S F Elena

..However, little is known about the mechanisms and pattern of PepMV molecular evolution and about the role of individual proteins in host-pathogen interactions...

..Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs...

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..In this paper, we propose and employ a new mathematical approach that allows a more complete description of multi-way interactions and provides new insights into the structure of fitness landscapes...

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..Finally, we discuss the possibility that viruses might exploit cellular buffering mechanisms for their own benefit, producing a sort of extrinsic robustness...

..coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5-2 million years ago...

..However, several issues related to robustness remain poorly understood, such as its implications for evolvability (the ability to produce adaptive evolutionary innovations)...

..These results are independent of whether genomes were constrained to their original length or allowed to change in size...

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..Recent results suggest that the effects of deleterious mutations can, instead, sometimes be ameliorated in stressful environments...

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..Here, we review studies identifying host genes regulated by viruses and discuss how these genes integrate in host regulatory and interaction networks, with a particular focus on the physical properties of these networks...

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..However, the magnitude of this effect is larger if replication occurs geometrically than if it proceeds linearly...

..In good agreement with our previous finding of an evolutionary trend toward increased robustness, we now found a trend toward reduced antagonistic epistasis...

..Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness...

..Thus, mixed infections appear to be contributing to shaping the genetic structure and dynamics of PepMV populations...

..Reproducibility was assessed by running multiple competition experiments for the same genotype. Sensitivity was assessed by comparing the results of competition experiments against TEV-PC1 of 24 single-nucleotide substitutions mutants...

..Finally, we discussed the evolution of incoherent regulations in terms of multifunctionality and robustness...

..We also show that genomic redundancy can contribute to the robustness of these simple RNA genomes...

..Viroids elicit RNA-silencing phenomena, which might mediate some of their biological properties, including pathogenesis. As some viroids behave as catalytic RNAs, they are regarded as remnants of the RNA world...

..Finally, we briefly discuss the modular designability of gene regulatory networks and its potential application in biotechnology...

..Second, the concept of resistance genes may only be valid for a well-defined viral genotype but not for polymorphic viral populations...

..We propose that antagonistic epistasis might be a property of compact genomes with few nonpleiotropic biological functions, whereas in complex genomes, synergism might emerge from mutational robustness...

..The MP and CP of APLPV possess most of the functional motifs described for other members of the genus Ilarvirus...

..In addition, high levels of viral fitness in horizontally transmitted populations were explained by competition among viral variants...

..Genomic consensus sequences were obtained for each lineage at the end time point. The potential relevance for the evolution of virulence and virus fitness of the characterized mutations is discussed...

..Our results suggest that the emergence of replication fidelity was critical for the evolution of complexity in the early history of life...

..We have also found that the region in the parameter space (mu,gamma) in which the master sequence survives is reduced when DIPs are introduced into the system...

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..A major difference is that genes involved in stress and pathogen response are not activated upon infection with the evolved virus, suggesting that selection has favored viral strategies to escape from host defenses...

..Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts...

..Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels...

..4% increases. Interestingly, the only mutations showing a significant effect on virulence were hypervirulent. Competitive fitness and virulence were uncorrelated traits...

..Finally, a phylogenetic network was constructed reflecting these genetic exchanges. The network confirmed the taxonomic status of the different genera within the family, despite the phylogenetic noise introduced by genetic exchange...

..The application of the method to different human immunodeficiency virus type 1 and to foot-and-mouth disease virus genes confirms the action of positive selection on previously described regions as well as on new regions...

..Temporal fitness fluctuations were not explained by random noise but reflected more complex underlying processes related to emergence and self-organization phenomena...

..The implications of these results for the taxonomy of this important family of plant viruses are discussed...

..However, the infectivity of each virus was not affected by the presence of the other, and no symptom synergism was observed...

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..Finally, we discuss these findings in the light of what is already known about the implication of certain sites and domains in structure and protein-protein and RNA-protein interactions...

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..In contrast, the slow-growth species was able to outcompete the fast species when the mutation rate was increased. These experimental results were supported by an in silico model of competing viroid quasispecies...

..Negative epistatic effects among beneficial mutations as well as decompensatory epistasis also play an important role during compensatory evolution of RNA-silencing suppression...

..Together, our results contribute to the rational management of amiR-based antiviral resistance in plants...

..As a consequence of lower viral accumulation, plants infected with virus bearing a hyposuppressor allele also accumulate less virus-derived siRNA...

..The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations...

..Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution...

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..Furthermore, it is shown that space, which involves a lower critical mutation rate, broadens the conditions at which the survival-of-the-flattest may occur...

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..Finally, and as another factor imposing a limit to their speed of adaptation, I review results showing that clonal interference also plays an important role during viral evolution...

..In contrast, positive selection does not seem to be the mechanism responsible for the evolution of patient-specific sequences...

..This finding has important implications for applied evolutionary research in both biological and computational realms...

..Evolution in presence of sub-inhibitory concentrations of antivirals compensated for the reduction in fitness in presence of antiviral therapy...

..These results suggest that, on average, deleterious mutations act multiplicatively with each other but in synergy with infection in determining fitness...

..Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations...

..This model may offer a simple and widely applicable alternative to complex metabolic network models, in particular for making evolutionary predictions...

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..The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection...

..In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components...

..Similarly, viral populations evolved at high density showed reduced fitness at low density. Finally, we compare our results with those obtained for other RNA viruses...