly, resulting in long periods of slow growth (the so-called “lag phase”) and large differences between individual cells within the population. We exploit this natural heterogeneity to evolve a set of mutants that demonstrate how the frequency and duration of changes in carbon source can favor different carbon catabolite repression strategies. At one end of this spectrum are “specialist” strategies that display high rates of growth in stable environments, with more stringent catabolite repression and slower transcriptional reprogramming. The other mutants display less stringent catabolite repression, resulting in leaky expression of genes that are not required for growth in glucose. This “generalist” strategy reduces fitness in glucose, but allows faster transcriptional reprogramming and shorter lag phases when the cells need to shift to alternative carbon sources. Whole-genome sequencing of these mutants reveals that mutations in key regulatory genes such as HXK2 and STD1 adjust the regulation and transcriptional noise of metabolic genes, with some mutations leading to alternative gene regulatory strategies that allow “stochastic sensing” of the environment. Together, our study unmasks how variable and stable environments favor distinct strategies of transcriptional reprogramming and growth. PMID:24453942

Reexamining the Efficacy and Value of Percutaneous Coronary Intervention for Patients With Stable Ischemic Heart Disease

PubMed Central

Weintraub, William S.; Boden, William E.

2017-01-01

Percutaneous coronary intervention (PCI) continues to be performed frequently for patients with stable ischemic heart disease, despite uncertain efficacy. Individual randomized trial data and meta-analyses have not demonstrated that PCI in addition to optimal medical therapy reduces the incidence of death or myocardial infarction in patients with stable disease. The Clinical Outcomes Utilizing Revascularization and Aggressive Drug Evaluation (COURAGE) Trial did not show benefit for cardiovascular outcomes or mortality but did find a modest improvement in quality of life that did not persist at 3 years. Long-term follow-up from COURAGE (up to 15 years) found no differences in mortality, consistent with other published literature. How PCI could reduce long-term mortality or prevent myocardial infarction is not clear because sites of future plaque rupture leading to myocardial infarction are unpredictable and PCI can only treat localized anatomic segments of obstructive atherosclerosis. In addition, PCI is expensive, and the value to society of PCI for stable disease has not been demonstrated. The ISCHEMIA trial will assess the role of PCI for stable ischemic heart disease using newer technology and in patients with greater ischemic burden than in COURAGE. After nearly a decade, the COURAGE trial and other studies have given us pause to critically reexamine the role of PCI for patients with stable ischemic heart disease. Until further research can show that PCI can reduce cardiovascular events in these patients, a first-line strategy of optimal medical therapy is known to be safe, effective, and noninferior to PCI, and our practice should more closely follow this strategy. PMID:27380178

Coronary computed tomography versus exercise testing in patients with stable chest pain: comparative effectiveness and costs.

PubMed

Genders, Tessa S S; Ferket, Bart S; Dedic, Admir; Galema, Tjebbe W; Mollet, Nico R A; de Feyter, Pim J; Fleischmann, Kirsten E; Nieman, Koen; Hunink, M G Myriam

2013-08-20

To determine the comparative effectiveness and costs of a CT-strategy and a stress-electrocardiography-based strategy (standard-of-care; SOC-strategy) for diagnosing coronary artery disease (CAD). A decision analysis was performed based on a well-documented prospective cohort of 471 outpatients with stable chest pain with follow-up combined with best-available evidence from the literature. Outcomes were correct classification of patients as CAD- (no obstructive CAD), CAD+ (obstructive CAD without revascularization) and indication for Revascularization (using a combination reference standard), diagnostic costs, lifetime health care costs, and quality-adjusted life years (QALY). Parameter uncertainty was analyzed using probabilistic sensitivity analysis. For men (and women), diagnostic cost savings were €245 (€252) for the CT-strategy as compared to the SOC-strategy. The CT-strategy classified 82% (88%) of simulated men (women) in the appropriate disease category, whereas 83% (85%) were correctly classified by the SOC-strategy. The long-term cost-effectiveness analysis showed that the SOC-strategy was dominated by the CT-strategy, which was less expensive (-€229 in men, -€444 in women) and more effective (+0.002 QALY in men, +0.005 in women). The CT-strategy was cost-saving (-€231) but also less effective compared to SOC (-0.003 QALY) in men with a pre-test probability of ≥ 70%. The CT-strategy was cost-effective in 100% of simulations, except for men with a pre-test probability ≥ 70% in which case it was 59%. The results suggest that a CT-based strategy is less expensive and equally effective compared to SOC in all women and in men with a pre-test probability <70%. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Stochastic evolutionary voluntary public goods game with punishment in a Quasi-birth-and-death process.

PubMed

Quan, Ji; Liu, Wei; Chu, Yuqing; Wang, Xianjia

2017-11-23

Traditional replication dynamic model and the corresponding concept of evolutionary stable strategy (ESS) only takes into account whether the system can return to the equilibrium after being subjected to a small disturbance. In the real world, due to continuous noise, the ESS of the system may not be stochastically stable. In this paper, a model of voluntary public goods game with punishment is studied in a stochastic situation. Unlike the existing model, we describe the evolutionary process of strategies in the population as a generalized quasi-birth-and-death process. And we investigate the stochastic stable equilibrium (SSE) instead. By numerical experiments, we get all possible SSEs of the system for any combination of parameters, and investigate the influence of parameters on the probabilities of the system to select different equilibriums. It is found that in the stochastic situation, the introduction of the punishment and non-participation strategies can change the evolutionary dynamics of the system and equilibrium of the game. There is a large range of parameters that the system selects the cooperative states as its SSE with a high probability. This result provides us an insight and control method for the evolution of cooperation in the public goods game in stochastic situations.

An intermittent control model of flexible human gait using a stable manifold of saddle-type unstable limit cycle dynamics

PubMed Central

Fu, Chunjiang; Suzuki, Yasuyuki; Kiyono, Ken; Morasso, Pietro; Nomura, Taishin

2014-01-01

Stability of human gait is the ability to maintain upright posture during walking against external perturbations. It is a complex process determined by a number of cross-related factors, including gait trajectory, joint impedance and neural control strategies. Here, we consider a control strategy that can achieve stable steady-state periodic gait while maintaining joint flexibility with the lowest possible joint impedance. To this end, we carried out a simulation study of a heel-toe footed biped model with hip, knee and ankle joints and a heavy head-arms-trunk element, working in the sagittal plane. For simplicity, the model assumes a periodic desired joint angle trajectory and joint torques generated by a set of feed-forward and proportional-derivative feedback controllers, whereby the joint impedance is parametrized by the feedback gains. We could show that a desired steady-state gait accompanied by the desired joint angle trajectory can be established as a stable limit cycle (LC) for the feedback controller with an appropriate set of large feedback gains. Moreover, as the feedback gains are decreased for lowering the joint stiffness, stability of the LC is lost only in a few dimensions, while leaving the remaining large number of dimensions quite stable: this means that the LC becomes saddle-type, with a low-dimensional unstable manifold and a high-dimensional stable manifold. Remarkably, the unstable manifold remains of low dimensionality even when the feedback gains are decreased far below the instability point. We then developed an intermittent neural feedback controller that is activated only for short periods of time at an optimal phase of each gait stride. We characterized the robustness of this design by showing that it can better stabilize the unstable LC with small feedback gains, leading to a flexible gait, and in particular we demonstrated that such an intermittent controller performs better if it drives the state point to the stable manifold, rather than directly to the LC. The proposed intermittent control strategy might have a high affinity for the inverted pendulum analogy of biped gait, providing a dynamic view of how the step-to-step transition from one pendular stance to the next can be achieved stably in a robust manner by a well-timed neural intervention that exploits the stable modes embedded in the unstable dynamics. PMID:25339687

An intermittent control model of flexible human gait using a stable manifold of saddle-type unstable limit cycle dynamics.

PubMed

Fu, Chunjiang; Suzuki, Yasuyuki; Kiyono, Ken; Morasso, Pietro; Nomura, Taishin

2014-12-06

Stability of human gait is the ability to maintain upright posture during walking against external perturbations. It is a complex process determined by a number of cross-related factors, including gait trajectory, joint impedance and neural control strategies. Here, we consider a control strategy that can achieve stable steady-state periodic gait while maintaining joint flexibility with the lowest possible joint impedance. To this end, we carried out a simulation study of a heel-toe footed biped model with hip, knee and ankle joints and a heavy head-arms-trunk element, working in the sagittal plane. For simplicity, the model assumes a periodic desired joint angle trajectory and joint torques generated by a set of feed-forward and proportional-derivative feedback controllers, whereby the joint impedance is parametrized by the feedback gains. We could show that a desired steady-state gait accompanied by the desired joint angle trajectory can be established as a stable limit cycle (LC) for the feedback controller with an appropriate set of large feedback gains. Moreover, as the feedback gains are decreased for lowering the joint stiffness, stability of the LC is lost only in a few dimensions, while leaving the remaining large number of dimensions quite stable: this means that the LC becomes saddle-type, with a low-dimensional unstable manifold and a high-dimensional stable manifold. Remarkably, the unstable manifold remains of low dimensionality even when the feedback gains are decreased far below the instability point. We then developed an intermittent neural feedback controller that is activated only for short periods of time at an optimal phase of each gait stride. We characterized the robustness of this design by showing that it can better stabilize the unstable LC with small feedback gains, leading to a flexible gait, and in particular we demonstrated that such an intermittent controller performs better if it drives the state point to the stable manifold, rather than directly to the LC. The proposed intermittent control strategy might have a high affinity for the inverted pendulum analogy of biped gait, providing a dynamic view of how the step-to-step transition from one pendular stance to the next can be achieved stably in a robust manner by a well-timed neural intervention that exploits the stable modes embedded in the unstable dynamics.

Evolutionarily conserved coupling of adaptive and excitable networks mediates eukaryotic chemotaxis

NASA Astrophysics Data System (ADS)

Tang, Ming; Wang, Mingjie; Shi, Changji; Iglesias, Pablo A.; Devreotes, Peter N.; Huang, Chuan-Hsiang

2014-10-01

Numerous models explain how cells sense and migrate towards shallow chemoattractant gradients. Studies show that an excitable signal transduction network acts as a pacemaker that controls the cytoskeleton to drive motility. Here we show that this network is required to link stimuli to actin polymerization and chemotactic motility and we distinguish the various models of chemotaxis. First, signalling activity is suppressed towards the low side in a gradient or following removal of uniform chemoattractant. Second, signalling activities display a rapid shut off and a slower adaptation during which responsiveness to subsequent test stimuli decline. Simulations of various models indicate that these properties require coupled adaptive and excitable networks. Adaptation involves a G-protein-independent inhibitor, as stimulation of cells lacking G-protein function suppresses basal activities. The salient features of the coupled networks were observed for different chemoattractants in Dictyostelium and in human neutrophils, suggesting an evolutionarily conserved mechanism for eukaryotic chemotaxis.

The presence of the ancestral insect telomeric motif in kissing bugs (Triatominae) rules out the hypothesis of its loss in evolutionarily advanced Heteroptera (Cimicomorpha)

PubMed Central

Pita, Sebastián; Panzera, Francisco; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Lorite, Pedro

2016-01-01

Abstract Next-generation sequencing data analysis on Triatoma infestans Klug, 1834 (Heteroptera, Cimicomorpha, Reduviidae) revealed the presence of the ancestral insect (TTAGG)n telomeric motif in its genome. Fluorescence in situ hybridization confirms that chromosomes bear this telomeric sequence in their chromosomal ends. Furthermore, motif amount estimation was about 0.03% of the total genome, so that the average telomere length in each chromosomal end is almost 18 kb long. We also detected the presence of (TTAGG)n telomeric repeat in mitotic and meiotic chromosomes in other three species of Triatominae: Triatoma dimidiata Latreille, 1811, Dipetalogaster maxima Uhler, 1894, and Rhodnius prolixus Ståhl, 1859. This is the first report of the (TTAGG)n telomeric repeat in the infraorder Cimicomorpha, contradicting the currently accepted hypothesis that evolutionarily recent heteropterans lack this ancestral insect telomeric sequence. PMID:27830050

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras.

PubMed

Stein, R William; Mull, Christopher G; Kuhn, Tyler S; Aschliman, Neil C; Davidson, Lindsay N K; Joy, Jeffrey B; Smith, Gordon J; Dulvy, Nicholas K; Mooers, Arne O

2018-02-01

In an era of accelerated biodiversity loss and limited conservation resources, systematic prioritization of species and places is essential. In terrestrial vertebrates, evolutionary distinctness has been used to identify species and locations that embody the greatest share of evolutionary history. We estimate evolutionary distinctness for a large marine vertebrate radiation on a dated taxon-complete tree for all 1,192 chondrichthyan fishes (sharks, rays and chimaeras) by augmenting a new 610-species molecular phylogeny using taxonomic constraints. Chondrichthyans are by far the most evolutionarily distinct of all major radiations of jawed vertebrates-the average species embodies 26 million years of unique evolutionary history. With this metric, we identify 21 countries with the highest richness, endemism and evolutionary distinctness of threatened species as targets for conservation prioritization. On average, threatened chondrichthyans are more evolutionarily distinct-further motivating improved conservation, fisheries management and trade regulation to avoid significant pruning of the chondrichthyan tree of life.

IQ and the values of nations.

PubMed

Kanazawa, Satoshi

2009-07-01

The origin of values and preferences is an unresolved theoretical question in behavioural and social sciences. The Savanna-IQ Interaction Hypothesis, derived from the Savanna Principle and a theory of the evolution of general intelligence, suggests that more intelligent individuals may be more likely to acquire and espouse evolutionarily novel values and preferences (such as liberalism and atheism and, for men, sexual exclusivity) than less intelligent individuals, but that general intelligence may have no effect on the acquisition and espousal of evolutionarily familiar values. Macro-level analyses show that nations with higher average intelligence are more liberal (have greater highest marginal individual tax rate and, as a result, lower income inequality), less religious (a smaller proportion of the population believes in God or considers themselves religious) and more monogamous. The average intelligence of a population appears to be the strongest predictor of its level of liberalism, atheism and monogamy.

Saccharomyces cerevisiae metabolism in ecological context.

PubMed

Jouhten, Paula; Ponomarova, Olga; Gonzalez, Ramon; Patil, Kiran R

2016-11-01

The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype-environment-phenotype relationships. © FEMS 2016.

H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis.

PubMed

Wang, Liying; Cao, Chunwei; Wang, Fang; Zhao, Jianguo; Li, Wei

2017-09-03

RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiologic functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adaptor with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiologic functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiologic functions of RNF20 during meiosis.

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

PubMed

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Saccharomyces cerevisiae metabolism in ecological context

PubMed Central

Jouhten, Paula; Ponomarova, Olga; Gonzalez, Ramon

2016-01-01

The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype–metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype–phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype–environment–phenotype relationships. PMID:27634775

Rx for low cash yields.

PubMed

Tobe, Chris

2003-10-01

Certain strategies can offer not-for-profit hospitals potentially greater investment yields while maintaining stability and principal safety. Treasury inflation-indexed securities can offer good returns, low volatility, and inflation protection. "Enhanced cash" strategies offer liquidity and help to preserve capital. Stable value "wrappers" allow hospitals to pursue higher-yielding fixed-income securities without an increase in volatility.

Strategies for the Synthesis of Higher Acenes

PubMed Central

Dorel, Ruth

2016-01-01

The outstanding performance of pentacene‐based molecules in molecular electronics, as well as the predicted enhanced semiconducting properties of extended acenes, have stimulated the development of new synthetic methods and functionalization strategies for the preparation of stable and soluble acenes larger than tetracene with the aim of obtaining improved functional materials. PMID:28747846

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes.

PubMed

Kawai, Mikihiko; Uchiyama, Ikuo; Takami, Hideto; Inagaki, Fumio

2015-04-01

Spore formation is considered to be one of the microbial strategies for long-term survival in subseafloor sedimentary habitats. However, our knowledge of the genetic and physiological characteristics of subseafloor microbes is limited. Here, we studied the distribution and frequency of genes that are related to endospore formation in 10 subseafloor sedimentary metagenomes from Site C9001 off Japan and Site 1229 off Peru. None or very low frequencies of endospore-specific genes (e.g. dpaA, dpaB, sspA, spo0A, spoIIGA, spoIIM, spoIIIAB, spoIVA, spoIVB, yabP, yunB, spoVM) were observed in the subseafloor metagenomes. Based on the number of universally conserved single copy genes, the frequency ratio of putative endospore-formers was estimated to be < 10%, which is consistent with the frequency of Clostridia-derived genomes (2-4%) but is lower than previous estimates based on the concentration of dipicolinic acid. Conceivable explanations for this discrepancy are as follows: the efficiency of lysis and DNA extraction of subseafloor endospore cells may have been lower than those of vegetative cells, conversion factor of dipicolinic acid content per cell may differ, and/or sporulation-related genes and other functional strategies for long-term survival in the deep subseafloor biosphere are evolutionarily distinct from known spore-forming gene repertoires. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution.

PubMed

Price, Christopher T D; Richards, Ashley M; Von Dwingelo, Juanita E; Samara, Hala A; Abu Kwaik, Yousef

2014-02-01

Legionella pneumophila, the causative agent of Legionnaires' disease, invades and proliferates within a diverse range of free-living amoeba in the environment, but upon transmission to humans, the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host, but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. Legionella pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Perchlorate and Halogen-Free High Energy Dense Oxidizers (HEDO)

DTIC Science & Technology

2011-06-01

nitric acid indicate that the covalent oxalic acid dinitrate ester should be more stable than the ionic dinitronium oxalate . The following three...synthetic strategies were developed to generate compound 11 (Scheme 17). Strategy I is the nitration of anhydrous oxalic acid with nitric acid (100...temperatures (25 to –30 °C) and in all dry solvents used. Scheme 17: Synthetic strategies for the production of oxalic acid dinitrate ester (11

The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages

PubMed Central

Imanian, Behzad; Keeling, Patrick J

2007-01-01

Background The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them. Results We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate. Conclusion Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport. PMID:17892581

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

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

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCEPost-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

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

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

Differential sensitivity of Chironomus and human hemoglobin to gamma radiation

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

Gaikwad, Pallavi S.; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085; Panicker, Lata

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb.more » Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study. -- Highlights: •Comparison of radiation tolerant Chironomus Hb and radiation sensitive Human Hb. •Amino acid composition of midge and human heme confer differential hydrophobicity. •Heme pocket of evolutionarily ancient midge Hb provide gamma radiation resistivity.« less

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

DOE PAGES

Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.; ...

2017-11-28

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggestmore » that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.« less

WFIRST: Managing Telescope Wavefront Stability to Meet Coronagraph Performance

NASA Astrophysics Data System (ADS)

Noecker, Martin; Poberezhskiy, Ilya; Kern, Brian; Krist, John; WFIRST System Engineering Team

2018-01-01

The WFIRST coronagraph instrument (CGI) needs a stable telescope and active wavefront control to perform coronagraph science with an expected sensitivity of 8x10-9 in the exoplanet-star flux ratio (SNR=10) at 200 milliarcseconds angular separation. With its subnanometer requirements on the stability of its input wavefront error (WFE), the CGI employs a combination of pointing and wavefront control loops and thermo-mechanical stability to meet budget allocations for beam-walk and low-order WFE, which enable stable starlight speckles on the science detector that can be removed by image subtraction. We describe the control strategy and the budget framework for estimating and budgeting the elements of wavefront stability, and the modeling strategy to evaluate it.

Development of a Freeze-Dried, Heat-Stable Influenza Subunit Vaccine Formulation

PubMed Central

Flood, Alexander; Chen, Dexiang

2016-01-01

An influenza pandemic remains a major public health concern. A key strategy to prevent a pandemic is to stockpile and pre-position stable influenza vaccine to allow rapid deployment in response to an outbreak. However, most influenza vaccines today are formulated as liquids that are stable only within a temperature range of 2°C to 8°C and require use of a cold chain, making vaccine transportation, distribution, and storage complicated and expensive, particularly for developing countries. To support the National Strategy for Pandemic Influenza preparedness in the United States and internationally, we developed two lead dry formulations of stable H1N1 influenza subunit vaccines using freeze-drying technology. The stable formulations contain an excipient combination of a disaccharide, such as sucrose or trehalose, and glycine, in addition to a surfactant and phosphate buffer. The freeze-dried vaccines were shown to be safe and remained immunogenic in an in vivo study in mice. Moreover, the lead formulations demonstrated no significant loss of activity after 40 months at storage temperatures of 25°C and 37°C. This stability can be particularly attractive as it could eliminate the need to use a cold chain for vaccine deployment and facilitate integration of vaccine distribution with general drug distribution where appropriate. These freeze-dried thermostable influenza subunit vaccines could also reduce the frequency of vaccine stockpile turnover, offering a cost-effective option for pandemic preparedness. PMID:27851765

Development of a Freeze-Dried, Heat-Stable Influenza Subunit Vaccine Formulation.

PubMed

Flood, Alexander; Estrada, Marcus; McAdams, David; Ji, Yuhua; Chen, Dexiang

2016-01-01

An influenza pandemic remains a major public health concern. A key strategy to prevent a pandemic is to stockpile and pre-position stable influenza vaccine to allow rapid deployment in response to an outbreak. However, most influenza vaccines today are formulated as liquids that are stable only within a temperature range of 2°C to 8°C and require use of a cold chain, making vaccine transportation, distribution, and storage complicated and expensive, particularly for developing countries. To support the National Strategy for Pandemic Influenza preparedness in the United States and internationally, we developed two lead dry formulations of stable H1N1 influenza subunit vaccines using freeze-drying technology. The stable formulations contain an excipient combination of a disaccharide, such as sucrose or trehalose, and glycine, in addition to a surfactant and phosphate buffer. The freeze-dried vaccines were shown to be safe and remained immunogenic in an in vivo study in mice. Moreover, the lead formulations demonstrated no significant loss of activity after 40 months at storage temperatures of 25°C and 37°C. This stability can be particularly attractive as it could eliminate the need to use a cold chain for vaccine deployment and facilitate integration of vaccine distribution with general drug distribution where appropriate. These freeze-dried thermostable influenza subunit vaccines could also reduce the frequency of vaccine stockpile turnover, offering a cost-effective option for pandemic preparedness.

Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives

PubMed Central

Bose, Himadri; Satyanarayana, Tulasi

2017-01-01

All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA) is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed. PMID:28890712

Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives.

PubMed

Bose, Himadri; Satyanarayana, Tulasi

2017-01-01

All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA) is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO 3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed.

Efficacy and safety of strategies to preserve stable extracorporeal life support flow during simulated hypovolemia.

PubMed

Simons, A P; Lindelauf, A A M A; Ganushchak, Y M; Maessen, J G; Weerwind, P W

2014-01-01

Without volume-buffering capacity in extracorporeal life support (ELS) systems, hypovolemia can acutely reduce support flow. This study aims at evaluating efficacy and safety of strategies for preserving stable ELS during hypovolemia. Flow and/or pressure-guided servo pump control, a reserve-driven control strategy and a volume buffer capacity (VBC) device were evaluated with respect to pump flow, venous line pressure and arterial gaseous microemboli (GME) during simulated normovolemia and hypovolemia. Normovolemia resulted in a GME-free pump flow of 3.1 ± 0.0 L/min and a venous line pressure of -10 ± 1 mmHg. Hypovolemia without servo pump control resulted in a GME-loaded flow of 2.3 ± 0.4 L/min with a venous line pressure of -114 ± 52 mmHg. Servo control resulted in an unstable and GME-loaded flow of 1.5 ± 1.2 L/min. With and without servo pump control, the VBC device stabilised flow (SD = 0.2 and 0.0 L/min, respectively) and venous line pressure (SD=51 and 4 mmHg, respectively) with near-absent GME activity. Reserve-driven pump control combined with a VBC device restored a near GME-free flow of 2.7 ± 0.0 L/min with a venous line pressure of -9 ± 0 mmHg. In contrast to a reserve-driven pump control strategy combined with a VBC device, flow and pressure servo control for ELS show evident deficits in preserving stable and safe ELS flow during hypovolemia.

Controlling the Active Sites of Sulfur-Doped Carbon Nanotube-Graphene Nanolobes for Highly Efficient Oxygen Evolution and Reduction Catalysis

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

El-Sawy, Abdelhamid M.; Mosa, Islam M.; Su, Dong

Controlling active sites of metal-free catalysts is an important strategy to enhance activity of the oxygen evolution reaction (OER). We made many attempts have been made to develop metal-free catalysts, but the lack of understanding of active-sites at the atomic-level has slowed the design of highly active and stable metal-free catalysts. We also developed a sequential two-step strategy to dope sulfur into carbon nanotube–graphene nanolobes. This bidoping strategy introduces stable sulfur–carbon active-sites. Fluorescence emission of the sulfur K-edge by X-ray absorption near edge spectroscopy (XANES) and scanning transmission electron microscopy electron energy loss spectroscopy (STEM-EELS) mapping and spectra confirm thatmore » increasing the incorporation of heterocyclic sulfur into the carbon ring of CNTs not only enhances OER activity with an overpotential of 350 mV at a current density of 10 mA cm -2, but also retains 100% of stability after 75 h. Furthermore, the bidoped sulfur carbon nanotube–graphene nanolobes behave like the state-of-the-art catalysts for OER but outperform those systems in terms of turnover frequency (TOF) which is two orders of magnitude greater than (20% Ir/C) at 400 mV overpotential with very high mass activity 1000 mA cm -2 at 570 mV. Moreover, the sulfur bidoping strategy shows high catalytic activity for the oxygen reduction reaction (ORR). Stable bifunctional (ORR and OER) catalysts are low cost, and light-weight bidoped sulfur carbon nanotubes are potential candidates for next-generation metal-free regenerative fuel cells.« less

Controlling the Active Sites of Sulfur-Doped Carbon Nanotube-Graphene Nanolobes for Highly Efficient Oxygen Evolution and Reduction Catalysis

DOE PAGES

El-Sawy, Abdelhamid M.; Mosa, Islam M.; Su, Dong; ...

2015-12-03

Controlling active sites of metal-free catalysts is an important strategy to enhance activity of the oxygen evolution reaction (OER). We made many attempts have been made to develop metal-free catalysts, but the lack of understanding of active-sites at the atomic-level has slowed the design of highly active and stable metal-free catalysts. We also developed a sequential two-step strategy to dope sulfur into carbon nanotube–graphene nanolobes. This bidoping strategy introduces stable sulfur–carbon active-sites. Fluorescence emission of the sulfur K-edge by X-ray absorption near edge spectroscopy (XANES) and scanning transmission electron microscopy electron energy loss spectroscopy (STEM-EELS) mapping and spectra confirm thatmore » increasing the incorporation of heterocyclic sulfur into the carbon ring of CNTs not only enhances OER activity with an overpotential of 350 mV at a current density of 10 mA cm -2, but also retains 100% of stability after 75 h. Furthermore, the bidoped sulfur carbon nanotube–graphene nanolobes behave like the state-of-the-art catalysts for OER but outperform those systems in terms of turnover frequency (TOF) which is two orders of magnitude greater than (20% Ir/C) at 400 mV overpotential with very high mass activity 1000 mA cm -2 at 570 mV. Moreover, the sulfur bidoping strategy shows high catalytic activity for the oxygen reduction reaction (ORR). Stable bifunctional (ORR and OER) catalysts are low cost, and light-weight bidoped sulfur carbon nanotubes are potential candidates for next-generation metal-free regenerative fuel cells.« less

New Strategies To Promote Stable Employment and Career Progression: An Introduction to the Employment Retention and Advancement Project.

ERIC Educational Resources Information Center

Bloom, Dan; Anderson, Jacquelyn; Wavelet, Melissa; Gardiner, Karen N.; Fishman, Michael E.

The Employment Retention and Advancement (ERA) project was undertaken to identify effective strategies for helping low-income parents work more steadily and advance in the labor market. The 15 ERA demonstration projects that were operating in nine states (California, Florida, Illinois, Minnesota, New York, Oregon, South Carolina; Tennessee, and…

A Phenomenological Study of Effective Reading Strategies for Children of Poverty in Nonmetropolitan: Stable School Settings

ERIC Educational Resources Information Center

Reyenga, Billy Shane

2017-01-01

This phenomenological narrative study explored the effective reading strategies that successful Kindergarten and 1st Grade teachers used for economically disadvantaged students. The researcher used face-to-face interviews to glean data from 10 successful Kindergarten and 1st Grade teachers. The study findings lead to the conclusion that despite…

A four-phase strategy for the implementation of reflectance confocal microscopy in dermatology.

PubMed

Hoogedoorn, L; Gerritsen, M J P; Wolberink, E A W; Peppelman, M; van de Kerkhof, P C M; van Erp, P E J

2016-08-01

Reflectance confocal microscopy (RCM) is gradually implemented in dermatology. Strategies for further implementation and practical 'hands on' guidelines are lacking. The primary outcome was to conduct a general strategy for further implementation of RCM. The secondary outcome was the diagnosis of psoriasis and differentiation of stable from unstable psoriatic plaques by means of the 'hands on' protocol, derived from the strategy. We used a four-phased model; an exploring phase, a systematic literature search, a clinical approach and, finally, an integration phase to develop a clinical guideline for RCM in psoriasis. Receiver operating characteristic curve statistics was applied to define the accuracy for the diagnosis of unstable psoriasis. A general strategy for further implementation of RCM and practical approach was developed to examine psoriasis by RCM and to distinguish stable from unstable psoriasis. Unstable psoriasis was diagnosed by epidermal inflammatory cell counts with a sensitivity and specificity of 91.7% and 98.3%, respectively, and with an accuracy of 0.92 (area under the curve). In addition, a monitoring model was proposed. This is the first study that shows a method for implementation of RCM in dermatology. The strategy and hands on protocol for psoriasis may serve as a model for other dermatological entities and additionally may lead to specialized ready-to-use RCM protocols for clinical dermatological practice. © 2016 European Academy of Dermatology and Venereology.

Beating the thermodynamic limit with photo-activation of n-doping in organic semiconductors

NASA Astrophysics Data System (ADS)

Lin, Xin; Wegner, Berthold; Lee, Kyung Min; Fusella, Michael A.; Zhang, Fengyu; Moudgil, Karttikay; Rand, Barry P.; Barlow, Stephen; Marder, Seth R.; Koch, Norbert; Kahn, Antoine

2017-12-01

Chemical doping of organic semiconductors using molecular dopants plays a key role in the fabrication of efficient organic electronic devices. Although a variety of stable molecular p-dopants have been developed and successfully deployed in devices in the past decade, air-stable molecular n-dopants suitable for materials with low electron affinity are still elusive. Here we demonstrate that photo-activation of a cleavable air-stable dimeric dopant can result in kinetically stable and efficient n-doping of host semiconductors, whose reduction potentials are beyond the thermodynamic reach of the dimer’s effective reducing strength. Electron-transport layers doped in this manner are used to fabricate high-efficiency organic light-emitting diodes. Our strategy thus enables a new paradigm for using air-stable molecular dopants to improve conductivity in, and provide ohmic contacts to, organic semiconductors with very low electron affinity.

Stable Nighttime Light Decreased in Protected Area of California: Findings from DMSP-OLS Observations and the Importance for Protected Area Policy Making

NASA Astrophysics Data System (ADS)

Jia, S.; Gillespie, T. W.

2016-12-01

Stable nighttime light, an indicator of persisting human activity and light pollution is a well-recognized disturbance to the wilderness of protected areas (PAs). Mostly supported by in situ observations, very limited studies of light pollution for PAs focused at a regional level and on a continuous time span to support policy making effectively. DMSP-OLS stable nighttime series provide continuous observation of nightlight and have been widely applied in studies focusing on human activities. In this study, we employed inter-calibrated DMSP-OLS nightlight series from 1992 to 2012 to evaluate the change of intensity and extension of stable nighttime light inside California PAs. We observed a decrease of stable nighttime light and a shrinkage in spatial extent in PAs located in all ecoregions from 1992 to 2012, especially before 2004. Such decrease and shrinkage occurred mostly in southern California and the Bay Area where mega metropolitan clusters locate. The successful application of protecting strategies in PAs and the improved technologies of lighting may contribute to the relieving of light pollution in PAs. However, the stable nighttime light slightly increased since 2004, when there was limited room for stricter protective regulations and the pressure from population growth persisted. Population density explained most spatial distribution of nightlight in years with census tract level demographic data available, except PAs with the highest wilderness such as Sierra Nevada Mts. We anticipate to improve the models with the newest remote sensing nighttime product from NASA Suomi-NPP and annually updated demographic data from American Community Survey at census tract level in the future to provide a cost-effective evaluation on protecting strategies. Such evaluation will support land managers of PAs and local policy-makers for modification and proposal of policies.

Investigating Extreme Lifestyles through Mangrove Transcriptomics

ERIC Educational Resources Information Center

Dassanayake, Maheshi

2009-01-01

Mangroves represent phylogenetically diverse taxa in tropical coastal terrestrial habitats. They are extremophiles, evolutionarily adapted to tolerate flooding, anoxia, high temperatures, wind, and high and extremely variable salt conditions in typically resource-poor environments. The genetic basis for these adaptations is, however, virtually…

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2014 CFR

2014-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2014 CFR

2014-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2011 CFR

2011-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2013 CFR

2013-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2012 CFR

2012-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2011 CFR

2011-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2013 CFR

2013-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2012 CFR

2012-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.211 - Critical habitat for Seven Evolutionarily Significant Units (ESUs) of Salmon (Oncorhynchus spp...

Code of Federal Regulations, 2010 CFR

2010-10-01

... form and maintain physical habitat conditions and support juvenile growth and mobility; (ii) Water...); Fossil Creek (39.9447, -123.0403); Middle Fork Eel River (40.0780, -123.0442); North Fork Middle Fork Eel...

50 CFR 226.212 - Critical habitat for 13 Evolutionarily Significant Units (ESUs) of salmon and steelhead...

Code of Federal Regulations, 2010 CFR

2010-10-01

... floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and... endpoint(s) in: Crooked Creek (46.3033, -123.6222); East Fork Grays River (46.4425, -123.4081); Fossil...

Lactation Biology Symposium: Lactocrine signaling and developmental programming

USDA-ARS?s Scientific Manuscript database

Lactocrine signaling is defined as transmission of bioactive factors from mother to offspring as a consequence of nursing. Lactocrine transmission of signaling molecules may be an evolutionarily conserved process through which bioactive factors necessary for support of neonatal development are deliv...

Phylogenetic conservatism in plant phenology

USGS Publications Warehouse

Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

2013-01-01

Synthesis. Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conser ved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species’ shared evolutionary histories.

Feedback control of flow vorticity at low Reynolds numbers.

PubMed

Zeitz, Maria; Gurevich, Pavel; Stark, Holger

2015-03-01

Our aim is to explore strategies of feedback control to design and stabilize novel dynamic flow patterns in model systems of complex fluids. To introduce the control strategies, we investigate the simple Newtonian fluid at low Reynolds number in a circular geometry. Then, the fluid vorticity satisfies a diffusion equation. We determine the mean vorticity in the sensing area and use two control strategies to feed it back into the system by controlling the angular velocity of the circular boundary. Hysteretic feedback control generates self-regulated stable oscillations in time, the frequency of which can be adjusted over several orders of magnitude by tuning the relevant feedback parameters. Time-delayed feedback control initiates unstable vorticity modes for sufficiently large feedback strength. For increasing delay time, we first observe oscillations with beats and then regular trains of narrow pulses. Close to the transition line between the resting fluid and the unstable modes, these patterns are relatively stable over long times.

Three strategies to stabilise nearly monodispersed silver nanoparticles in aqueous solution

NASA Astrophysics Data System (ADS)

Stevenson, Amadeus PZ; Blanco Bea, Duani; Civit, Sergi; Antoranz Contera, Sonia; Iglesias Cerveto, Alberto; Trigueros, Sonia

2012-02-01

Silver nanoparticles are extensively used due to their chemical and physical properties and promising applications in areas such as medicine and electronics. Controlled synthesis of silver nanoparticles remains a major challenge due to the difficulty in producing long-term stable particles of the same size and shape in aqueous solution. To address this problem, we examine three strategies to stabilise aqueous solutions of 15 nm citrate-reduced silver nanoparticles using organic polymeric capping, bimetallic core-shell and bimetallic alloying. Our results show that these strategies drastically improve nanoparticle stability by distinct mechanisms. Additionally, we report a new role of polymer functionalisation in preventing further uncontrolled nanoparticle growth. For bimetallic nanoparticles, we attribute the presence of a higher valence metal on the surface of the nanoparticle as one of the key factors for improving their long-term stability. Stable silver-based nanoparticles, free of organic solvents, will have great potential for accelerating further environmental and nanotoxicity studies. PACS: 81.07.-b; 81.16.Be; 82.70.Dd.

A Novel Hybrid Iron Regulation Network Combines Features from Pathogenic and Nonpathogenic Yeasts

PubMed Central

Gerwien, Franziska; Safyan, Abu; Wisgott, Stephanie; Hille, Fabrice; Kaemmer, Philipp; Linde, Jörg; Brunke, Sascha; Kasper, Lydia

2016-01-01

ABSTRACT Iron is an essential micronutrient for both pathogens and their hosts, which restrict iron availability during infections in an effort to prevent microbial growth. Successful human pathogens like the yeast Candida glabrata have thus developed effective iron acquisition strategies. Their regulation has been investigated well for some pathogenic fungi and in the model organism Saccharomyces cerevisiae, which employs an evolutionarily derived system. Here, we show that C. glabrata uses a regulation network largely consisting of components of the S. cerevisiae regulon but also of elements of other pathogenic fungi. Specifically, similarly to baker’s yeast, Aft1 is the main positive regulator under iron starvation conditions, while Cth2 degrades mRNAs encoding iron-requiring enzymes. However, unlike the case with S. cerevisiae, a Sef1 ortholog is required for full growth under iron limitation conditions, making C. glabrata an evolutionary intermediate to SEF1-dependent fungal pathogens. Therefore, C. glabrata has evolved an iron homeostasis system which seems to be unique within the pathogenic fungi. PMID:27795405

Broad spectrum antiretroviral activity of 2',3'-dideoxynucleosides.

PubMed Central

Dahlberg, J E; Mitsuya, H; Blam, S B; Broder, S; Aaronson, S A

1987-01-01

Certain dideoxynucleosides have been shown to markedly inhibit the infectivity of human T-lymphotropic virus type III/lymphadenopathy-associated virus, the causative agent of acquired immunodeficiency syndrome (AIDS). Our present studies demonstrate that these drugs are broad spectrum antiretroviral agents capable of inhibiting the infectivity of evolutionarily divergent mammalian type C and animal lentiviruses. Under some conditions, virus infectivity could be inhibited by more than six orders of magnitude. However, the potency of these agents was shown to be greatly influenced by cell-specified determinants. Drug exposure during the initial 24 hr was almost as effective as prolonged treatment on the inhibition of a single cycle of virus infection and expression. Moreover, virus infection was shown directly to be inhibited at the level of proviral DNA synthesis. Thus the time period during which reverse transcription and provirus integration occur is the critical period required for drug action. Our findings have implications concerning strategies to be considered in attempts to utilize 2',3'-dideoxynucleosides in control and treatment of retrovirus-induced diseases of animals and humans. Images PMID:3470806

Comprehensive identification and profiling of host miRNAs in response to Singapore grouper iridovirus (SGIV) infection in grouper (Epinephelus coioides).

PubMed

Guo, Chuanyu; Cui, Huachun; Ni, Songwei; Yan, Yang; Qin, Qiwei

2015-10-01

microRNAs (miRNAs) are an evolutionarily conserved class of non-coding RNA molecules that participate in various biological processes. Employment of high-throughput screening strategies greatly prompts the investigation and profiling of miRNAs in diverse species. In recent years, grouper (Epinephelus spp.) aquaculture was severely affected by iridoviral diseases. However, knowledge regarding the host immune responses to viral infection, especially the miRNA-mediated immune regulatory roles, is rather limited. In this study, by employing Solexa deep sequencing approach, we identified 116 grouper miRNAs from grouper spleen-derived cells (GS). As expected, these miRNAs shared high sequence similarity with miRNAs identified in zebrafish (Danio rerio), pufferfish (Fugu rubripes), and other higher vertebrates. In the process of Singapore grouper iridovirus (SGIV) infection, 45 and 43 miRNAs with altered expression (>1.5-fold) were identified by miRNA microarray assays in grouper spleen tissues and GS cells, respectively. Furthermore, target prediction revealed 189 putative targets of these grouper miRNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bile salt receptor complex activates a pathogenic type III secretion system

DOE PAGES

Li, Peng; Rivera-Cancel, Giomar; Kinch, Lisa N.; ...

2016-07-05

Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure ofmore » VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.« less

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.

PubMed

Matthew, Ashley N; Zephyr, Jacqueto; Hill, Caitlin J; Jahangir, Muhammad; Newton, Alicia; Petropoulos, Christos J; Huang, Wei; Kurt-Yilmaz, Nese; Schiffer, Celia A; Ali, Akbar

2017-07-13

A substrate envelope-guided design strategy is reported for improving the resistance profile of HCV NS3/4A protease inhibitors. Analogues of 5172-mcP1P3 were designed by incorporating diverse quinoxalines at the P2 position that predominantly interact with the invariant catalytic triad of the protease. Exploration of structure-activity relationships showed that inhibitors with small hydrophobic substituents at the 3-position of P2 quinoxaline maintain better potency against drug resistant variants, likely due to reduced interactions with residues in the S2 subsite. In contrast, inhibitors with larger groups at this position were highly susceptible to mutations at Arg155, Ala156, and Asp168. Excitingly, several inhibitors exhibited exceptional potency profiles with EC 50 values ≤5 nM against major drug resistant HCV variants. These findings support that inhibitors designed to interact with evolutionarily constrained regions of the protease, while avoiding interactions with residues not essential for substrate recognition, are less likely to be susceptible to drug resistance.

Biology of flower-infecting fungi.

PubMed

Ngugi, Henry K; Scherm, Harald

2006-01-01

The ability to infect host flowers offers important ecological benefits to plant-parasitic fungi; not surprisingly, therefore, numerous fungal species from a wide range of taxonomic groups have adopted a life style that involves flower infection. Although flower-infecting fungi are very diverse, they can be classified readily into three major groups: opportunistic, unspecialized pathogens causing necrotic symptoms such as blossom blights (group 1), and specialist flower pathogens which infect inflorescences either through the gynoecium (group 2) or systemically through the apical meristem (group 3). This three-tier system is supported by life history attributes such as host range, mode of spore transmission, degree of host sterilization as a result of infection, and whether or not the fungus undergoes an obligate sexual cycle, produces resting spores in affected inflorescences, and is r- or K-selected. Across the three groups, the flower as an infection court poses important challenges for disease management. Ecologically and evolutionarily, terms and concepts borrowed from the study of venereal (sexually transmitted) diseases of animals do not adequately capture the range of strategies employed by fungi that infect flowers.

Reconsolidation or extinction: transcription factor switch in the determination of memory course after retrieval.

PubMed

de la Fuente, Verónica; Freudenthal, Ramiro; Romano, Arturo

2011-04-13

In fear conditioning, aversive stimuli are readily associated with contextual features. A brief reexposure to the training context causes fear memory reconsolidation, whereas a prolonged reexposure induces memory extinction. The regulation of hippocampal gene expression plays a key role in contextual memory consolidation and reconsolidation. However, the mechanisms that determine whether memory will reconsolidate or extinguish are not known. Here, we demonstrate opposing roles for two evolutionarily related transcription factors in the mouse hippocampus. We found that nuclear factor-κB (NF-κB) is required for fear memory reconsolidation. Conversely, calcineurin phosphatase inhibited NF-κB and induced nuclear factor of activated T-cells (NFAT) nuclear translocation in the transition between reconsolidation and extinction. Accordingly, the hippocampal inhibition of both calcineurin and NFAT independently impaired memory extinction, whereas inhibition of NF-κB enhanced memory extinction. These findings represent the first insight into the molecular mechanisms that determine memory reprocessing after retrieval, supporting a transcriptional switch that directs memory toward reconsolidation or extinction. The precise molecular characterization of postretrieval processes has potential importance to the development of therapeutic strategies for fear memory disorders.

Reducing signs of aging and increasing lifespan by drug synergy.

PubMed

Huang, Xinhe; Liu, Jun; Withers, Bradley R; Samide, Aaron J; Leggas, Markos; Dickson, Robert C

2013-08-01

Disease incidence rises rapidly with age and increases both human suffering and economic hardship while shortening life. Advances in understanding the signaling pathways and cellular processes that influence aging support the possibility of reducing the incidence of age-related diseases and increasing lifespan by pharmacological intervention. Here, we demonstrate a novel pharmacological strategy that both reduces signs of aging in the budding yeast Saccharomyces cerevisiae and generates a synergistic increase in lifespan. By combining a low dose of rapamycin, to reduce activity of the target of rapamycin complex 1 (TORC1) protein kinase, and myriocin, to reduce sphingolipid synthesis, we show enhancement of autophagy, genomic stability, mitochondrial function, and AMP kinase pathway activity. These processes are controlled by evolutionarily conserved signal transduction pathways that are vital for maintaining a healthy state and promoting a long life. Thus, our data show that it ought to be possible to find pharmacological approaches to generate a synergistic reduction in the incidence of human age-related diseases to improve health quality in the elderly and enhance lifespan. © 2013 John Wiley & Sons Ltd and the Anatomical Society.

An in-advance stable isotope labeling strategy for relative analysis of multiple acidic plant hormones in sub-milligram Arabidopsis thaliana seedling and a single seed.

PubMed

Sun, Xiaohong; Ouyang, Yue; Chu, Jinfang; Yan, Jing; Yu, Yan; Li, Xiaoqiang; Yang, Jun; Yan, Cunyu

2014-04-18

A sensitive and reliable in-advance stable isotope labeling strategy was developed for simultaneous relative quantification of 8 acidic plant hormones in sub-milligram amount of plant materials. Bromocholine bromide (BETA) and its deuterated counterpart D9-BETA were used to in-advance derivatize control and sample extracts individually, which were then combined and subjected to solid-phase extraction (SPE) purification followed by UPLC-MS/MS analysis. Relative quantification of target compounds was obtained by calculation of the peak area ratios of BETA/D9-BETA labeled plant hormones. The in-advance stable isotope labeling strategy realized internal standard-based relative quantification of multiple kinds of plant hormones independent of availability of internal standard of every analyte with enhanced sensitivity of 1-3 orders of magnitude. Meanwhile, the in-advance labeling contributes to higher sample throughput and more reliability. The method was successfully applied to determine 8 plant hormones in 0.8mg DW (dry weight) of seedlings and 4 plant hormones from single seed of Arabidopsis thaliana. The results show the potential of the method in relative quantification of multiple plant hormones in tiny plant tissues or organs, which will advance the knowledge of the crosstalk mechanism of plant hormones. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative Glycomics Strategies*

PubMed Central

Mechref, Yehia; Hu, Yunli; Desantos-Garcia, Janie L.; Hussein, Ahmed; Tang, Haixu

2013-01-01

The correlations between protein glycosylation and many biological processes and diseases are increasing the demand for quantitative glycomics strategies enabling sensitive monitoring of changes in the abundance and structure of glycans. This is currently attained through multiple strategies employing several analytical techniques such as capillary electrophoresis, liquid chromatography, and mass spectrometry. The detection and quantification of glycans often involve labeling with ionic and/or hydrophobic reagents. This step is needed in order to enhance detection in spectroscopic and mass spectrometric measurements. Recently, labeling with stable isotopic reagents has also been presented as a very viable strategy enabling relative quantitation. The different strategies available for reliable and sensitive quantitative glycomics are herein described and discussed. PMID:23325767

An unconditionally stable staggered algorithm for transient finite element analysis of coupled thermoelastic problems

NASA Technical Reports Server (NTRS)

Farhat, C.; Park, K. C.; Dubois-Pelerin, Y.

1991-01-01

An unconditionally stable second order accurate implicit-implicit staggered procedure for the finite element solution of fully coupled thermoelasticity transient problems is proposed. The procedure is stabilized with a semi-algebraic augmentation technique. A comparative cost analysis reveals the superiority of the proposed computational strategy to other conventional staggered procedures. Numerical examples of one and two-dimensional thermomechanical coupled problems demonstrate the accuracy of the proposed numerical solution algorithm.

To eject or to abandon? Life history traits of hosts and parasites interact to influence the fitness payoffs of alternative anti-parasite strategies.

PubMed

Servedio, M R; Hauber, M E

2006-09-01

Hosts either tolerate avian brood parasitism or reject it by ejecting parasitic eggs, as seen in most rejecter hosts of common cuckoos, Cuculus canorus, or by abandoning parasitized clutches, as seen in most rejecter hosts of brown-headed cowbirds, Molothrus ater. What explains consistent variation between alternative rejection behaviours of hosts within the same species and across species when exposed to different types of parasites? Life history theory predicts that when parasites decrease the fitness of host offspring, but not the future reproductive success of host adults, optimal clutch size should decrease. Consistent with this prediction, evolutionarily old cowbird hosts, but not cuckoo hosts, have lower clutch sizes than related rarely- or newly parasitized species. We constructed a mathematical model to calculate the fitness payoffs of egg ejector vs. nest abandoner hosts to determine if various aspects of host life history traits and brood parasites' virulence on adult and young host fitness differentially influence the payoffs of alternative host defences. These calculations showed that in general egg ejection was a superior anti-parasite strategy to nest abandonment. Yet, increasing parasitism rates and increasing fitness values of hosts' eggs in both currently parasitized and future replacement nests led to switch points in fitness payoffs in favour of nest abandonment. Nonetheless, nest abandonment became selectively more favourable only at lower clutch sizes and only when hosts faced parasitism by a cowbird- rather than a cuckoo-type brood parasite. We suggest that, in addition to evolutionary lag and gape-size limitation, our estimated fitness differences based on life history trait variation provide new insights for the consistent differences observed in the anti-parasite rejection strategies between many cuckoo- and cowbird-hosts.

Cooperation prevails when individuals adjust their social ties.

PubMed

Santos, Francisco C; Pacheco, Jorge M; Lenaerts, Tom

2006-10-20

Conventional evolutionary game theory predicts that natural selection favours the selfish and strong even though cooperative interactions thrive at all levels of organization in living systems. Recent investigations demonstrated that a limiting factor for the evolution of cooperative interactions is the way in which they are organized, cooperators becoming evolutionarily competitive whenever individuals are constrained to interact with few others along the edges of networks with low average connectivity. Despite this insight, the conundrum of cooperation remains since recent empirical data shows that real networks exhibit typically high average connectivity and associated single-to-broad-scale heterogeneity. Here, a computational model is constructed in which individuals are able to self-organize both their strategy and their social ties throughout evolution, based exclusively on their self-interest. We show that the entangled evolution of individual strategy and network structure constitutes a key mechanism for the sustainability of cooperation in social networks. For a given average connectivity of the population, there is a critical value for the ratio W between the time scales associated with the evolution of strategy and of structure above which cooperators wipe out defectors. Moreover, the emerging social networks exhibit an overall heterogeneity that accounts very well for the diversity of patterns recently found in acquired data on social networks. Finally, heterogeneity is found to become maximal when W reaches its critical value. These results show that simple topological dynamics reflecting the individual capacity for self-organization of social ties can produce realistic networks of high average connectivity with associated single-to-broad-scale heterogeneity. On the other hand, they show that cooperation cannot evolve as a result of "social viscosity" alone in heterogeneous networks with high average connectivity, requiring the additional mechanism of topological co-evolution to ensure the survival of cooperative behaviour.

The nature of species interactions shifts profoundly between time periods

USDA-ARS?s Scientific Manuscript database

Species interactions change through time, for example ontogenetically, successionally, and evolutionarily. They also change as environmental conditions change, both within years (seasonally) and between years (year effects). The former are relatively well-studied, but the latter have received less a...

Evolutionarily Engineered Ethanologenic Yeast Detoxifies Lignocellulosic Biomass Conversion Inhibitors by Reprogrammed Pathways

USDA-ARS?s Scientific Manuscript database

Lignocellulosic biomass conversion inhibitors furfural and HMF inhibit microbial growth and interfere with subsequent fermentation of ethanol, posing significant challenges for a sustainable cellulosic ethanol conversion industry. Numerous yeast genes were found to be associated with the inhibitor ...

Species delimitation: A case study in a problematic ant taxon

USDA-ARS?s Scientific Manuscript database

Species delimitation has been invigorated as a discipline in systematics by an influx of new character sets, analytical methods, and conceptual advances. We use genetic data from 68 markers, combined with distributional, bioclimatic, and coloration information, to distinguish evolutionarily indepe...

Cyanobacteria, Toxins and Indicators: Field Monitoring, Treatment Facility Monitoring and Treatment Studies

EPA Science Inventory

Cyanobacteria, formerly known as blue green algae, are an evolutionarily ancient and ubiquitous class of micro-organisms. Under a combination of conditions that include nutrient availability, warm temperatures, stagnant water and high solar irradiance, these organisms have the p...

Rare but evolutionarily consequential outcrossing in a highly inbred zoonotic parasite

USDA-ARS?s Scientific Manuscript database

Recurrent self-mating can result in nearly clonal propagation of biological lineages, but even occasional outcrossing can serve to redistribute variation in future generations, providing cohesion among regional populations. The zoonotic parasite Trichinella spiralis has been suspected to undergo fr...

Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

PubMed

Flegr, Jaroslav

2010-01-13

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

Improved immunization strategy to reduce energy consumption on nodes traffic

NASA Astrophysics Data System (ADS)

Yuan, Jiazheng; Zhao, Dongyan; Long, Keping; Zheng, Yongrong

2017-04-01

The increasing requirement of transmission network sizes would result in huge energy consumption with communication traffic. Green communication technologies are expected to help in reducing energy consumption impact to environment. Therefore, it is important to design energy-efficient strategy that can decrease energy consumption. This paper proposes to use the acquaintance and improved targeted immunization strategies from complex systems to resolve energy consumption issues and uses traffic as measure standard to obtain a stable threshold. The simulation results show that the improved control strategy is better and more effective to save as much energy as possible.

Quantum Prisoner’s Dilemma game on hypergraph networks

NASA Astrophysics Data System (ADS)

Pawela, Łukasz; Sładkowski, Jan

2013-02-01

We study the possible advantages of adopting quantum strategies in multi-player evolutionary games. We base our study on the three-player Prisoner’s Dilemma (PD) game. In order to model the simultaneous interaction between three agents we use hypergraphs and hypergraph networks. In particular, we study two types of networks: a random network and a SF-like network. The obtained results show that in the case of a three-player game on a hypergraph network, quantum strategies are not necessarily stochastically stable strategies. In some cases, the defection strategy can be as good as a quantum one.

Combining stable insect cell lines with baculovirus-mediated expression for multi-HA influenza VLP production.

PubMed

Sequeira, Daniela P; Correia, Ricardo; Carrondo, Manuel J T; Roldão, António; Teixeira, Ana P; Alves, Paula M

2018-05-24

Safer and broadly protective vaccines are needed to cope with the continuous evolution of circulating influenza virus strains and promising approaches based on the expression of multiple hemagglutinins (HA) in a virus-like particle (VLP) have been proposed. However, expression of multiple genes in the same vector can lead to its instability due to tandem repetition of similar sequences. By combining stable with transient expression systems we can rationally distribute the number of genes to be expressed per platform and thus mitigate this risk. In this work, we developed a modular system comprising stable and baculovirus-mediated expression in insect cells for production of multi-HA influenza enveloped VLPs. First, a stable insect High Five cell population expressing two different HA proteins from subtype H3 was established. Infection of this cell population with a baculovirus vector encoding three other HA proteins from H3 subtype proved to be as competitive as traditional co-infection approaches in producing a pentavalent H3 VLP. Aiming at increasing HA expression, the stable insect cell population was infected at increasingly higher cell concentrations (CCI). However, cultures infected at CCI of 3×10 6 cells/mL showed lower HA titers per cell in comparison to standard CCI of 2×10 6 cells/mL, a phenomenon named "cell density effect". To lessen the negative impact of this phenomenon, a tailor-made refeed strategy was designed based on the exhaustion of key nutrients during cell growth. Noteworthy, cultures supplemented and infected at a CCI of 4×10 6 cells/mL showed comparable HA titers per cell to those of CCI of 2×10 6 cells/mL, thus leading to an increase of up to 4-fold in HA titers per mL. Scalability of the modular strategy herein proposed was successfully demonstrated in 2L stirred tank bioreactors with comparable HA protein levels observed between bioreactor and shake flasks cultures. Overall, this work demonstrates the suitability of combining stable with baculovirus-mediated expression in insect cells as an efficient platform for production of multi-HA influenza VLPs, surpassing the drawbacks of traditional co-infection strategies and/or the use of larger, unstable vectors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Feeding strategies of four dominant copepod species in Prydz Bay, Antarctica: Insights from a combined fatty acid biomarker and stable isotopic approach

NASA Astrophysics Data System (ADS)

Yang, Guang; Li, Chaolun; Guilini, Katja; Peng, Quancai; Wang, Yanqing; Zhang, Ye; Zhang, Yongshan

2016-08-01

Using fatty acid biomarkers and stable isotopic signatures, we investigated the feeding strategies and dietary preferences of four dominant copepod species (Calanoides acutus, Calanus propinquus, Metridia gerlachei and Rhincalanus gigas) sampled during the late austral summer in Prydz Bay, Antarctica. Our results show that diatoms, dinoflagellates and ciliates dominated copepod food sources (hypothesized to be phytoplankton and particulate organic matter) in the inner bay regions more than in the oceanic regions of Prydz Bay. Regional differences in the composition and abundance of food sources were also reflected in the fatty acid biomarkers and stable isotopic values. In the inner bay region, the total fatty acid contents of these food sources were nearly twofold higher, including greater contributions from fatty acids of dinoflagellate origin; these samples also had higher δ13C and δ15N values. Fatty acid biomarkers and stable isotopic values in copepod species roughly mirrored the spatial patterns in food sources. As found in the primary producers, the concentrations of dinoflagellate fatty acids and δ13C and δ15N values were higher in copepods from the inner bay regions. Additionally, there were inter-species differences in the fatty acids and stable isotopic values of copepods. C. acutus and C. propinquus did not exhibit significant regional differences in their total fatty acid contents. In contrast, M. gerlachei from the inner bay region had higher fatty acid values. C. acutus and C. propinquus had higher compositions of the long chain fatty acids 20:1n-9, 22:1n-9 and 22:1n-1, while docosahexaenoic acid (DHA) was higher in M. gerlachei. The δ15N values indicate that C. acutus occupies a higher trophic level than the other copepod species. Similarly, higher fatty acid ratios in M. gerlachei, including DHA/EPA(eicosapntemacnioc acid) and 18:1n-9/18:1n-7, indicate that this species feeds more opportunistically and prefers a carnivorous diet. Insights from this combined fatty acid and stable isotopic approach suggest that the dominant copepod species in Prydz Bay, Antarctica, have flexible feeding strategies that vary by food source during the late austral summer.

That's a good one! Belief in efficacy of mnemonic strategies contributes to age-related increase in associative memory.

PubMed

Daugherty, Ana M; Ofen, Noa

2015-08-01

The development of associative memory during childhood may be influenced by metacognitive factors. Here, one aspect of metamemory function--belief in strategy efficacy-was tested for a role in the effective use of encoding strategies. A sample of 61 children and adults (8-25 years of age) completed an associative recognition memory test and were assessed on belief in the efficacy of encoding strategies. Independent of age, belief ratings identified two factors: "deep" and "shallow" encoding strategies. Although the strategy factor structure was stable across age, adolescents and adults were more likely to prefer using a deep encoding strategy, whereas children were equally likely to prefer a shallow strategy. Belief ratings of deep encoding strategies increased with age and, critically, accounted for better associative recognition. Copyright © 2015 Elsevier Inc. All rights reserved.

Chicken bile Matrix metalloproteinase; its characterization and significance

USDA-ARS?s Scientific Manuscript database

Previous studies from our lab had shown that the avian bile was rich in matrix metalloproteinase (MMP), enzymes implicated in the degradation of extracellular matrices (ECM) such as collagens and proteoglycans. We hypothesized that bile MMP may be evolutionarily associated with the digestion of ECM ...

Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection

USDA-ARS?s Scientific Manuscript database

Staphylococcus aureus is a Gram-positive pathogen relevant for both human and animal health. With multi-drug resistant S. aureus strains becoming increasingly prevalent, alternative therapeutics are urgently needed. Bacteriophage endolysins (peptidoglycan hydrolases, PGH) are capable of killing Gra...

Haplogroups as Evolutionary Markers of Cognitive Ability

ERIC Educational Resources Information Center

Rindermann, Heiner; Woodley, Michael A.; Stratford, James

2012-01-01

Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal…

77 FR 476 - Endangered and Threatened Species; Recovery Plan Southern Oregon/Northern California Coast Coho...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-05

... and Threatened Species; Recovery Plan Southern Oregon/ Northern California Coast Coho Salmon... Oregon/Northern California Coast (SONCC) Coho Salmon (Oncorhynchus kisutch) Evolutionarily Significant... 95521, Attn: Recovery Coordinator/SONCC Coho Salmon Public Draft Recovery Plan Comments. Hand delivered...

Myosin1D is an evolutionarily conserved regulator of animal left-right asymmetry.

PubMed

Juan, Thomas; Géminard, Charles; Coutelis, Jean-Baptiste; Cerezo, Delphine; Polès, Sophie; Noselli, Stéphane; Fürthauer, Maximilian

2018-05-16

The establishment of left-right (LR) asymmetry is fundamental to animal development, but the identification of a unifying mechanism establishing laterality across different phyla has remained elusive. A cilia-driven, directional fluid flow is important for symmetry breaking in numerous vertebrates, including zebrafish. Alternatively, LR asymmetry can be established independently of cilia, notably through the intrinsic chirality of the acto-myosin cytoskeleton. Here, we show that Myosin1D (Myo1D), a previously identified regulator of Drosophila LR asymmetry, is essential for the formation and function of the zebrafish LR organizer (LRO), Kupffer's vesicle (KV). Myo1D controls the orientation of LRO cilia and interacts functionally with the planar cell polarity (PCP) pathway component VanGogh-like2 (Vangl2), to shape a productive LRO flow. Our findings identify Myo1D as an evolutionarily conserved regulator of animal LR asymmetry, and show that functional interactions between Myo1D and PCP are central to the establishment of animal LR asymmetry.

Modality and morphology: what we write may not be what we say.

PubMed

Rapp, Brenda; Fischer-Baum, Simon; Miozzo, Michele

2015-06-01

Written language is an evolutionarily recent human invention; consequently, its neural substrates cannot be determined by the genetic code. How, then, does the brain incorporate skills of this type? One possibility is that written language is dependent on evolutionarily older skills, such as spoken language; another is that dedicated substrates develop with expertise. If written language does depend on spoken language, then acquired deficits of spoken and written language should necessarily co-occur. Alternatively, if at least some substrates are dedicated to written language, such deficits may doubly dissociate. We report on 5 individuals with aphasia, documenting a double dissociation in which the production of affixes (e.g., the -ing in jumping) is disrupted in writing but not speaking or vice versa. The findings reveal that written- and spoken-language systems are considerably independent from the standpoint of morpho-orthographic operations. Understanding this independence of the orthographic system in adults has implications for the education and rehabilitation of people with written-language deficits. © The Author(s) 2015.

Cellular microbiology and molecular ecology of Legionella-amoeba interaction.

PubMed

Richards, Ashley M; Von Dwingelo, Juanita E; Price, Christopher T; Abu Kwaik, Yousef

2013-05-15

Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

DOE PAGES

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.; ...

2016-09-20

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

In silico discovery of terpenoid metabolism in Cannabis sativa.

PubMed

Massimino, Luca

2017-01-01

Due to their efficacy, cannabis based therapies are currently being prescribed for the treatment of many different medical conditions. Interestingly, treatments based on the use of cannabis flowers or their derivatives have been shown to be very effective, while therapies based on drugs containing THC alone lack therapeutic value and lead to increased side effects, likely resulting from the absence of other pivotal entourage compounds found in the Phyto-complex. Among these compounds are terpenoids, which are not produced exclusively by cannabis plants, so other plant species must share many of the enzymes involved in their metabolism. In the present work, 23,630 transcripts from the canSat3 reference transcriptome were scanned for evolutionarily conserved protein domains and annotated in accordance with their predicted molecular functions. A total of 215 evolutionarily conserved genes encoding enzymes presumably involved in terpenoid metabolism are described, together with their expression profiles in different cannabis plant tissues at different developmental stages. The resource presented here will aid future investigations on terpenoid metabolism in Cannabis sativa .

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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

Hawkes, Emily J.; Hennelly, Scott P.; Novikova, Irina V.

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. Here, we investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probingmore » and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.« less

Evolutionarily Conserved, Multitasking TRP Channels: Lessons from Worms and Flies

PubMed Central

Venkatachalam, Kartik; Luo, Junjie; Montell, Craig

2015-01-01

The Transient Receptor Potential (TRP) channel family is comprised of a large group of cation-permeable channels, which display an extraordinary diversity of roles in sensory signaling. TRPs allow animals to detect chemicals, mechanical force, light, and changes in temperature. Consequently, these channels control a plethora of animal behaviors. Moreover, their functions are not limited to the classical senses, as they are cellular sensors, which are critical for ionic homeostasis and metabolism. Two genetically tractable invertebrate model organisms, Caenorhabditis elegans and Drosophila melanogaster, have led the way in revealing a wide array of sensory roles and behaviors that depend on TRP channels. Two overriding themes have emerged from these studies. First, TRPs are multitasking proteins, and second, many functions and modes of activation of these channels are evolutionarily conserved, including some that were formerly thought to be unique to invertebrates, such as phototransduction. Thus, worms and flies offer the potential to decipher roles for mammalian TRPs, which would otherwise not be suspected. PMID:24961975

Cellular microbiology and molecular ecology of Legionella–amoeba interaction

PubMed Central

Richards, Ashley M.; Von Dwingelo, Juanita E.; Price, Christopher T.; Abu Kwaik, Yousef

2013-01-01

Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer. PMID:23535283

The HMMER Web Server for Protein Sequence Similarity Search.

PubMed

Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

2017-12-08

Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Chaotification of complex networks with impulsive control.

PubMed

Guan, Zhi-Hong; Liu, Feng; Li, Juan; Wang, Yan-Wu

2012-06-01

This paper investigates the chaotification problem of complex dynamical networks (CDN) with impulsive control. Both the discrete and continuous cases are studied. The method is presented to drive all states of every node in CDN to chaos. The proposed impulsive control strategy is effective for both the originally stable and unstable CDN. The upper bound of the impulse intervals for originally stable networks is derived. Finally, the effectiveness of the theoretical results is verified by numerical examples.

A strategy with novel evolutionary features for the iterated prisoner's dilemma.

PubMed

Li, Jiawei; Kendall, Graham

2009-01-01

In recent iterated prisoner's dilemma tournaments, the most successful strategies were those that had identification mechanisms. By playing a predetermined sequence of moves and learning from their opponents' responses, these strategies managed to identify their opponents. We believe that these identification mechanisms may be very useful in evolutionary games. In this paper one such strategy, which we call collective strategy, is analyzed. Collective strategies apply a simple but efficient identification mechanism (that just distinguishes themselves from other strategies), and this mechanism allows them to only cooperate with their group members and defect against any others. In this way, collective strategies are able to maintain a stable population in evolutionary iterated prisoner's dilemma. By means of an invasion barrier, this strategy is compared with other strategies in evolutionary dynamics in order to demonstrate its evolutionary features. We also find that this collective behavior assists the evolution of cooperation in specific evolutionary environments.

Genetic and morphological differences among populations of the Bonin Islands White-eye in Japan.

PubMed

Kawakami, Kazuto; Harada, Sachiko; Suzuki, Tadashi; Higuchi, Hiroyoshi

2008-09-01

The Bonin Islands White-eye, Apalopteron familiare , is the sole endemic avian species surviving on the Bonin Islands. The current distribution of this species is limited to only three islands of the Hahajima Island group: Hahajima, Imotojima, and Mukohjima. Imotojima and Mukohjima, which are small satellite islands of Hahajima, are about 3.6 km and 5.5 km, respectively, from the larger island. To investigate genetic and morphological differences among A. familiare populations on these islands, we assayed 634 bp of mitochondrial control region sequence for 132 birds from five locations among the three islands. We detected five haplotypes: two endemic haplotypes each on Hahajima and Imotojima and one on Mukohjima. Principal component analysis based on eight morphological characters of 162 birds from the three island populations revealed that birds from the small satellite islands had significantly different beak morphological characters. Our findings indicate that over-sea dispersal is rare in A. familiare , even when islands are separated by only a few kilometers, and suggest that little movement occurs on Hahajima. Thus, each population on each island should be conserved as an evolutionarily significant unit. The low dispersal ability of this species suggests that it is vulnerable to habitat fragmentation. Although the populations are currently stable and do not require rapid countermeasures, they should be monitored, especially those on the smaller islands.

Characterization of Ten Heterotetrameric NDP-Dependent Acyl-CoA Synthetases of the Hyperthermophilic Archaeon Pyrococcus furiosus

DOE PAGES

Scott, Joseph W.; Poole, Farris L.; Adams, Michael W. W.

2014-01-01

Tmore » he hyperthermophilic archaeon Pyrococcus furiosus grows by fermenting peptides and carbohydrates to organic acids. In the terminal step, acyl-CoA synthetase (ACS) isoenzymes convert acyl-CoA derivatives to the corresponding acid and conserve energy in the form of AP. ACS1 and ACS2 were previously purified from P. furiosus and have α 2 β 2 structures but the genome contains genes encoding three additional α -subunits. he ten possible combinations of α and β genes were expressed in E. coli and each resulted in stable and active α 2 β 2 isoenzymes. he α -subunit of each isoenzyme determined CoA-based substrate specificity and between them they accounted for the CoA derivatives of fourteen amino acids. he β -subunit determined preference for adenine or guanine nucleotides. he GP-generating isoenzymes are proposed to play a role in gluconeogenesis by producing GP for GP-dependent phosphoenolpyruvate carboxykinase and for other GP-dependent processes. ranscriptional and proteomic data showed that all ten isoenzymes are constitutively expressed indicating that both AP and GP are generated from the metabolism of most of the amino acids. A phylogenetic analysis showed that the ACSs of P. furiosus and other members of the hermococcales are evolutionarily distinct from those found throughout the rest of biology, including those of other hyperthermophilic archaea.« less

Identification of a molecular pH sensor in coral.

PubMed

Barott, Katie L; Barron, Megan E; Tresguerres, Martin

2017-11-15

Maintaining stable intracellular pH (pHi) is essential for homeostasis, and requires the ability to both sense pH changes that may result from internal and external sources, and to regulate downstream compensatory pH pathways. Here we identified the cAMP-producing enzyme soluble adenylyl cyclase (sAC) as the first molecular pH sensor in corals. sAC protein was detected throughout coral tissues, including those involved in symbiosis and calcification. Application of a sAC-specific inhibitor caused significant and reversible pHi acidosis in isolated coral cells under both dark and light conditions, indicating sAC is essential for sensing and regulating pHi perturbations caused by respiration and photosynthesis. Furthermore, pHi regulation during external acidification was also dependent on sAC activity. Thus, sAC is a sensor and regulator of pH disturbances from both metabolic and external origin in corals. Since sAC is present in all coral cell types, and the cAMP pathway can regulate virtually every aspect of cell physiology through post-translational modifications of proteins, sAC is likely to trigger multiple homeostatic mechanisms in response to pH disturbances. This is also the first evidence that sAC modulates pHi in any non-mammalian animal. Since corals are basal metazoans, our results indicate this function is evolutionarily conserved across animals. © 2017 The Author(s).

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

DOE PAGES

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; ...

2016-01-25

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

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

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor.

PubMed

Anandhakumar, Jayamani; Moustafa, Yara W; Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

2016-07-15

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the "anchor away" (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration

PubMed Central

Petersen, Hendrik O.; Höger, Stefanie K.; Looso, Mario; Lengfeld, Tobias; Kuhn, Anne; Warnken, Uwe; Nishimiya-Fujisawa, Chiemi; Schnölzer, Martina; Krüger, Marcus; Özbek, Suat; Simakov, Oleg; Holstein, Thomas W.

2015-01-01

The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration. PMID:25841488

Mating System Evolution under Strong Pollen Limitation: Evidence of Disruptive Selection through Male and Female Fitness in Clarkia xantiana.

PubMed

Briscoe Runquist, Ryan D; Geber, Monica A; Pickett-Leonard, Michael; Moeller, David A

2017-05-01

Selection on floral traits in hermaphroditic plants is determined by both male and female reproductive success. However, predictions regarding floral trait and mating system evolution are often based solely on female fitness. Selection via male fitness has the potential to affect the outcomes of floral evolution. In this study, we used paternity analysis to assess individual selfing rates and selection on floral traits via male and female fitness in an experimental population of Clarkia xantiana where pollen limitation of seed set was strong. We detected selection through both female and male fitness with reinforcing or noninterfering patterns of selection through the two sex functions. For female fitness, selection favored reduced herkogamy and protandry, traits that promote increased autonomous selfing. For male fitness, selection on petal area was disruptive, with higher trait values conferring greater pollinator attraction and outcross siring success and smaller trait values leading to higher selfed siring success. Combining both female and male fitness, selection on petal area and protandry was disruptive because intermediate phenotypes were less successful as both males and females. Finally, functional relationships among male and female fertility components indicated that selfing resulted in seed discounting and pollen discounting. Under these functional relationships, the evolutionarily stable selfing rate can be intermediate or predominantly selfing or outcrossing, depending on the segregating load of deleterious mutations.

The coevolution of long-term pair bonds and cooperation.

PubMed

Song, Z; Feldman, M W

2013-05-01

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

The Effect of Two Amino acid Residue Substitutions via RNA Editing on Dark-operative Protochlorophyllide Oxidoreductase in the Black Pine Chloroplasts.

PubMed

Yamamoto, Haruki; Kusumi, Junko; Yamakawa, Hisanori; Fujita, Yuichi

2017-05-24

Dark-operative protochlorophyllide oxidoreductase (DPOR) is a key enzyme to produce chlorophyll in the dark. Among photosynthetic eukaryotes, all three subunits chlL, chlN, and chlB are encoded by plastid genomes. In some gymnosperms, two codons of chlB mRNA are changed by RNA editing to codons encoding evolutionarily conserved amino acid residues. However, the effect of these substitutions on DPOR activity remains unknown. We first prepared cyanobacterial ChlB variants with amino acid substitution(s) to mimic ChlB translated from pre-edited mRNA. Their activities were evaluated by measuring chlorophyll content of dark-grown transformants of a chlB-lacking mutant of the cyanobacterium Leptolyngbya boryana that was complemented with pre-edited mimic chlB variants. The chlorophyll content of the transformant cells expressing the ChlB variant from the fully pre-edited mRNA was only one-fourth of the control cells. Co-purification experiments of ChlB with Strep-ChlN suggested that a stable complex with ChlN is greatly impaired in the substituted ChlB variant. We then confirmed that RNA editing efficiency was markedly greater in the dark than in the light in cotyledons of the black pine Pinus thunbergii. These results indicate that RNA editing on chlB mRNA is important to maintain appropriate DPOR activity in black pine chloroplasts.

A face for all seasons: Searching for context-specific leadership traits and discovering a general preference for perceived health

PubMed Central

Spisak, Brian R.; Blaker, Nancy M.; Lefevre, Carmen E.; Moore, Fhionna R.; Krebbers, Kleis F. B.

2014-01-01

Previous research indicates that followers tend to contingently match particular leader qualities to evolutionarily consistent situations requiring collective action (i.e., context-specific cognitive leadership prototypes) and information processing undergoes categorization which ranks certain qualities as first-order context-general and others as second-order context-specific. To further investigate this contingent categorization phenomenon we examined the “attractiveness halo”—a first-order facial cue which significantly biases leadership preferences. While controlling for facial attractiveness, we independently manipulated the underlying facial cues of health and intelligence and then primed participants with four distinct organizational dynamics requiring leadership (i.e., competition vs. cooperation between groups and exploratory change vs. stable exploitation). It was expected that the differing requirements of the four dynamics would contingently select for relatively healthier- or intelligent-looking leaders. We found perceived facial intelligence to be a second-order context-specific trait—for instance, in times requiring a leader to address between-group cooperation—whereas perceived health is significantly preferred across all contexts (i.e., a first-order trait). The results also indicate that facial health positively affects perceived masculinity while facial intelligence negatively affects perceived masculinity, which may partially explain leader choice in some of the environmental contexts. The limitations and a number of implications regarding leadership biases are discussed. PMID:25414653

Nuclear Localization of the ERK MAP Kinase Mediated by Drosophila αPS2βPS Integrin and Importin-7

PubMed Central

James, Brian P.; Bunch, Thomas A.; Krishnamoorthy, Srinivasan; Perkins, Lizabeth A.

2007-01-01

The control of gene expression by the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (ERK) requires its translocation into the nucleus. In Drosophila S2 cells nuclear accumulation of diphospho-ERK (dpERK) is greatly reduced by interfering double-stranded RNA against Drosophila importin-7 (DIM-7) or by the expression of integrin mutants, either during active cell spreading or after stimulation by insulin. In both cases, total ERK phosphorylation (on Westerns) is not significantly affected, and ERK accumulates in a perinuclear ring. Tyrosine phosphorylation of DIM-7 is reduced in cells expressing integrin mutants, indicating a mechanistic link between these components. DIM-7 and integrins localize to the same actin-containing peripheral regions in spreading cells, but DIM-7 is not concentrated in paxillin-positive focal contacts or stable focal adhesions. The Corkscrew (SHP-2) tyrosine phosphatase binds DIM-7, and Corkscrew is required for the cortical localization of DIM-7. These data suggest a model in which ERK phosphorylation must be spatially coupled to integrin-mediated DIM-7 activation to make a complex that can be imported efficiently. Moreover, dpERK nuclear import can be restored in DIM-7–deficient cells by Xenopus Importin-7, demonstrating that ERK import is an evolutionarily conserved function of this protein. PMID:17699602

Parental effects alter the adaptive value of an adult behavioural trait

PubMed Central

Kilner, Rebecca M; Boncoraglio, Giuseppe; Henshaw, Jonathan M; Jarrett, Benjamin JM; De Gasperin, Ornela; Attisano, Alfredo; Kokko, Hanna

2015-01-01

The parents' phenotype, or the environment they create for their young, can have long-lasting effects on their offspring, with profound evolutionary consequences. Yet, virtually no work has considered how such parental effects might change the adaptive value of behavioural traits expressed by offspring upon reaching adulthood. To address this problem, we combined experiments on burying beetles (Nicrophorus vespilloides) with theoretical modelling and focussed on one adult behavioural trait in particular: the supply of parental care. We manipulated the early-life environment and measured the fitness payoffs associated with the supply of parental care when larvae reached maturity. We found that (1) adults that received low levels of care as larvae were less successful at raising larger broods and suffered greater mortality as a result: they were low-quality parents. Furthermore, (2) high-quality males that raised offspring with low-quality females subsequently suffered greater mortality than brothers of equivalent quality, which reared larvae with higher quality females. Our analyses identify three general ways in which parental effects can change the adaptive value of an adult behavioural trait: by influencing the associated fitness benefits and costs; by consequently changing the evolutionary outcome of social interactions; and by modifying the evolutionarily stable expression of behavioural traits that are themselves parental effects. DOI: http://dx.doi.org/10.7554/eLife.07340.001 PMID:26393686

Avian Egg and Egg Coat.

PubMed

Okumura, Hiroki

2017-01-01

An ovulated egg of vertebrates is surrounded by unique extracellular matrix, the egg coat or zona pellucida, playing important roles in fertilization and early development. The vertebrate egg coat is composed of two to six zona pellucida (ZP) glycoproteins that are characterized by the evolutionarily conserved ZP-domain module and classified into six subfamilies based on phylogenetic analyses. Interestingly, investigations of biochemical and functional features of the ZP glycoproteins show that the roles of each ZP-glycoprotein family member in the egg-coat formation and the egg-sperm interactions seemingly vary across vertebrates. This might be one reason why comprehensive understandings of the molecular basis of either architecture or physiological functions of egg coat still remain elusive despite more than 3 decades of intensive investigations. In this chapter, an overview of avian egg focusing on the oogenesis are provided in the first section, and unique features of avian egg coat, i.e., perivitelline layer, including the morphology, biogenesis pathway, and physiological functions are discussed mainly on chicken and quail in terms of the characteristics of ZP glycoproteins in the following sections. In addition, these features of avian egg coat are compared to mammalian zona pellucida, from the viewpoint that the structural and functional varieties of ZP glycoproteins might be associated with the evolutionary adaptation to their reproductive strategies. By comparing the egg coat of birds and mammals whose reproductive strategies are largely different, new insights into the molecular mechanisms of vertebrate egg-sperm interactions might be provided.

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

PubMed Central

Woldring, Daniel R.; Holec, Patrick V.; Zhou, Hong; Hackel, Benjamin J.

2015-01-01

Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3–3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site. PMID:26383268

Contextual influences on animal decision-making: Significance for behavior-based wildlife conservation and management.

PubMed

Owen, Megan A; Swaisgood, Ronald R; Blumstein, Daniel T

2017-01-01

Survival and successful reproduction require animals to make critical decisions amidst a naturally dynamic environmental and social background (i.e. "context"). However, human activities have pervasively, and rapidly, extended contextual variation into evolutionarily novel territory, potentially rendering evolved animal decision-making mechanisms and strategies maladaptive. We suggest that explicitly focusing on animal decision-making (ADM), by integrating and applying findings from studies of sensory ecology, cognitive psychology, behavioral economics and eco-evolutionary strategies, may enhance our understanding of, and our ability to predict how, human-driven changes in the environment and population demography will influence animal populations. Fundamentally, the decisions animals make involve evolved mechanisms, and behaviors emerge from the combined action of sensory integration, cognitive mechanisms and strategic rules of thumb, and any of these processes may have a disproportionate influence on behavior. Although there is extensive literature exploring ADM, it generally reflects a canalized, discipline-specific approach that lacks a unified conceptual framework. As a result, there has been limited application of ADM theory and research findings into predictive models that can enhance management outcomes, even though it is likely that the relative resilience of species to rapid environmental change is fundamentally a result of how ADM is linked to contextual variation. Here, we focus on how context influences ADM, and highlight ideas and results that may be most applicable to conservation biology. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

PubMed Central

Wang, Minglei; Yafremava, Liudmila S.; Caetano-Anollés, Derek; Mittenthal, Jay E.; Caetano-Anollés, Gustavo

2007-01-01

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya. PMID:17908824

Two Arabidopsis AGC kinases are critical for the polarized growth of pollen tubes

USDA-ARS?s Scientific Manuscript database

Reproduction of flowering plants requires the growth of pollen tubes to deliver immotile sperm for fertilization. Pollen tube growth resembles that of polarized metazoan cells, in that some molecular mechanisms underlying cell polarization and growth are evolutionarily conserved, including the funct...

Fruits

USDA-ARS?s Scientific Manuscript database

In a botanical sense, fruits are the developed part of the seed-containing ovary. Evolutionarily speaking, plants have developed fruit with the goal of attracting insects, birds, reptiles and mammals to spread the seeds. Fruit can be dry such as the pod of a pea, or fleshy such as a peach. As humans...

The Social Conquest of General Education

ERIC Educational Resources Information Center

Helfand, David J.

2013-01-01

The dominant model of university education featuring one-way communication in a desocialized setting that celebrates competition is fundamentally at odds with the evolutionarily attuned attributes of the human brain. Quest University Canada represents an alternative of engaged, collaborative learning that builds on the eusocial nature of our…

Importance of Gait Training

MedlinePlus

... natural tendency to find the most stable and energy-efficient way to walk. The physical therapist and prosthetist may try either or both of these strategies to get the best outcome. Communication and teamwork ...

Transition-Metal-Free Oxidative C(sp2 )-H Hydroxylation of Terpyridines: A HOMO-Raising Strategy for the Construction of a New Super-Stable Terpyridine Chromophores.

PubMed

Huang, Jiang-Bo; Bai, Xing-Feng; Li, Li; Zheng, Zhan-Jiang; Xu, Zheng; Cui, Yu-Ming; Cao, Jian; Xu, Li-Wen

2017-03-23

Direct functionalization of terpyridines is an increasingly important topic in the field of dyes and catalysis as well as supramolecular chemistry, but its synthesis and transformation is usually challenging. Herein, a HOMO-raising strategy is reported for the construction of a super-stable novel terpyridine chromophores, in which the selective oxidation of terpyridines at its 3-position was determined successfully to the synthesis of phenol-functionalization of terpyridines (TPyOHs) bearing a hydrogen bonding group. The corresponding TPyOHs displayed strong aggregation-induced emission and exhibited highly selective and visual detection of Zn II cation with a record green terpyridine-based luminophore with nanomolar sensitivity (125 nm). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.