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PubMed1999

Archaeabacterial seryl-tRNA synthetases: adaptation to extreme environments and evolutionary analysis.

The aminoacyl-tRNA synthetases are ubiquitous enzymes which catalyze a crucial step of the cell life, the specific attachment of amino acids to their cognate tRNA. The amino acid sequences of three archaeal seryl-tRNA synthetases (SerRS) from Haloarcula marismortui and Methanococcus jannaschii, both belonging to the group of Euryarchaeota, and from Sulfolobus solfataricus, of the group of Crenarchaeota, were aligned with other eubacterial and eukaryal available SerRS sequences. In an attempt to identify some features of adaptation to extreme environments of these organisms, amino acid composition and amino acid substitutions between mesophilic and thermophilic SerRS were analyzed. In addition, universal phylogenetic trees of SerRS including the three known archaeal sequences, rooted by the threonyl-tRNA synthetases were inferred. Amino acid analyses of the SerRS revealed two ways of adaptation to thermophilic environments between the Eubacteria and the Archaea; most of the usually described amino acid substitutions were nonsignificant in the case of archaeal thermophilic SerRS and most amino acid composition biases seemed to be linked to the genome G+C content pressure. The phylogenetic analysis of the SerRS showed the Archaea to be paraphyletic, H. marismortui emerging with the Gram-positive Bacteria, M. jannaschii being near the root of the tree, and S. solfataricus branching with Eucarya.

Adaptation, Physiological↗
PubMed2004

Parasite-induced surfacing in the cockle Austrovenus stuchburyi: adaptation or not?

Parasite manipulation of host behaviour is a compelling example of the extended phenotype. However, in many cases, such manipulation may be incorrectly assumed. Previous work has demonstrated that Austrovenus stuchburyi cockles stranded on mud-flat surfaces due to an inability to re-burrow both contain significantly more metacercariae of the trematode Curtuteria australis and are predated by the definitive host of this parasite at a faster rate than burrowed cockles. These results have been interpreted as strong evidence for a manipulation of cockle behaviour by the trematode to facilitate transmission to the definitive host. The model presented here, however, indicates that the selective advantage to the parasite of the altered host behaviour is currently of a negligible level at our study site that is highly unlikely to have been realized as an adaptation over evolutionary time. Hence, there are no grounds on which the more parsimonious explanation, that the altered host behaviour observed is simply an incidental side-effect of infection, can be rejected. We thus maintain that for any change in the behaviour of infected hosts to be confirmed as potentially a parasite trait that has evolved in response to selection, the adaptive benefit taking into account the entire parasite life cycle may need to be considered.

Adaptation, Physiological↗
PubMedDate not supplied

[Comparative analysis of vestibular system development in various groups of mammals living under different environmental conditions].

We have conducted for the first time a comparative study of the prenatal development of the vestibular system in representatives of pinnipeds (Phocidae, Otariidae, Odobenidae) and cetaceans (Odontoceti, Mysticeti) in comparison with terrestrial mammals. This allowed us to perform a detailed study of the structural organization of the inner ear in species with different ecological specialization, to find out adaptive aspects and stages of the formation of cochlear and vestibular structures in each of the studied species, and to correlate it with the properties of the environment. Studies on early embryogenesis of the labyrinth in cetaceans and pinnipeds, which represent a special direction in the evolution of placentates, give a significant contribution to the solution of problem about the evolutionary origin of the labyrinth in mammals studied. Sensory systems clearly demonstrate the scope of evolutionary and adaptive transformations, which appear in mammals during the transition from the terrestrial to the aquatic mode of life. At the same time, these results may provide help in understanding the general trends of the development of structure and function of the inner ear in mammals as a whole.

Animals↗
PubMed2005

Evolutionary-based grouping of haplotypes in association analysis.

Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNPs, and are considered as a more informative format of data in association analysis. To model haplotypes requires high degrees of freedom, which could decrease power and limit a model's capacity to incorporate other complex effects, such as gene-gene interactions. Even within haplotype blocks, high degrees of freedom are still a concern unless one chooses to discard rare haplotypes. To increase the efficiency and power of haplotype analysis, we adapt the evolutionary concepts of cladistic analyses and propose a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes. The algorithm determines the cluster bases by preserving common haplotypes using a criterion built on the Shannon information content. Each haplotype is then assigned to its appropriate clusters probabilistically according to the cladistic relationship. Through this algorithm, we perform association analysis based on groups of haplotypes. Simulation results indicate power increases for performing tests on the haplotype clusters when compared to tests using original haplotypes or the truncated haplotype distribution.

Algorithms↗
PubMed2005

Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene.

Throughout North America, rabies virus (RV) is endemic in bats. Distinct RV variants exist that are closely associated with infection of individual host species, such that there is little or no sustained spillover infection away from the primary host. Using Bayesian methodology, nucleotide substitution rates were estimated from alignments of partial nucleoprotein (N) gene sequences of nine distinct bat RV variants from North America. Substitution rates ranged from 2.32 x 10(-4) to 1.38 x 10(-3) substitutions per site per year. A maximum-likelihood (ML) molecular clock model was rejected for only two of the nine datasets. In addition, using sequences from bat RV variants across the Americas, the evolutionary rate for the complete N gene was estimated to be 2.32 x 10(-4). This rate was used to scale trees using Bayesian and ML methods, and the time of the most recent common ancestor for current bat RV variant diversity in the Americas was estimated to be 1660 (range 1267-1782) and 1651 (range 1254-1773), respectively. Our reconstructions suggest that RV variants currently associated with infection of bats from Latin America (Desmodus and Tadarida) share the earliest common ancestor with the progenitor RV. In addition, from the ML tree, times were estimated for the emergence of the three major lineages responsible for bat rabies cases in North America. Adaptation to infection of the colonial bat species analysed (Eptesicus fuscus, Myotis spp.) appears to have occurred much quicker than for the solitary species analysed (Lasionycteris noctivagans, Pipistrellus subflavus, Lasiurus borealis, Lasiurus cinereus), suggesting that the process of virus adaptation may be dependent on host biology.

Adaptation, Biological↗
PubMed1994

Does cancer kill the individual and save the species?

I have argued that most germline mutations are due to endogenous process. I speculate that endogenous control of germline mutation serves an important biological function. A certain rate of mutation is required to generate sufficient variation for adaptation during evolutionary time. Sexual reproduction and recombination may serve to enhance variation, but ultimately new germline mutation is required to replenish variant alleles lost secondary to negative selection, genetic drift, and population bottlenecks. Unfortunately, the requisite mutation rates carry a terrible price: for each advantageous mutation, there are many disadvantageous ones. Thus, all mammals are plagued with substantial Mendelian and multifactorial disease. Consequently, the optimal mutation rate should be at a level just sufficient to maintain the requisite variation needed for adaptation. In this view, mechanisms for negative selection are necessary to keep the mutation rate in check. If a high germline mutation rate produces a high mutation rate in somatic tissues, cancer may be an important mediator of negative selection. The multiple mutations necessary to produce cancer serve to amplify relatively small differences in the mutation rate, thereby providing an efficient selection against individuals with germline mutations that result in a high mutation rate. This hypothesis can account for the general similarity of the longevity-corrected cancer incidence profile and the small but significant prevalence of cancer before and during the reproductive period. While this hypothesis must presently be viewed as speculative, it integrates certain previously disjointed observations and suggests an alternative to the general assumption that cancer represents a breakdown in normal physiology.

Animals↗
PubMed1993

Bone and bones, architecture and stress, fossils and osteoporosis.

The combined use of architectural and stress technologies in osteological studies is starting to provide the basic biomechanical underpinnings to both evolutionary and applied medical investigations of bone. The architectural investigations, though tested using invasive methods, are aimed at non-invasive ways of obtaining information from radiographs of bones, fossils and people. They include optical (Fourier) data analysis (ODA) and computational Fourier transformations (FFT). The stress studies, though initially involving older techniques such as photoelastic stress analysis, now employ finite element analysis (FEA) and, most recently, fast Lagrangian analysis of continua (FLAC). Taken together, these methods are capable of providing more detailed knowledge of bone form and function that is important (a) in revealing functional adaptation in evolutionary studies of fossils and (b) for making early diagnosis and understanding pathological fractures in the late stages of osteoporosis.

Animals↗
PubMed2006

Dental morphometric variation between African and Asian colobines, with special reference to the other Old World monkeys.

In order to reveal differences between Asian and African colobines (nonhuman primates) in terms of dietary adaptation and evolutionary development, a large number of the species of the cercopithecoids (Old World monkeys) was analyzed with morphometric methods. In addition to the raw data and ratios, deviations of the colobines, predicted from allometric baselines derived from the cercopithecines, were analyzed by univariate and multivariate analyses. Some results indicated that there exists significant differentiation between colobines and cercopithecines; the latter exhibit a larger dental scale relative to body size, and the less developed front teeth of the colobines may be related to their fewer frequent incisal use, compared with those of the cercopithecines. With regard to variations between the two subtribes of the colobines, which are found in African (Colobina) and Asia (Presbytina), the Asian subtribe displays a larger scale of postcanine teeth, referring to the results of the raw data. This may correspond to their larger body size. While ratios were considered, the variation between Presbytina and Colobina was diminished greatly. This implies that, unlike the scenario postulated to reflect the relationships between colobines and cercopithecines--which supposes that their differentiation is in both size and shape--the variation between the two subtribes is principally size associated: relative to body size Colobina exhibits more emphasized incisors, but less developed postcanine teeth--with the exception of width of M3s. In other words, the relationships between teeth and body size of the African colobines are more similar to those of the cercopithecines. This implies, compared to their Asian partners, that African colobines share more similarities with cercopithecines. This may be related to the episodes in which African species underwent a longer period of sharing environmental and climatic patterns with the cercopithecines that moved to Asia about 5 or 8 million years ago. Canines were found to be important in distinguishing colobines from cercopithecines and in separating one subtribe from the other.

Adaptation, Physiological↗
PubMed1976

Arch form, tooth size, and occlusomandibular kinesis in the Ceboidea.

Correlations between dental morphology, arch configuration, and jaw movement patterns were quantitatively investigated in 23 ceboid species to elucidate integrative aspects of occlusal functional anatomy in an adaptive and evolutionary context. Differential maxillary-mandibular arch widths are primary in guiding lateral jaw movements. These movements are characterized according to their associated condylar shifts as either predominantly translatory or rotational. Predominantly translatory movements result from peripheral contact relationships between maxillary arches which are considerably wider posteriorly than their opposing mandibular arches. The greatest degree of mandibular movement is in the molar region in functional association with wide "primitive" maxillary molars, narrow mandibular molars, constricted maxillary intercanine widths, and narrow maxillary incisors. In contrast, predominantly rotational masticatory jaw movements results from differential arch widths which are greatest in the maxillary canine and incisor regions. Here most jaw movement is in the anterior segment and this is reflected in small maxillary-mandibular molar widths differences, a high degree of premolarization, wide-set maxillary canine teeth, and wide maxillary incisors. Possible selectional factors in the putative evolution of rotational predominance in mastication from the more primitive translatory pattern are discussed.

Animals↗
PubMed2001

A molecular model for the evolution of endothermy in the theropod-bird lineage.

Ectothermy is a primitive state; therefore, a shared common ancestor of crocodiles, dinosaurs, and birds was at some point ectothermic. Birds, the extant descendants of the dinosaurs, are endothermic. Neither the metabolic transition within this lineage nor the place the dinosaurs held along the ectothermic-endothermic continuum is defined. This paper presents a conceptual model for the evolution of endothermy in the theropod-bird lineage. It is recognized that other animals (some fish, insects, etc.) are functionally endothermic. However, endothermy in other clades is beyond the scope of this paper, and we address the onset of endothermy in only the theropod/bird clade. The model begins with simple changes in a single gene of a common ancestor, and it includes a series of concomitant physiological and morphological changes, beginning perhaps as early as the first archosaurian common ancestor of dinosaurs and crocodiles. These changes continued to accumulate within the theropod-avian lineage, were maintained and refined through selective forces, and culminated in extant birds. Metabolic convergence or homoplasy is evident in the inherent differences between the endothermy of mammals and the endothermy of extant birds. The strength and usefulness of this model lie in the phylogenetic, genetic, evolutionary, and adaptive plausibility of each of the suggested developmental steps toward endothermy. The model, although conceptual in nature, relies on an extensive knowledge base developed by numerous workers in each of these areas. In addition, the model integrates known genetic, metabolic, and developmental aspects of extant taxa that phylogenetically bracket theropod dinosaurs for comparison with information derived from the fossil record of related extinct taxa.

Adaptation, Physiological↗
PubMed2006

An evolutionary model for identifying genetic adaptation to high altitude.

Coordinated maternal/fetal responses to pregnancy are required to ensure continuous O2 delivery to the developing organism. Mammals employ distinctive reproductive strategies that afford their young an improved chance of survival through the completion or the reproductive period. Thus, mortality prior to the end of the reproductive period is concentrated in the earliest phases of the lifecycle. At high altitude, fetal growth restriction reduces birth weight and likely compromises survival during the early postnatal period. Population variation in the frequency of the altitude-associated increase in intrauterine growth restriction (IUGR) demonstrates that multigenerational Tibetan and Andean high-altitude populations are protected compared with shorter duration, European or Han (Chinese) residents. This experiment of nature permits testing the hypothesis that genetic factors (a) influence susceptibility to altitude-associated IUGR, (b) act on maternal vascular adjustments to pregnancy determining uteroplacental blood flow, and (c) involve genes which regulate and/or are regulated by hypoxia-inducible factors (HIFs). Serial, studies during pregnancy as well as postpartum in Andean and European residents of high (3600 m) and low (300 m) altitude will permit evaluation of whether uteroplacental O2 delivery is lower in the European than Andean women and, if so, the physiological factors responsible. Comparisons of HIF-targeted vasoactive substances and SNPs in or near HIF-regulatory or targeted genes will permit determination of whether these regions are distinctive in the Andean population. Studies coupling genetic and genomic approaches with more traditional physiological measures may be productively employed for determining the genetic mechanisms influencing physiological adaptation to high altitude.

Adolescent↗
PubMed2005

Predatory search algorithm with restriction of solution distance.

A variety of methods and algorithms have been developed to solve NP-Hard problems in recent decades. In this paper, we are concerned with a relatively new algorithm based on animal behavioral adaptability and evolutionary computation, namely predatory search. When first introduced, the algorithm was implemented with restrictions based on solution cost as a simplification of distance adopted by search-intensive predators. Our research concentrates on exploring the possibility of using distance to restrict search area. Based on the research of Boese et al. (1994), we propose a type of predatory search algorithm restricted by solution distance (particularly bond distance), and compare it with the original algorithm based on three benchmark traveling salesman problems. The results indicate that both algorithms are suitable for solving the traveling salesman problems, while our proposed algorithm either outperforms or at least matches its predecessor with respect to both the running time and the quality of solutions. In addition, further experiments suggest that there exists a certain relationship between the two algorithms.

Algorithms↗
PubMed2026

Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.

The conquest of land by vertebrates has been a pivotal moment in evolutionary history. Adapting to the new habitats necessitated numerous changes in vertebrate anatomy and physiology, creating an enduring imprint on the developmental gene regulatory networks (GRNs) of tetrapods. The increase of high-quality genomic resources over the past decade has made it possible to study the genomic legacy of the water-to-land transition. While much attention has been given to the highly conserved non-coding elements (CNEs) of the genome that share high levels of similarity across evolutionarily diverged clades, recent evidence suggests that perhaps comparable attention should be given to "missing" CNE-s, conserved sequence patches present in extant stem gnathostomes and actinopterygian fishes that have become undetectable in tetrapods during the adaptation to terrestrial life, whether through true sequence loss or divergence beyond alignability. These sequences could help us reveal the relaxation of certain developmental constraints, related to the aquatic lifestyle, that made reaching new adaptive peaks in the developmental landscape possible. In this paper, we search for such CNEs and characterize them in comparison with pan-Gnathostome CNEs, using the zebrafish (Danio rerio) genome as a reference. Our results suggest that the rewiring of developmental networks related to pigmentation and muscle structure formation has left the largest genomic imprint. We also find that components of canonical Wnt and Hedgehog signalling, are enriched among CNEs retained in fish.

cis-regulatory evolution↗
PubMed1982

Characteristics of leucine transport by isolated hepatocytes of Antarctic fish at low temperatures.

Hepatocytes prepared by collagenase perfusion from Antarctic nototheniid fish of genus Trematomus are active in uptake of [14C]leucine at 0, 5, and 10 degrees C. The system is saturable with apparent Km about 1.0 mM. Isoleucine and phenylalanine were major competitors, valine was about one-half as effective, while alanine, glycine and histidine had no effect. Temperature dependency of rates in the 0-10 degrees C range yielded Ea = 65 kJ/mol (Q10 = 2.7). The average first-order rate constant at 0 degrees C was 0.1 min-1, one-third the value of 0.3 min-1 estimated for clearance of [14C]leucine by liver of these species in vivo. Affinity and specificity agreed well with in vivo data on liver clearance of leucine, both in Antarctic fish at 0 degrees C and in temperate fish acclimated to 10 degrees C and 20 degrees C. The results indicate similar modifications of leucine transport associated with evolutionary cold adaptation and seasonal acclimation in fish.

Amino Acids↗
PubMed2006

Rapid discrimination of visual scene content in the human brain.

The rapid evaluation of complex visual environments is critical for an organism's adaptation and survival. Previous studies have shown that emotionally significant visual scenes, both pleasant and unpleasant, elicit a larger late positive wave in the event-related brain potential (ERP) than emotionally neutral pictures. The purpose of the present study was to examine whether neuroelectric responses elicited by complex pictures discriminate between specific, biologically relevant contents of the visual scene and to determine how early in the picture processing this discrimination occurs. Subjects (n = 264) viewed 55 color slides differing in both scene content and emotional significance. No categorical judgments or responses were required. Consistent with previous studies, we found that emotionally arousing pictures, regardless of their content, produce a larger late positive wave than neutral pictures. However, when pictures were further categorized by content, anterior ERP components in a time window between 200 and 600 ms following stimulus onset showed a high selectivity for pictures with erotic content compared to other pictures regardless of their emotional valence (pleasant, neutral, and unpleasant) or emotional arousal. The divergence of ERPs elicited by erotic and non-erotic contents started at 185 ms post-stimulus in the fronto-central midline region, with a later onset in parietal regions. This rapid, selective, and content-specific processing of erotic materials and its dissociation from other pictures (including emotionally positive pictures) suggests the existence of a specialized neural network for prioritized processing of a distinct category of biologically relevant stimuli with high adaptive and evolutionary significance.

Adolescent↗
PubMed2005

Thermodynamics of microbial growth and metabolism: an analysis of the current situation.

This paper attempts to review in how far thermodynamic analysis can be used to understand and predict the performance of microorganisms with respect to growth and bio-product synthesis. In the first part, a simple thermodynamic model of microbial growth is developed which explains the relationship between the driving force for growth in terms of Gibbs energy dissipation and biomass yield. From the currently available literature, it appears that the Gibbs energy dissipation per C-mol of biomass grown, which represents the driving force for chemotrophic growth, may have been adapted by evolutionary processes to strike a reasonable compromise between metabolic rate and growth efficiency. Based on empirical correlations of the C-molar Gibbs energy dissipation, the wide variety of biomass yields observed in nature can be explained and roughly predicted. This type of analysis may be highly useful in environmental applications, where such wide variations occur. It is however not able to predict biomass yields in very complex systems such as mammalian cells nor is it able to predict or to assess bio-product or recombinant protein yields. For this purpose, a much more sophisticated treatment that accounts for individual metabolic pathways separately is required. Based on glycolysis as a test example, it is shown in the last part that simple thermodynamic analysis leads to erroneous conclusions even in well-known, simple cases. Potential sources for errors have been analyzed and can be used to identify the most important needs for future research.

Bacteria↗
PubMed2005

Trauma and resulting sensitization effects are modulated by psychological factors.

Traumas have both immediate consequences and proactive consequences. Examples include learned helplessness, HPA-axis responsivity, gastrointestinal vulnerability to ulcer, and other correlates of anxiety disorders. Both immediate and proactive consequences may be modulated by behavioral and cognitive evolutionary evolved adaption processes, among which are forms of learning that enable 'coping'. Examples of associative and non-associative forms of coping and effects on learned helplessness, HPA-axis responsivity, and gastrointestinal vulnerability are presented. The importance of attention to behavioral contingencies in situations in which potentially traumatic events occur is emphasized as critical to understanding that it is not the physical event(s) per se that determine the immediate and long term consequences.

Adaptation, Psychological↗