Página 6 dos resultados de 7455 itens digitais encontrados em 0.033 segundos

‣ Harnessing evolutionary biology to combat infectious disease

Little, Tom J.; Allen, Judith E.; Babayan, Simon A.; Matthews, Keith R.; Colegrave, Nick
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 06/02/2012 Português
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Pathogens exhibit remarkable abilities to flout therapeutic intervention. This outcome is driven by evolution, either as a direct response to intervention (e.g. the evolution of antibiotic resistance), or through long-term coevolution generating host or parasite traits that interact with therapy in undesirable or unpredicted ways. To make progress, the concepts and techniques of evolutionary biology must be deeply integrated with traditional approaches to immunology and pathogen biology. An interdisciplinary approach can inform control strategies, or even patient treatment, positioning us to meet the current and future challenges of controlling infectious diseases.

‣ Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration

Levin, Michael
Fonte: Blackwell Science Inc Publicador: Blackwell Science Inc
Tipo: Artigo de Revista Científica
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Pattern formation, as occurs during embryogenesis or regeneration, is the crucial link between genotype and the functions upon which selection operates. Even cancer and aging can be seen as challenges to the continuous physiological processes that orchestrate individual cell activities toward the anatomical needs of an organism. Thus, the origin and maintenance of complex biological shape is a fundamental question for cell, developmental, and evolutionary biology, as well as for biomedicine. It has long been recognized that slow bioelectrical gradients can control cell behaviors and morphogenesis. Here, I review recent molecular data that implicate endogenous spatio-temporal patterns of resting potentials among non-excitable cells as instructive cues in embryogenesis, regeneration, and cancer. Functional data have implicated gradients of resting potential in processes such as limb regeneration, eye induction, craniofacial patterning, and head-tail polarity, as well as in metastatic transformation and tumorigenesis. The genome is tightly linked to bioelectric signaling, via ion channel proteins that shape the gradients, downstream genes whose transcription is regulated by voltage, and transduction machinery that converts changes in bioelectric state to second-messenger cascades. However...

‣ Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

Wang, Jiguang; Khiabanian, Hossein; Rossi, Davide; Fabbri, Giulia; Gattei, Valter; Forconi, Francesco; Laurenti, Luca; Marasca, Roberto; Del Poeta, Giovanni; Foà, Robin; Pasqualucci, Laura; Gaidano, Gianluca; Rabadan, Raul
Fonte: eLife Sciences Publications, Ltd Publicador: eLife Sciences Publications, Ltd
Tipo: Artigo de Revista Científica
Publicado em 11/12/2014 Português
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Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

‣ Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila Melanogaster Euchromatin

Fontanillas, Pierre; Reuter, Max; Malik, Harmit S; Hartl, Daniel L.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection against new insertions. Understanding the distribution of TEs therefore provides insights into the forces shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic regions with low gene density and low recombination rate. However, little is known about the factors modulating insertion rates across the genome and their evolutionary significance. One candidate factor is gene expression, which has been suggested to increase local insertion rate by rendering DNA more accessible. We test this hypothesis by comparing the TE density around germline- and soma-expressed genes in the euchromatin of Drosophila melanogaster. Because only insertions that occur in the germline are transmitted to the next generation, we predicted a higher density of TEs around germline-expressed genes than soma-expressed genes. We show that the rate of TE insertions is greater near germline- than soma-expressed genes. However, this effect is partly offset by stronger selection for genome compactness (against excess noncoding DNA) on germline-expressed genes. We also demonstrate that the local genome organization in clusters of coexpressed genes plays a fundamental role in the genomic distribution of TEs. Our analysis shows that—in addition to recombination rate—the distribution of TEs is shaped by the interaction of gene expression and genome organization. The important role of selection for compactness sheds a new light on the role of TEs in genome evolution. Instead of making genomes grow passively...

‣ Melanism in Peromyscus Is Caused by Independent Mutations in Agouti

Wiley, Christopher D.; Kingsley, Evan Prentice; Hoekstra, Hopi E.; Manceau, Marie C.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Identifying the molecular basis of phenotypes that have evolved independently can provide insight into the ways genetic and developmental constraints influence the maintenance of phenotypic diversity. Melanic (darkly pigmented) phenotypes in mammals provide a potent system in which to study the genetic basis of naturally occurring mutant phenotypes because melanism occurs in many mammals, and the mammalian pigmentation pathway is well understood. Spontaneous alleles of a few key pigmentation loci are known to cause melanism in domestic or laboratory populations of mammals, but in natural populations, mutations at one gene, the melanocortin-1 receptor (Mc1r), have been implicated in the vast majority of cases, possibly due to its minimal pleiotropic effects. To investigate whether mutations in this or other genes cause melanism in the wild, we investigated the genetic basis of melanism in the rodent genus Peromyscus, in which melanic mice have been reported in several populations. We focused on two genes known to cause melanism in other taxa, Mc1r and its antagonist, the agouti signaling protein (Agouti). While variation in the Mc1r coding region does not correlate with melanism in any population, in a New Hampshire population, we find that a 125-kb deletion...

‣ Phylogenetic Targeting of Research Effort in Evolutionary Biology

Arnold, Christian; Nunn, Charles Lindsay
Fonte: University of Chicago Press Publicador: University of Chicago Press
Tipo: Artigo de Revista Científica
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Many questions in comparative biology require that new data be collected, either to build a comparative database for the first time or to augment existing data. Given resource limitations in collecting data, the question arises as to which species should be studied to increase the size of comparative data sets. By taking hypotheses, existing data relevant to the hypotheses, and a phylogeny, we show that a method of “phylogenetic targeting” can systematically guide data collection while taking into account potentially confounding variables and competing hypotheses. Phylogenetic targeting selects potential candidates for future data collection, using a flexible scoring system based on differences in pairwise comparisons. We used simulations to assess the performance of phylogenetic targeting, as compared with the less systematic approach of randomly selecting species (as might occur when data have been collected without regard to phylogeny and variation in the traits of interest). The simulations revealed that phylogenetic targeting increased the statistical power to detect correlations and that power increased with the number of species in the tree, even when the number of species studied was held constant. We also developed a Web‐based computer program called PhyloTargeting to implement the approach (http://phylotargeting.fas.harvard.edu).; Human Evolutionary Biology

‣ A Veritable Menagerie of Heritable Bacteria from Ants, Butterflies, and Beyond: Broad Molecular Surveys and a Systematic Review

Russell, Jacob A.; Funaro, Colin F.; Giraldo, Ysabel M.; Goldman-Huertas, Benjamin; Suh, David; Kronauer, Daniel J. C.; Moreau, Corrie S.; Pierce, Naomi Ellen
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Maternally transmitted bacteria have been important players in the evolution of insects and other arthropods, affecting their nutrition, defense, development, and reproduction. Wolbachia are the best studied among these and typically the most prevalent. While several other bacteria have independently evolved a heritable lifestyle, less is known about their host ranges. Moreover, most groups of insects have not had their heritable microflora systematically surveyed across a broad range of their taxonomic diversity. To help remedy these shortcomings we used diagnostic PCR to screen for five groups of heritable symbionts—Arsenophonus spp., Cardinium hertigii, Hamiltonella defensa, Spiroplasma spp., and Wolbachia spp.—across the ants and lepidopterans (focusing, in the latter case, on two butterfly families—the Lycaenidae and Nymphalidae). We did not detect Cardinium or Hamiltonella in any host. Wolbachia were the most widespread, while Spiroplasma (ants and lepidopterans) and Arsenophonus (ants only) were present at low levels. Co-infections with different Wolbachia strains appeared especially common in ants and less so in lepidopterans. While no additional facultative heritable symbionts were found among ants using universal bacterial primers...

‣ Architecture and evolutionary stability of yeast signaling pathways

Gritton, Jeffrey S
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 45 leaves
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I have researched the effect that selection for the function of the High Osmolarity Glycerol (HOG) pathway has on the evolutionary stability of the pheromone response pathway in the yeast Saccharomyces cerevisiae. I first set out to demonstrate that, because the pheromone and HOG response pathways share protein components, selection for HOG function will enrich a population for cells capable of pheromone response. I performed experiments in both continuous and batch culture to demonstrate this effect. I then characterized the decay of the pheromone response pathway first, by measuring its mutation rate and second, by measuring the fitness of a series of strains with pheromone response gene deletions. I conclude with thoughts on possible experiments that may be used to further this research.; by Jeffrey S. Gritton.; Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biology, 2006.; "September 2006."; Includes bibliographical references (leaves 37-38).

‣ Evolutionary Cycles of Cooperation and Defection

Imhof, Lorens A.; Fudenberg, Drew; Nowak, Martin A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The main obstacle for the evolution of cooperation is that natural selection favors defection in most settings. In the repeated prisoner's dilemma, two individuals interact several times, and, in each round, they have a choice between cooperation and defection. We analyze the evolutionary dynamics of three simple strategies for the repeated prisoner's dilemma: always defect (ALLD), always cooperate (ALLC), and tit-for-tat (TFT). We study mutation–selection dynamics in finite populations. Despite ALLD being the only strict Nash equilibrium, we observe evolutionary oscillations among all three strategies. The population cycles from ALLD to TFT to ALLC and back to ALLD. Most surprisingly, the time average of these oscillations can be entirely concentrated on TFT. In contrast to the classical expectation, which is informed by deterministic evolutionary game theory of infinitely large populations, stochastic evolution of finite populations need not choose the strict Nash equilibrium and can therefore favor cooperation over defection.; Mathematics; Organismic and Evolutionary Biology

‣ Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

Xi, Zhenxiang; Wang, Yuguo; Bradley, Robert K.; Sugumaran, M.; Marx, Christopher J; Rest, Joshua S.; Davis, Charles Cavender
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e....

‣ Darwin would have loved DNA: celebrating Darwin 200

Bromham, Lindell
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
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Analysis of DNA sequences now plays a key role in evolutionary biology research. If Darwin were to come back today, I think he would be absolutely delighted with molecular evolutionary genetics, for three reasons. First, it solved one of the greatest problems for his theory of evolution by natural selection. Second, it gives us a tool that can be used to investigate many of the questions he found the most fascinating. And third, DNA data confirm Darwin's grand view of evolution.

‣ Seven reasons (not) to neglect niche construction

Sterelny, Kim; Laland, Kevin
Fonte: Society for the Study of Evolution Publicador: Society for the Study of Evolution
Tipo: Artigo de Revista Científica
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The niche-construction perspective within evolutionary biology places emphasis on the changes that organisms bring about in their selective environments. Advocates of this viewpoint argue that there is both accuracy and utility in treating niche construct

‣ Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods

Primack, Richard B.; Miller-Rushing, Abraham J.; Willis, Charles G.; Ruhfel, Brad R; Losos, Jonathan; Davis, Charles
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes than native species. Recent evidence indicates that species that respond to climate change by adjusting their phenology (i.e., the timing of seasonal activities, such as flowering) have historically increased in abundance. The extent to which non-native species success is similarly linked to a favorable climate change response, however, remains untested. We analyzed a dataset initiated by the conservationist Henry David Thoreau that documents the long-term phenological response of native and non-native plant species over the last 150 years from Concord, Massachusetts (USA). Our results demonstrate that non-native species, and invasive species in particular, have been far better able to respond to recent climate change by adjusting their flowering time. This demonstrates that climate change has likely played, and may continue to play, an important role in facilitating non-native species naturalization and invasion at the community level.; Organismic and Evolutionary Biology

‣ On Energy-efficiency in Wireless Networks: A Game-theoretic Approach to Cooperation Inspired by Evolutionary Biology

Utkovski, Zoran; Gajduk, Andrej; Basnarkov, Lasko; Bosnakovski, Darko; Kocarev, Ljupco
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/05/2014 Português
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We develop a game-theoretic framework to investigate the effect of cooperation on the energy efficiency in wireless networks. We address two examples of network architectures, resembling ad-hoc network and network with central infrastructure node. Most present approaches address the issue of energy efficiency in communication networks by using complex algorithms to enforce cooperation in the network, followed by extensive signal processing at the network nodes. Instead, we address cooperative communication scenarios which are governed by simple, evolutionary-like, local rules, and do not require strategic complexity of the network nodes. The approach is motivated by recent results in evolutionary biology which suggest that cooperation can emerge in Nature by evolution, i. e. can be favoured by natural selection, if certain mechanism is at work. As result, we are able to show by experiments that cooperative behavior can indeed emerge and persist in wireless networks, even if the behavior of the individual nodes is driven by selfish decision making. The results from this work indicate that uncomplicated local rules, followed by simple fitness evaluation, can promote cooperation and generate network behavior which yields global energy efficiency in certain wireless networks.; Comment: This work has been submitted to the IEEE/ACM Transactions on Networking

‣ Evolutionary Dynamics for Persistent Cooperation in Structured Populations

Li, Yan; Liu, Xinsheng; Claussen, Jens Christian; Guo, Wanlin
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 19/05/2015 Português
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The emergence and maintenance of cooperative behavior is a fascinating topic in evolutionary biology and social science. The public goods game (PGG) is a paradigm for exploring cooperative behavior. In PGG, the total resulting payoff is divided equally among all participants. This feature still leads to the dominance of defection without substantially magnifying the public good by a multiplying factor. Much effort has been made to explain the evolution of cooperative strategies, including a recent model in which only a portion of the total benefit is shared by all the players through introducing a new strategy named persistent cooperation. A persistent cooperator is a contributor who is willing to pay a second cost to retrieve the remaining portion of the payoff contributed by themselves. In a previous study, this model was analyzed in the framework of well-mixed populations. This paper focuses on discussing the persistent cooperation in lattice-structured populations. The evolutionary dynamics of the structured populations consisting of three types of competing players (pure cooperators, defectors and persistent cooperators) are revealed by theoretical analysis and numerical simulations. In particular, the approximate expressions of fixation probabilities for strategies are derived on one-dimensional lattices. The phase diagrams of stationary states...

‣ Clades and clans: a comparison study of two evolutionary models

Zhu, Sha; Than, Cuong; Wu, Taoyang
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 15/07/2014 Português
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The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1

‣ The contribution of epistasis to the architecture of fitness in an RNA virus

Sanjuán, Rafael; Moya, Andrés; Elena, Santiago F.
Fonte: National Academy of Sciences (U.S.) Publicador: National Academy of Sciences (U.S.)
Tipo: Artículo Formato: 203 bytes; text/plain
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4 pages, 2 figures.-- PMID: 15492220 [PubMed].-- PMCID: PMC524436.-- Additional information (Suppl. table S1: Relevant information about each single- and double-nucleotide substitution mutant created) available at: http://www.pnas.org/content/101/43/15376/suppl/DC1; The tendency for genetic architectures to exhibit epistasis among mutations plays a central role in the modern synthesis of evolutionary biology and in theoretical descriptions of many evolutionary processes. Nevertheless, few studies unquestionably show whether, and how, mutations typically interact. Beneficial mutations are especially difficult to identify because of their scarcity. Consequently, epistasis among pairs of this important class of mutations has, to our knowledge, never before been explored. Interactions among genome components should be of special relevance in compacted genomes such as those of RNA viruses. To tackle these issues, we first generated 47 genotypes of vesicular stomatitis virus carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were determined. Several pairs exhibited significant interactions for fitness, including antagonistic and synergistic epistasis. Synthetic lethals represented 50% of the latter. In a second set of experiments...

‣ Introduction. Evolutionary dynamics of wild populations: The use of long-term pedigree data

Kruuk, Loeske; Hill, W.G.
Fonte: Royal Society of London Publicador: Royal Society of London
Tipo: Artigo de Revista Científica
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Studies of populations in the wild can provide unique insights into the forces driving evolutionary dynamics. This themed issue of Proc. R. Soc. B focuses on new developments in long-term analyses of animal populations where pedigree information has been

‣ Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses

Guenther Witzany
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
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Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms...

‣ Evolutionary descent of prion genes from a ZIP metal ion transport ancestor

Gerold Schmitt-Ulms; Sepehr Ehsani; Joel C. Watts; David Westaway; Holger Wille
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
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In the more than 20 years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into the function of PrP may be obtained through a characterization of its molecular neighborhood. Quantitative interactome data revealed the spatial proximity of a subset of metal ion transporters of the ZIP family to mammalian prion proteins. A subsequent bioinformatic analysis revealed the presence of a prion-like protein sequence within the N-terminal, extracellular domain of a phylogenetic branch of ZIPs. Additional structural threading and ortholog sequence alignment analyses consolidated the conclusion that the prion protein gene family is phylogenetically derived from a ZIP-like ancestor molecule. Our data explain structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The connection to ZIP proteins is expected to open new avenues to elucidate the biology of the prion protein in health and disease.