Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum.
... Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with ... be attributed to independent evolution of the two copies after an ancient duplication event although the mechanism behind this is not clearly understood. Contrasting evolutionary patterns have been reported in the albatross, Thalassarche albatrosses, where one part of CRs evolved independently while the other showed concerted evolution . Variation ... [3,4,14–16]. Despite the increasing reports of concerted evolution of CRs, contradictory data have been reported in the mt genome of the Amazona parrot, PLOS ONE | www.plosone.org 1 December 2013 | Volume 8 | Issue 12 | e82854 Evolution of CRs in Platysternon megacephalum indicate concerted evolution. Similar patterns were detected in sea birds .
Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS.
... in our experimental evolution. All of the evolution in our DrpoS lines was mediated by IS10. While this constancy may be unusual, IS elements have been frequently found as the causes of adaptive mutations in experimental evolution [27–29]. In addition, comparative genomics suggests that IS elements play an important role in genome evolution [30–32]. ... promoters. Nucleic Acids Res 35: 771–788. 24. Lenski RE, Bennett AF (1993) Evolutionary response of Escherichia coli to thermal stress. Am Nat 142: S47–S64. 25. Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution 52: 935–949. 26. Fisher RA (1930) The genetical theory of natural ... www.plosgenetics.org 5 October 2009 | Volume 5 | Issue 10 | e1000671 Evolution in an rpoS Mutant Figure 6. The position of 21 mutants that upregulate an otsB::lacZY fusion. The 19 IS10 insertions between +12 and +13 are in the same position as those recovered from the experimental evolution, and all 19 mutants have IS10 inserted with POUT oriented reading
Climate-vegetation-soil interactions and long-term hydrologic partitioning: signatures of catchment co-evolution
... suggest climate-landscape co -evolution that impact hydrologic response at the catchment scale. More research, including more catchments and possibly other model parameterizations, is needed to provide further evidence for these observations. Hydrol. Earth Syst. Sci., 17, 2209–2217, 2013 P. A. Troch et al.: Signatures of catchment co -evolution Recent opinion ... results suggest that their exists strong interactions between climate, vegetation and soil properties that lead to specific hydrologic partitioning at the catchment scale. This co -evolution of catchment vegetation and soils with climate needs to be further explored to improve our capabilities to predict hydrologic partitioning in ungauged basins. 1 Introduction Catchment ... different climatic and geologic settings: deep rooting strategies in Western Australia Hydrol. Earth Syst. Sci., 17, 2209–2217, 2013 P. A. Troch et al.: Signatures of catchment co -evolution with a strong Mediterranean climate (Silberstein et al., 2001), and over-storey-under-storey dynamics in Darwin, Northern Australia, with a tropical climate (Schymanski
Clonal dissemination, emergence of mutator lineages and antibiotic resistance evolution in Pseudomonas aeruginosa cystic fibrosis chronic lung infection.
... their potential for unexpected short-term sequence type evolution, illustrating the complexity of P. aeruginosa population biology in CF. Citation: López-Causapé C, Rojo-Molinero E, Mulet X, Cabot G, Moyà B, et al. (2013) Clonal Dissemination, Emergence of Mutator Lineages and Antibiotic Resistance Evolution in Pseudomonas aeruginosa Cystic Fibrosis ... e12669. 17. Luján AM, Maciá MD, Yang L, Molin S, Oliver A, et al. (2011) Evolution and adaptation in Pseudomonas aeruginosa biofilms driven by mismatch repair systemdeficient mutators. PLoS One 6: e27842. 18. Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S (2009) Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary ... Clonal Dissemination, Emergence of Mutator Lineages and Antibiotic Resistance Evolution in Pseudomonas aeruginosa Cystic Fibrosis Chronic Lung Infection Carla López-Causapé1., Estrella Rojo-Molinero1., Xavier Mulet1, Gabriel Cabot1, Bartolomé Moyà1, Joan
Evolution and adaptation in Pseudomonas aeruginosa biofilms driven by mismatch repair system-deficient mutators.
... evidence for mutator-driven adaptive evolution in the biofilm mode of growth. This work helps to understand the basis for the specific high proportion and role of mutators in chronic infections, where P. aeruginosa develops in biofilm communities. Citation: Luján AM, Maciá MD, Yang L, Molin S, Oliver A, et al. (2011) Evolution and Adaptation in Pseudomonas ... Evolution and Adaptation in Pseudomonas aeruginosa Biofilms Driven by Mismatch Repair System-Deficient Mutators Adela M. Luján1., Marı́a D. Maciá2., Liang Yang3, Søren Molin3, ... phenotype known as the hypermutator or just mutator phenotype [1,2]. Since mutation is the substrate for natural selection, the potential role of mutator phenotypes in adaptive evolution has attracted a huge biological and medical interest for decades. Indeed, early in vitro experiments, using Escherichia coli as model organism, indicated that the occurrence
Ecotype evolution in Glossina palpalis subspecies, major vectors of sleeping sickness.
... to "débusquer la bête". Infection Genetics and Evolution 7: 308–332. PMID: 16949350 30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731–2739. doi: 10.1093/molbev/msr121 ... specialisation, habitat preference and parasites. In: Poulin R, Morand S, Skorping A, editors. Evolutionary Biology of Host Parasite Relationships: Theory Meets Reality. Amsterdam.: Elsevier. pp. 27–42. 3. Kempf F, Boulinier T, De Meeûs T, Arnathau C, McCoy KD (2009) Recent evolution of host-associated divergence in the seabird tick Ixodes uriae. Molecular Ecology ... DOI:10.1371/journal.pntd.0003497 March 16, 2015 13 / 16 Ecotype Evolution in Glossina palpalis 4. De Meeûs T, Koffi BB, Barré N, de Garine-Wichatitsky M, Chevillon C (2010) Swift sympatric adaptation of a species of cattle tick to a new deer host in New-Caledonia. Infection Genetics and Evolution 10: 976–983. doi: 10.1016/j.meegid.2010.06.005 PMID:
Hamiltonian approach to the derivation of evolution equations for wave trains in weakly unstable media
Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum.
... minimized (Text S7). Rapid evolution and degradation of CRISPRs The CRISPR dynamics we observed in House Finch MG differ from that seen in other pathogen and bacterial populations. A recent study of Y. pestis CRISPR arrays from 131 strains  indicated a slower pace of CRISPR evolution than observed in MG and pattern of evolution in which acquisition ... required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs. Citation: Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, et al. (2012) Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel ... France ¤b Current address: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America rapid spread throughout eastern North America in exceptional detail, making it one of the best documented wildlife pathogen outbreaks [3–7]. Although previous genome-wide studies have clarified rates of measurable evolution in viral pathogens
Facilitated variation: how evolution learns from past environments to generalize to new environments.
... e1000206 Evolution of Facilitated Phenotypic Variation Figure 2. Schematic view of evolutionary goals and phenotypes in the two model systems. (A–B) Logic circuit model. (A) A typical circuit evolved by fixed-goal evolution toward goal G1. Each gate in the circuit represents a NAND gate. (B) Modular circuit evolved under modularly varying goal evolution ... Biology | www.ploscompbiol.org Evolution of Novelty within the MVG ‘Modularity Language’ So far, we analyzed the adaptation to previously seen goals introduced along MVG evolution history, which highlighted the 5 November 2008 | Volume 4 | Issue 11 | e1000206 Evolution of Facilitated Phenotypic Variation Figure 4. Evolution of genetic triggers. ... such systematically varying Author Summary One of the striking features of evolution is the appearance of novel structures in organisms. The origin of the ability to generate novelty is one of the main mysteries in evolutionary theory. The molecular mechanisms that enhance the evolution of novelty were recently integrated by Kirschner and Gerhart in
Reflected Adaptive Differential Evolution with Two External Archives for Large-Scale Global Optimization
... Transactions on Evolutionary Computation, vol. 12, no. 3, pp. 107–125, 2008.  L. Tang, Y. Dong, and J. Liu, “Differential evolution with an individualdependent mechanism,” Evolutionary Computation, IEEE Transactions on, vol. 19, no. 4, pp. 560–574, 2015.  J. Brest, A. Zamuda, B. Boskovic, S. Greiner, and V. Zumer, Advances in Differential Evolution, ... in Differential Evolution.  Z. Yang, K. Tang, and X. Yao, “Self-adaptive differential evolution with neighborhood search,” in IEEE Congress on Evolutionary Computation (CEC 2008). Singapore: IEEE Press, 2008.  J. Brest, A. Zamuda, I. Fister, and B. Boskovic, “Some improvements of the self-adaptive jde algorithm,” in Differential Evolution (SDE), ... K. Qin and P. N. Suganthan, “Self adaptive differential evolution algorithm for numerical optimization,” in IEEE Congress on Evolutionary Computation (2005), vol. 2, 2005, pp. 1785–1791.  J. Zhang and A. C. Sanderson, “Jade: adaptive differential evolution with optional external archive,” Evolutionary Computation, IEEE Transactions on, vol. 13,
A Differential Evolution for Operon Prediction
... TUB (2) B. Differential Evolution The differential evolution algorithm (DE) was proposed by Storn and Price in 1995  and has been shown to have superior solving ability. The DE algorithm is similar to the genetic algorithm (GA) and particle swarm optimization (PSO); all are optimized algorithms. The differential evolution TABLE I INTERVALS ... differential evolution algorithm includes three steps: mutation, recombination and selection. In selection, DE uses a one-to-one elimination mechanism to update the chromosome, which is similar to the recording of the best experience in PSO. DE considers the correlation between multiple variables; this coupling has an advantage over PSO. The differential evolution ... 0.963, respectively. A comparison with other methods in the other literature is proves that our method can effectively be used for operon prediction. Index Terms—operon prediction, Differential Evolution, intergenic distance, metabolic pathway, cluster of orthologous groups. I. INTRODUCTION N prokaryotic organisms operons of bacterial genomes Icontain valuable information,
Grey Relation Entropy based Dynamic Evaluation Model of Product Lifecycle Information System Evolution
... the evolution of the whole system is called order parameter, which determines degree of order in a system. So order degree and evolution direction of a system can be described by the order parameter. The result of “synergetic theory” research indicates that synergy results in order, non-synergy results in disorder. Since order parameter determines the evolution ... of the product lifecycle information system and estimate its evolution direction. PLIS is an organism which consists of subsystems such as product needs analysis, concept design, structure design, engineering analysis, manufacture and service support and so on. Every subsystem has its own evolution discipline and is constrained by other factors. These ... sound development and evolution process, and user’s demands can be reasonably met. If ΔS = 0 , it indicates that entropy stays unchanged within a certain period, the system state is the same as the beginning. At this time further in-depth research of the system is needed, and technology strategy adjustments should be made to make the evolution directed
Papio Cranium from the Hominin-Bearing Site of Malapa: Implications for the Evolution of Modern Baboon Cranial Morphology and South African Plio-Pleistocene Biochronology.
... Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, United States of America, 3 New York Consortium in Evolutionary Primatology, New York, NY, United States of America, 4 Evolutionary Studies Institute, University of the Witwatersrand, Private Bag 3, Wits 2050, Johannesburg, Republic of South Africa * email@example.com OPEN ... paleoecology, biochronology, and mammalian evolution during the African Plio-Pleistocene. In this paper, we describe the only known non-hominin primate specimen from Malapa, UW 88–886, a specimen of the fossil baboon Papio angusticeps. Furthermore, we evaluate Papio angusticeps in the broader context of modern baboon craniodental evolution and South African Plio-Pleistocene ... angusticeps at Malapa has broader implications for baboon evolution and hominin biochronology as well. Modern baboons (extant P. hamadryas ssp.) represent one of the most successful living primate radiations, with populations distributed all across sub-Saharan Africa and into the Arabian Peninsula. Despite their evolutionary success, modern baboon origins in
TRENDS IN THE EVOLUTION OF WORLDWIDE FOREIGN DIRECT INVESTMENTS
... the paper is to analyze the evolution of worldwide foreign direct investment (FDI) inflows, before and after the onset of the global economic crisis. Keywords: foreign direct investment; FDI inflows; financial crisis. JEL Classification: F210. INTRODUCTION The year 2008 marked the beginning of a new period in the evolution of the global economy, ... TRENDS IN THE EVOLUTION OF WORLDWIDE FOREIGN DIRECT INVESTMENTS Maria Ramona Sarbu* Iuliana Mazur (Gavrea) Abstract: The flows of foreign direct investments constitutes a major component of ... 2 135 liberalization and promotion. Over two thirds of the measures taken, in 2010, in the field of FDI policies, were of this nature (Bonciu, 2012). The aim of this paper is to analyze the evolution of worldwide FDI inflows, before and after the onset of the global economic crisis. The analysis of the internal flows is important because it offers an indication regarding
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.
... both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular ... the complex evolutionary history of most protein families, which includes also gene losses and lateral gene transfers, limits the application of purely phylogenetic approaches in interpreting function divergence. At the same time, other mechanisms, including convergent evolution of the same functions, are also possible. Among plausible evolutionary ... include instances of convergent evolution in which the same functional specificity is reinvented in distinct groups of species through lineage-specific expansions and specialization events. For example, the latter model was inferred for the evolution of some receptors in the innate immune system . An extreme case of convergent evolution of essentially identical
Evolution of the aging brain transcriptome and synaptic regulation.
... macaques and humans (category III). Also indicated is the evolutionary time of divergence in years for each pair of species based on analysis of protein sequence alignments . doi:10.1371/journal.pone.0003329.g002 PLoS ONE | www.plosone.org 3 October 2008 | Volume 3 | Issue 10 | e3329 Evolution of the Aging Brain Table 1. Age-regulated ... humans and rhesus macaques that may alter neural networks and contribute to age-related cognitive changes. Citation: Loerch PM, Lu T, Dakin KA, Vann JM, Isaacs A, et al. (2008) Evolution of the Aging Brain Transcriptome and Synaptic Regulation. PLoS ONE 3(10): e3329. doi:10.1371/journal.pone.0003329 Editor: Laszlo Orban, Temasek Life Sciences Laboratory, ... changes in gene expression, cortical samples from 13 young (#40 years old) and 15 aged ($70 years PLoS ONE | www.plosone.org 1 October 2008 | Volume 3 | Issue 10 | e3329 Evolution of the Aging Brain old) humans were hybridized to Affymetrix U133plus 2.0 arrays, 5-month-old (n = 5) and 30-month-old mice (n = 5) were hybridized to Affymetrix Mouse
Amino acid properties conserved in molecular evolution.
... right set for describing protein evolution has not been found. There is no fundamental reason why the properties that we can measure should be the most convenient ones for modelling the process of evolution. PLOS ONE | www.plosone.org 5 June 2014 | Volume 9 | Issue 6 | e98983 Amino Acid Properties and Molecular Evolution Figure 4. The optimal ... molecular evolution was proposed very soon after the discovery of the latter [1–4]. It has been shown that the most frequently occurring single nucleotide mutations of DNA lead to amino acid changes that conserve certain amino acid properties [3,5]. It has also been suggested that this property of the genetic code was acquired in the process of evolution ... correlations . These findings are good evidence supporting the role amino acid properties play in molecular evolution. Nevertheless, while the fact that the properties of amino acids are decisive in determining protein structure, function and evolution on the molecular level is now universally accepted, and even considered self-evident, the support
The Evolution of beliefs and opinions on matters related to marriage and sexual behaviour among French-speaking Catholic Quebecers and English-speaking Protestant Ontarians
... Catholics. Using data from Gallup polls, the authors compare the evolution of the opinions of French-speaking Quebec Catholics and Englishspeaking Ontario Protestants on matters related to sexual and family behaviour from the 1950s to the beginning of the 2000s. The general result is that the evolution of the differences between the two groups is compatible ... article, we begin by describing the evolution of certain demographic behaviours in Quebec, as compared with Ontario. We present, in a condensed form, the rationale for our hypothesis. We then formulate specific empirical hypotheses, outline our data sources and methods, provide our results and present a discussion. 211 The Evolution of Beliefs and Opinions ... whereas this is the case in less than one out of ten two-parent families in Ontario. Figures 1 to 4 give an overview of the evolution of certain demographic behaviours in Quebec and Ontario over several decades. Figure 1 shows the evolution of the crude marriage rate in Quebec and Ontario from 1950 to 2003. From 1950 to the mid-1960s, the crude marriage
Patterning of the dorsal-ventral axis in echinoderms: insights into the evolution of the BMP-chordin signaling network.
... that an inversion of the D/V axis has occurred in the course of evolution [6,7]. Echinoderms offer interesting models for the comparative analysis of the mechanisms of axis specification. Their position at the basis of the deuterostome lineage makes them a valuable model to reconstruct the evolution of deuterostomes from an ancestral metazoan and to understand ... information is established along the dorsal-ventral axis of the sea urchin embryo, and more generally on how a BMP morphogen gradient is established in a multicellular embryo. From an evolutionary point of view, it highlights that although the genes used for dorsal-ventral patterning are highly conserved in bilateria, there are considerable variations, even ... these genes are used to shape a BMP morphogen gradient. Citation: Lapraz F, Besnardeau L, Lepage T (2009) Patterning of the Dorsal-Ventral Axis in Echinoderms: Insights into the Evolution of the BMP-Chordin Signaling Network. PLoS Biol 7(11): e1000248. doi:10.1371/journal.pbio.1000248 Academic Editor: Hiroshi Hamada, Osaka University, Japan Received
Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance.
... exhaustively consider all evolutionary trajectories but instead highlighted only those that arose in a small number of replicates; further, the authors do not consider how evolution may proceed once a second drug is applied and whether resistance can then emerge. Model Overview In this study we present a model that abstracts the evolutionary dynamics ... predicting evolutionary trajectories. This allows us to efficiently determine evolutionary trajectories and to consider trajectories either at the patient scale or at the whole clinic scale as in Goulart et al , although without explicit knowledge of the population parameters we are unable to predict the time taken to traverse these evolutionary ... combinations predicted to minimize the probability of evolution to the most resistant genotype in the PLOS Computational Biology | DOI:10.1371/journal.pcbi.1004493 September 11, 2015 6 / 19 Steering Evolution to Prevent the Emergence of Drug Resistance Fig 1. Example fitness landscapes. The evolutionary graphs for the fitness landscapes of E.
Evoluţia diversităţii structurale şi compoziţionale a arboretelor cu ajutorul indicelui UMF: un studiu de caz la nivel de unitate de producţie[The evolution of stand structural and compositional diversity assessed with the UMF index: A case study at produ
... structurale şi compoziţionale a arboretelor cu ajutorul indicelui UMF: un studiu de caz la nivel de unitate de producţie M. C. Burlui, R. Cenuşă Burlui M. C., Cenuşă R., 2014. The evolution of stand structural and compositional diversity assessed with the UMF index: A case study at the production unit. Bucov. For. 14(1): 29-39, 2014. Abstract. In this article ... and compositional diversity of a given area, using data from forest management plans. The results can be analyzed for longer periods of time and may indicate the direction of evolution of an area in relation with anthropogenic changes: from even-aged structure to uneven-aged, from monocultures to mixed stands. Keywords unevere aged, mixed forest, diversity,
Chromosomal characterization of the three subgenomes in the polyploids of Hordeum murinum L.: new insight into the evolution of this complex.
... the hexaploid level. Genome remodelling and polyploidy Allopolyploidy has been an important mechanism in the rapid genomic evolution of the members of Triticeae [29–31]. The present work contributes to our understanding of the coevolution of the Xu, Xv and Xw subgenomes following the polyploidization process. In general, the chromosomes of the same (sub)genome ... recognition. Citation: Cuadrado A´ , Carmona A, Jouve N (2013) Chromosomal Characterization of the Three Subgenomes in the Polyploids of Hordeum murinum L.: New Insight into the Evolution of This Complex. PLoS ONE 8(12): e81385. doi:10.1371/journal.pone.0081385 Editor: Christos A. Ouzounis, The Centre for Research and Technology, Hellas, Greece Received ... manuscript. Competing Interests: The author have declared that no competing interests exist. * E-mail: firstname.lastname@example.org Introduction Polyploidy has been particularly important in the evolution of the family Poaceae . Certainly, it has played an important role in the diversification of the genus Hordeum, which contains diploid, tetraploid and hexaploid taxa.
EVOLUTION OF THE ROMANIAN RESIDENTIAL MARKET AFTER OUTBREAK OF THE CURRENT ECONOMIC AND FINANCIAL CRISIS
... limited to the old buildings for sale. A key role in the analysis of the residential market belongs to the newly built homes. In fact, the evolution of these constructions may provide an important signal for the evolution of the entire economy. A favourable trend in the level of home construction may underlie the revival of a country’s economy, whereas ... world-wide state of affairs. This paper aims to briefly outline the trends on the Romanian residential market in the aftermath of the current crisis. Key words: residential market, evolution, prices, home constructions, First Home. JEL Classification: E31, L74, O18, R31 Introduction The residential market constitutes an extremely important segment of the ... purchase prices, as well as of value of mortgage loans. This paper attempts to perform a radiograph of the Romanian residential market. The paper contains data regarding the evolution of the new homes put into service, of the real estate trading prices, of the First Home scheme and of the luxury residential segment. For this purpose we used a series
Diversity and evolution of coral fluorescent proteins.
... parallel evolution of the color diversity in corals, provide the foundation for experimental studies of evolutionary processes that led to color diversification, and enable a comparative analysis of structural determinants of different colors. Citation: Alieva NO, Konzen KA, Field SF, Meleshkevitch EA, Hunt ME, et al. (2008) Diversity and Evolution ... with which coral FPs can be expressed and screened for phenotypic changes makes them ideal models for experimental studies in evolution of protein families, addressing in particular such important questions as convergent molecular evolution and the origins of molecular complexity [5,6]. Last but not least, coral FPs are major determinants of the coral ... residues in the reconstructed ancestral protein in the evolutionaryforward direction can prove that such modifications are also sufficient . We therefore reconstructed two ancestral proteins, all-coral ancestor and all-Faviina ancestor, which provide perspective to the history of coral color evolution. We found that both ancestral proteins, the
Meningite bacteriana no período neonatal evolução clínica e complicações em 109 casos: clinical evolution and complications in 109 cases.
... haver modificação no prognóstico a longo prazo. PALAVRAS-CHAVE: meningite, criança, recém-nascido, infecção bacteriana. Bacterial meningitis in neonatal p e r i o d : clinical evolution and c o m p l i c a t i o n s in 109 cases SUMMARY — Bacterial meningitis has special clinical features in the newborn infant. Major complications and sequelae result