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Results for “evolutionary potentiation”

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At least 523 records · Page 29Linked to original sources
PubMed2003

[Study on the evolutionary pressure on the env gene of the human immunodeficiency virus type 1 CRF01-AE strains circulating in China].

OBJECTIVE: To identify variations in the env gene of human immunodeficiency virus type 1 (HIV-1) subtype CRF01-AE strains circulating in China and to elucidate the potential relationship between genetic variation and evolutionary pressure. METHODS: Fragments of the HIV-1 env gene were amplified by nested-polymerase chain reaction (n-PCR) from the whole blood of HIV-1 infected individuals from four provinces in Southeast China (Guangdong, Hunan, Jiangsu and Jiangxi). The PCR products were then directly sequenced by ABI 377 DNA sequencers. The sequences covering the env V3-V4 region of 34 HIV-1 subtype CRF01-AE strains were selected to analyse phylogenetic trees and amino acid mutations. The accumulation of synonymous (Ks) and antonymous (Ka) substitutions as well as Ks/Ka ratios were calculated using DIVERGE. RESULTS: Phylogenetic trees showed that the 34 HIV-1 subtype CRF01-AE strains from China clustered with the Chinese AE reference strain (AE.97CNGX2F), as well as with the reference strains from Thailand (AE.CM240 and AE.93TH253). The amino acid sequences of the env V4 and C3 regions in the samples were highly variable, compared with those of V3 and V3-downstream regions. The V3 loop central motif in the majority (87.5%) of the strains was GPGQ. The majority of strains did not contain positively charged amino acids at positions 306 and 320 in V3 loop. The N-linked glycosylation sites in the V3-V4 region and flanking regions in these strains were relatively conserved. Analysis of the entire region showed that the mean Ks values were significantly higher than that of the Ka values (P < 0.001), with the Ks/Ka significantly higher than 1.0 (P < 0.001). In contrast, the Ks/Ka ratio in the V4 region was significantly lower than 1.0 (P < 0.01). CONCLUSIONS: Our study indicated that the majority of HIV-1 subtype CRF01-AE strains circulating in China were highly homogeneous. The amino acid sequences of the V4 and C3 regions were significantly more variable than those of the V3 loop. Our analysis also suggested that the phenotype of nearly all strains was likely to be non-syncytium inducing (NSI). Finally, the variation found in the V3-V4 sequence was significantly influenced by functional constraints as opposed to positive selective pressure, while the variability of the lone V4 region was strongly related to positive selective pressure.

Adult↗
PubMed2006

Ecosystem engineers as selective agents: the effects of leaf litter on emergence time and early growth in Impatiens capensis.

By physically modifying the abiotic environment, ecosystem engineers can have dramatic effects on the distribution and abundance of species in a community. However, ecosystem engineering can also change the selective environment and evolutionary dynamics of affected species, although this remains relatively understudied. Here, we examine the potential for an ecosystem engineer - oak trees - to affect the evolutionary dynamics of the herbaceous, understory annual, Impatiens capensis, through leaf litter deposition. Using a quantitative genetic experimental approach, we found that: (i) the presence of leaf litter significantly affected a suite of germination, growth and phenological traits in I. capensis; (ii) I. capensis does not exhibit performance trade-offs across litter and bare soil environments in the form of negative across-environment genetic correlations; (iii) the presence or absence of leaf litter significantly alters the pattern of natural selection germination timing and hypocotyl length; and (iv) the frequency of leaf litter environments can dramatically change which combinations of hypocotyl length lead to highest mean fitness across both bare soil and leaf litter environments. More generally, our results demonstrate the potential for ecosystem engineers to alter both the ecological and the evolutionary dynamics of the species they affect.

Ecosystem↗
PubMed2006

Towards a unified science of cultural evolution.

We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. Much potential exists for experimental simulations and field studies of cultural microevolution, where there are opportunities to borrow further methods and hypotheses from biology. Potential also exists for the cultural equivalent of molecular genetics in "social cognitive neuroscience," although many fundamental issues have yet to be resolved. It is argued that studying culture within a unifying evolutionary framework has the potential to integrate a number of separate disciplines within the social sciences.

Animals↗
PubMed1997

T cell repertoire: genomic or somatic bias toward recognition of major histocompatibility complex molecules?

The prevailing concept about a major influence of thymic positive selection on shaping the T cell repertoire during ontogeny is confronted with an old idea emphasizing a dominant role for genetic (evolutionary) factors in molding the recognition potential of mature T cells. Our recent results are not readily interpreted without introducing a new version of the old concept, according to which complementarity to the major histocompatibility complex peptide-binding site is a major evolutionary selective pressure on T cell antigen receptor variable genes, with alloreactivity being a reflection of this fact.

Animals↗
PubMed2004

Deafness in Claudin 11-null mice reveals the critical contribution of basal cell tight junctions to stria vascularis function.

Generation of a strong electrical potential in the cochlea is uniquely mammalian and may reflect recent evolutionary advances in cellular voltage-dependent amplifiers. This endocochlear potential is hypothesized to dramatically improve hearing sensitivity, a concept that is difficult to explore experimentally, because manipulating cochlear function frequently causes rapid degenerative changes early in development. Here, we examine the deafness phenotype in adult Claudin 11-null mice, which lack the basal cell tight junctions that give rise to the intrastrial compartment and find little evidence of cochlear pathology. Potassium ion recycling is normal in these mutants, but endocochlear potentials were below 30 mV and hearing thresholds were elevated 50 dB sound pressure level across the frequency spectrum. Together, these data demonstrate the central importance of basal cell tight junctions in the stria vascularis and directly verify the two-cell hypothesis for generation of endocochlear potential. Furthermore, these data indicate that endocochlear potential is an essential component of the power source for the mammalian cochlear amplifier.

Animals↗
PubMed2006

Novel knowledge-based mean force potential at the profile level.

BACKGROUND: The development and testing of functions for the modeling of protein energetics is an important part of current research aimed at understanding protein structure and function. Knowledge-based mean force potentials are derived from statistical analyses of interacting groups in experimentally determined protein structures. Current knowledge-based mean force potentials are developed at the atom or amino acid level. The evolutionary information contained in the profiles is not investigated. Based on these observations, a class of novel knowledge-based mean force potentials at the profile level has been presented, which uses the evolutionary information of profiles for developing more powerful statistical potentials. RESULTS: The frequency profiles are directly calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into binary profiles with a probability threshold. As a result, the protein sequences are represented as sequences of binary profiles rather than sequences of amino acids. Similar to the knowledge-based potentials at the residue level, a class of novel potentials at the profile level is introduced. We develop four types of profile-level statistical potentials including distance-dependent, contact, Phi/Psi dihedral angle and accessible surface statistical potentials. These potentials are first evaluated by the fold assessment between the correct and incorrect models generated by comparative modeling from our own and other groups. They are then used to recognize the native structures from well-constructed decoy sets. Experimental results show that all the knowledge-base mean force potentials at the profile level outperform those at the residue level. Significant improvements are obtained for the distance-dependent and accessible surface potentials (5-6%). The contact and Phi/Psi dihedral angle potential only get a slight improvement (1-2%). Decoy set evaluation results show that the distance-dependent profile-level potentials even outperform other atom-level potentials. We also demonstrate that profile-level statistical potentials can improve the performance of threading. CONCLUSION: The knowledge-base mean force potentials at the profile level can provide better discriminatory ability than those at the residue level, so they will be useful for protein structure prediction and model refinement.

Algorithms↗
PubMed2026

Historical metabolic adaptation potentiates the rapid evolution of flonicamid resistance in Myzus persicae.

Rapid adaptation to novel environments is often shaped not only by newly acquired mutations but also by historical genetic backgrounds established through prior evolutionary events. However, the extent to which such historical contingency contributes to the rapid evolution of insecticide resistance remains poorly understood. Here, we investigated the emergence of resistance to flonicamid, a recently deployed insecticide, in the green peach aphid, Myzus persicae. We show that constitutive overexpression of the P450 enzymes CYP6CY3 and CYP6CY4, already widespread in populations of M. persicae before flonicamid deployment, confers a previously cryptic tolerance phenotype to flonicamid. However, biochemical and transgenic analyses demonstrated that these metabolic adaptations provide only weak protection against flonicamid. Following flonicamid deployment, however, a novel target-site mutation, NaamV251I, in the recently identified molecular target of 4-trifluoromethylnicotinamide (TFNA-AM), emerged in M. persicae on a genetic background of CYP6CY3 or CYP6CY4 overexpression. Structural modeling, enzymatic assays, and CRISPR-Cas9 genome editing demonstrated that this mutation reduces target sensitivity and independently confers moderate resistance. Strikingly, combining the nicotinamidase (Naam) mutation with pre-existing CYP6CY3 or CYP6CY4 overexpression produced substantially elevated resistance phenotypes that far exceeded the effects of either mechanism alone. Our results demonstrate that the pre-existing metabolic background did not itself evolve further following flonicamid deployment but fundamentally altered the phenotypic consequences of a subsequently acquired target-site mutation. These findings provide direct evidence that historical adaptive variation can potentiate rapid resistance evolution to newly introduced insecticides and reveal how interactions between past and contemporary adaptations shape evolutionary responses to novel environmental challenges.

Animals↗
PubMed2025

The Arms Race Between Actinobacillus pleuropneumoniae and Its Genetic Environment: A Comprehensive Analysis of Its Defensome and Mobile Genetic Elements.

Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia in swine, a highly contagious and economically significant disease. The genetic variability of A. pleuropneumoniae complicates disease control efforts, as it enables rapid adaptation to various stressors, including antimicrobial treatments. To better understand the molecular mechanisms underlying this adaptability, we investigated the role of the bacterial defensome and its relationship with mobile genetic elements (MGEs), such as prophages, plasmids, and integrative conjugative elements (ICEs). Using bioinformatic tools, we identified a diverse and rich defensome in A. pleuropneumoniae, with an average of 16 different defense systems per strain. We found that CRISPR-Cas systems, along with other defense mechanisms, are actively involved in restricting the entry of foreign genetic material, playing a crucial role in bacterial adaptation. Additionally, we characterized several novel prophages and examined their distribution across different strains, revealing their potential contribution to the bacterium's evolutionary success. Our findings underscore the complex interplay between the bacterium's defense systems and MGEs, shedding light on how A. pleuropneumoniae maintains genetic diversity while also safeguarding itself against external threats. These insights provide a better understanding of the genetic factors that influence the pathogen's adaptability and highlight potential avenues for more effective disease control strategies.

Actinobacillus pleuropneumoniae↗
PubMed2006

Aggressive behaviour affects selection on morphology by influencing settlement patterns in a passerine bird.

The importance of behaviours as instigators or inhibitors of evolutionary change remains largely unresolved and this is in part because there are very few empirical examples of how behaviours affect evolutionary processes. By determining the environment of breeding, aggressive interactions over territories have the potential to strongly impact selection pressures experienced by individuals. Western bluebirds (Sialia mexicana) provide a unique opportunity to investigate the evolutionary importance of aggression, since their highly variable breeding habitat favours distinct foraging techniques and they also compete aggressively for nest boxes, a resource that is easy to manipulate. Here, I show experimentally that more aggressive males compete more effectively for territories with a high density of nest boxes and, as a consequence, aggressive and non-aggressive males are sorted into distinct breeding habitats that differ in the strength of selection on morphological traits. Specifically, males with longer tails and tarsi were favoured in open habitats where high agility is required to forage efficiently, whereas in forested habitats, where agility is less important, selection was weak. These results show that aggression can affect selection on a local scale by determining individual settlement patterns. More generally, because territorial interactions are important across a wide variety of taxa, these results suggest that aggressive behaviour has the potential to impact the evolutionary trajectory of many animal populations.

Aggression↗
PubMed2000

Embryology and evolution 1920-1960: worlds apart?

During the early part of the 20th century most embryologists were skeptical about the significance of Mendelian genetics to embryological development. A few embryologists began to study the developmental effects of Mendelian genes around 1940. Such work was a necessary step on the path to modern developmental biology. It occurred during the time when the Evolutionary Synthesis was integrating Mendelian and population genetics into a unified evolutionary theory. Why did the first embryological geneticists begin their study at that particular time? One possible explanation is that developmental genetics was a potential avenue of alliance between embryology and evolutionary biology, two fields that had been separated since the 1890s. To assess this possible motive it is necessary to explore the methodological contrasts that obtained between embryology and both Mendelian-chromosomal genetics and neo-Darwinian evolutionary theory. Some of these contrasts persist to the present day.

Animals↗
PubMed2005

Phylogenomics and the reconstruction of the tree of life.

As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.

Animals↗
PubMed2003

Molecular clocks and explosive radiations.

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.

Animals↗
PubMed2004

A new approach to prediction of short-range conformational propensities in proteins.

MOTIVATION: Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data. RESULTS: A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.

Algorithms↗
PubMed2002

Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.

BACKGROUND: In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data. RESULTS: Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger. CONCLUSIONS: In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.

Amino Acid Motifs↗
PubMed2004

Endosymbiotic origins of sex.

Understanding how complex sexual reproduction arose, and why sexual organisms have been more successful than otherwise similar asexual organisms, is a longstanding problem in evolutionary biology. Within this problem, the potential role of endosymbionts or intracellular pathogens in mediating primitive genetic transfers is a continuing theme. In recent years, several remarkable activities of mitochondria have been observed in the germline cells of complex eukaryotes, and it has been found that bacterial endosymbionts related to mitochondria are capable of manipulating diverse aspects of metazoan gametogenesis. An attempt is made here to rationalize these observations with an endosymbiotic model for the evolutionary origins of sex. It is hypothesized that the contemporary life cycle of germline cells has descended from the life cycle of the endosymbiotic ancestor of the mitochondrion. Through an actin-based motility that drove it from one cell to another, the rickettsial ancestor of mitochondria may have functioned as a primitive transducing particle, the evolutionary progenitor of sperm.

Animals↗
PubMed2002

Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind.

Evolutionary psychologists often overlook a wealth of information existing between the proximate genotypic level and the ultimate phenotypic level. This commonly ignored level of biological organization is the ongoing activity of neurobiological systems. In this paper, we extend our previous arguments concerning strategic weaknesses of evolutionary psychology by advocating a foundational view that focuses on similarities in brain, behavior, and various basic psychological features across mammalian species. Such an approach offers the potential to link the emerging discipline of evolutionary psychology to its parent scientific disciplines such as biochemistry, physiology, molecular genetics, developmental biology and the neuroscientific analysis of animal behavior. We detail an example of this through our impending work using gene microarray technology to characterize gene expression patterns in rats during aggressive and playful social interactions. Through a focus on functional homologies and the experimental analysis of conserved, subcortical emotional and motivational brain systems, neuroevolutionary psychobiology can reveal ancient features of the human mind that are still shared with other animals. Claims regarding evolved, uniquely human, psychological constructs should be constrained by the rigorous evidentiary standards that are routine in other sciences.

Adaptation, Psychological↗
PubMed2001

The genetic basis of modularity in the development and evolution of the vertebrate dentition.

The construction of organisms from units that develop under semi-autonomous genetic control (modules) has been proposed to be an important component of their ability to undergo adaptive phenotypic evolution. The organization of the vertebrate dentition as a system of repeated parts provides an opportunity to study the extent to which phenotypic modules, identified by their evolutionary independence from other such units, are related to modularity in the genetic control of development. The evolutionary history of vertebrates provides numerous examples of both correlated and independent evolution of groups of teeth. The dentition itself appears to be a module of the dermal exoskeleton, from which it has long been under independent genetic control. Region-specific tooth loss has been a common trend in vertebrate evolution. Novel deployment of teeth and reacquisition of lost teeth have also occurred, although less frequently. Tooth shape differences within the dentition may be discontinuous (referred to as heterodonty) or graded. The occurrence of homeotic changes in tooth shape provides evidence for the decoupling of tooth shape and location in the course of evolution. Potential mechanisms for region-specific evolutionary tooth loss are suggested by a number of mouse gene knockouts and human genetic dental anomalies, as well as a comparison between fully-developed and rudimentary teeth in the dentition of rodents. These mechanisms include loss of a tooth-type-specific initiation signal, alterations of the relative strength of inductive and inhibitory signals acting at the time of tooth initiation and the overall reduction in levels of proteins required for the development of all teeth. Ectopic expression of tooth initiation signals provides a potential mechanism for the novel deployment or reacquisition of teeth; a single instance is known of a gene whose ectopic expression in transgenic mice can lead to ectopic teeth. Differences in shape between incisor and molar teeth in the mouse have been proposed to be controlled by the region-specific expression of signalling molecules in the oral epithelium. These molecules induce the expression of transcription factors in the underlying jaw mesenchyme that may act as selectors of tooth type. It is speculated that shifts in the expression domains of the epithelial signalling molecules might be responsible for homeotic changes in tooth shape. The observation that these molecules are regionally restricted in the chicken, whose ancestors were not heterodont, suggests that mammalian heterodonty may have evolved through the use of patterning mechanisms already acting on skeletal elements of the jaws. In general, genetic and morphological approaches identify similar types of modules in the dentition, but the data are not yet sufficient to identify exact correspondences. It is speculated that modularity may be achieved by gene expression differences between teeth or by differences in the time of their development, causing mutations to have cumulative effects on later-developing teeth. The mammalian dentition, for which virtually all of the available developmental genetic data have been collected, represents a small subset of the dental diversity present in vertebrates as a whole. In particular, teleost fishes may have a much more extensive dentition. Extension of research on the genetic control of tooth development to this and other vertebrate groups has great potential to further the understanding of modularity in the dentition.

Animals↗
PubMed1992

Immune response to inactivated influenza virus vaccine: antibody reactivity with epidemic influenza B viruses of two highly distinct evolutionary lineages.

Vaccination of adults (healthy female employees potentially capable of transmitting influenza to high-risk persons; n = 104) in autumn 1990 with a trivalent influenza virus vaccine containing B/Yamagata/16/88 induced a low antibody response to B/Finland/150/90, a recent variant of B/Victoria/2/87-like viruses, as compared with the antibody response to B/Finland/172/91, a current variant in the lineage of B/Yamagata/16/88-like viruses. Up to the end of the epidemic season, the antibody status declined but was still significantly better than before the vaccination. The results suggest that the vaccine strain was appropriate for the outbreak of 1990 to 1991 in Finland, but may provide unsatisfactory protection against B/Victoria/2/87-like viruses. Evidence is given that use of Madin-Darby canine kidney (MDCK)-grown virus as an antigen in the haemagglutination inhibition test (HI) may provide more reliable information about the protective antibodies than use of untreated or ether-treated egg-grown viruses. Significantly higher postvaccination and postepidemic antibody titres were recorded among subjects who exhibited the antibody before vaccination than among seronegative subjects. A significantly higher response rate among initially seronegative people than among seropositive people was recorded for antibody to B/Finland/150/90, but no clear evidence was obtained that the pre-existing antibody could have had a negative effect on the antibody production.

Adult↗