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PubMed1995

Chromosome painting in mammals as an approach to comparative genomics.

Chromosome painting has become a routine tool in comparative cytogenetics. The utility of interspecies chromosome painting has been demonstrated in taxa characterized by highly rearranged karyotypes such as in rodents and lesser apes. Chromosome painting also provides a new level of precision in comparative genome analysis for eliminating errors of confounding convergence with homology. Recent results hold promise that molecular cytogenetics will make a significant contribution to the understanding of the major features of genome evolution.

Animals↗
PubMed2006

Emotional endophenotypes in evolutionary psychiatry.

Evolutionary psychiatry emerged from the conceptual successes of sociobiology and evolutionary psychology. It will need to avoid the many mistakes that biology-free Evolutionary Psychology has been prey to. It should not ignore the wealth of information that exists between the phenotypic expression of symptoms and the genotypic sources of core brain/mind processes that are disrupted in psychiatric disorders. Syndromal-conceptual thinking has become a barrier to illuminating the biological sources of psychiatric disorders. Endophenoytpic-biomarker approaches now offer robust alternatives for generating linkages between psychiatrically relevant psychological changes and the neurobiological infrastructure of disordered mentation. Here I summarize recent advances in endophenotypic thinking in biological psychiatry, and suggest that various core emotional-affective processes may be among the most important endophenotypes that need to be clarified at both neurobiological and genetic levels of analysis. To this end, I discuss strategies to link basic emotional processes that are commonly imbalanced in psychiatric disorders to neuroanatomical, neurochemical, neurophysiology, and molecular genetic levels of analysis. Conjoint animal behavioral-genetic and gene expression, microarray analyses can clarify a variety of key emotional endophenotypes and thereby provide a coherent infrastructure for psychiatric systematics. To further clarify the neurobiological dimensions of psychiatric disorders, we must also focus on psychosocial and environmental stress vectors that converge to create imbalanced emotional and motivational brain activities of psychiatric significance.

Animals↗
PubMedDate not supplied

The modes of action of colicins E5 and D, and related cytotoxic tRNases.

Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro, which accounts for their bactericidal actions through depletion of tRNAs and prevention of protein synthesis. The targets of colicin E5 are five tRNA species for four amino acids, tyrosine, histidine, asparagine and aspartic acid, and those of colicin D are four isoaccepting tRNAs for arginine. These two colicins represent a new class, the "tRNase-type", of the nuclease-type colicins, which previously comprised the DNase-type and ribotoxin-type (or rRNase-type). On the other hand, a certain clinical E. coli strain produces a potentially suicidal "anticodon-nuclease", PrrC, in response to phage T4 infection, which specifically cleaves its own lysine tRNA. For these three tRNases, i.e. colicins E5 and D, and PrrC, the substrates and reaction products, as well as their physiological consequences, are very similar to each other, but so many molecular features are different that these three proteins are assumed to have acquired similar functions through evolutionary convergence from different origins.

Bacterial Proteins↗
PubMed2004

The ground state tunneling splitting of malonaldehyde: accurate full dimensional quantum dynamics calculations.

Benchmark calculations of the tunneling splitting in malonaldehyde using the full dimensional potential proposed by Yagi et al. are reported. Two exact quantum dynamics methods are used: the multiconfigurational time-dependent Hartree (MCTDH) approach and the diffusion Monte Carlo based projection operator imaginary time spectral evolution (POITSE) method. A ground state tunneling splitting of 25.7+/-0.3 cm(-1) is calculated using POITSE. The MCTDH computation yields 25 cm(-1) converged to about 10% accuracy. These rigorous results are used to evaluate the accuracy of approximate dynamical approaches, e.g., the instanton theory.

Journal Article↗
PubMed2004

Critical scale invariance in a healthy human heart rate.

We demonstrate the robust scale-invariance in the probability density function (PDF) of detrended healthy human heart rate increments, which is preserved not only in a quiescent condition, but also in a dynamic state where the mean level of the heart rate is dramatically changing. This scale-independent and fractal structure is markedly different from the scale-dependent PDF evolution observed in a turbulentlike, cascade heart rate model. These results strongly support the view that a healthy human heart rate is controlled to converge continually to a critical state.

Computer Simulation↗
PubMed2005

Pollen and sperm heteromorphism: convergence across kingdoms?

Sperm competition theory predicts that males should produce many, similar sperm. However, in some species of animals and plants, males exhibit a heteromorphism that results in the production of at least two different types of sperm or pollen grains. In animals, sperm heteromorphism typically corresponds to the production of one fertile morph and one (or more) sterile morph(s), whereas in plants two or more pollen morphs (one of which can be either sterile or fertile) are produced in all flowers but sometimes in different anthers. Heteromorphism has arisen independently several times across phyla and at different phylogenetic levels. Here, we compare and contrast sperm and pollen heteromorphism and discuss the evolutionary hypotheses suggested to explain heteromorphism in these taxa. These hypotheses include facilitation, nutritive contribution, blocking, cheap filler, sperm flushing or killing for animals; outcrossing and precise cross-pollen transfer or bet-hedging strategy for plants; cryptic female choice for both. We conclude that heteromorphism in the two phyla is most likely linked to a general evolutionary response to sexual selection, either to increase one male's sperm or pollen success in competition with other males, or mediate male/female interactions. Therefore, although sperm and pollen are not homologous, we suggest that heteromorphism represents an example of convergence across kingdoms.

Animals↗
PubMed1995

Morphological correlates of auditory sensitivity in anuran amphibians.

It is largely unknown how the presence and morphology of various auditory structures, including extratympanic structures, affect auditory sensitivity in anuran amphibians. This study examines body size, tympanum size, the presence versus absence of the tympanum, the 'external' versus 'internal' status of the tympanum, and the amphibian and basilar papilla (AP and BP) hair cell counts, as they relate to physiological estimates of auditory sensitivity, within both AP- and BP-sensitive frequency ranges. The BP sensitivity is positively correlated with tympanum area, which is positively correlated with body size. The AP sensitivity is also correlated with body size, perhaps through mediation by extratympanic factors. Tympanum presence affects only BP sensitivity, whereas the external/internal status of the tympanum is irrelevant. Lastly, AP hair cell count correlates with AP sensitivity, irrespective of possible sensory convergence effects.

Animals↗
PubMed2004

Science and technology integration for increased human potential and societal outcomes.

Unifying science based on the material unity of nature at the nanoscale provides a new foundation for knowledge, innovation, and integration of technology. Revolutionary and synergistic advances at the interfaces between previously separated fields of science, engineering and areas of relevance are ready to create nano-bio-info-cogno (NBIC) transforming tools. Developments in systems approach, mathematics, and computation in conjunction with NBIC allow us to understand the natural world and scientific research as closely coupled, complex, hierarchical entities. At this unique moment of scientific and technical achievement, improvement of human performance at individual and group levels, as well as development of suitable revolutionary products, becomes possible and these are primary goals for converging new technologies. NBIC addresses long-term advances in key areas of human activity, including working, learning, aging, group interaction, organizations, and human evolution ((Roco and Bainbridge, 2003)). Fundamentally new tools, technologies, and products will be integrated into individual and social human architecture. This introductory chapter of the Annals outlines research and education trends, funding activities, and the potential of development of revolutionary products and services.

Biological Evolution↗
PubMed2006

An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20.

We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence.

Algorithms↗
PubMedDate not supplied

[Consciousness].

"Consciousness" is the feeling that each individual has of his own existence (self-awareness) and also the state which permits him to perceive his environment (consciousness and wakefulness). These two types of consciousness, apparently quite different, are in fact the two converging stems of the perceptions that the nervous system provides to the organism. To explain this better, it is necessary to refer to the evolution of the nervous system organization among the species and to imagine what perception the nervous system provides at each stage of this evolution, or in each species harbouring a nervous system corresponding to a given stage. At the beginning, the role of the nervous system is to protect the organism and only by an automatic and reflex organization. It corresponds to an unconscious alertness which permits to perceive the environment; it is the prefiguration of the future consciousness. Self-awareness seems to appear with the centrencephalic and limbic structures which are the highest part of the nervous system in the inferior mammals and the central part in man. At this stage, acquisition memory and affectivity with its different manifestations (emotions, mood, pain...) are established. This kind of consciousness is difficult to imagine since it is only sensorial and affective. Mental consciousness appears with the mental activity in the cerebral hemispheres. It is more than likely that it exists in the superior mammals though it is impossible to imagine what it corresponds to. It reaches the highest development in the man in whose the frontal lobes have the largest extent. Speech is the most striking figure of this development. At each stage of the evolution, consciousness expresses the nervous system activity, centered on a perception, the level of which corresponds to the improvements occurring at each stage and superadded to the previous ones. Hence it is obvious that consciousness has no specific center or pathway. It relies upon structures that participate in triggering and regulating the nervous activity and that utilize the particular centers of perception and analysis. These structures are: the reticular formation and the diffuse thalamic system.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2005

Evolution of male morphology in the ant genus Cardiocondyla.

The ant genus Cardiocondyla is characterized by a striking male polymorphism, with wingless, local fighter males (ergatoid males) with life-long spermatogenesis, and winged, peaceful disperser males with limited sperm supply. We examined the evolution of male morphology by reconstructing the phylogeny of Cardiocondyla from sequences of the mitochondrial COI/COII and 16S RNA genes from 13 of the 15 species, of which males are known. Data suggest that male polymorphism is ancestral and that winged males were lost convergently in several taxa, such as C. elegans, C. batesii, and C. mauritanica. Saber-shaped mandibles and lethal fighting among adult ergatoid males might probably have been the original condition, from which strong, shear-shaped mandibles and attacks directed predominantly against freshly eclosed, not yet sclerotized males might have evolved once. The evolution of queen number from ancestral polygyny to derived monogyny appears to be associated with a switch in the behavior of ergatoid males from fighting to mutual tolerance.

Animals↗
PubMed2006

Evolution of mitochondrial chaperones utilized in Fe-S cluster biogenesis.

Biogenesis of Fe-S clusters is an essential process [1]. In both Escherichia coli and Saccharomyces cerevisiae, insertion of clusters into an apoprotein requires interaction between a scaffold protein on which clusters are assembled and a molecular chaperone system--an unusually specialized mitochondrial Hsp70 (mtHsp70) and its J protein cochaperone [2]. It is generally assumed that mitochondria inherited their Fe-S cluster assembly machinery from prokaryotes via the endosymbiosis of a bacterium that led to formation of mitochondria. Indeed, phylogenetic analyses demonstrated that the S. cerevisiae J protein, Jac1, and the scaffold, Isu, are orthologous to their bacterial counterparts [3, 4]. However, our analyses indicate that the specialized mtHsp70, Ssq1, is only present in a subset of fungi; most eukaryotes have a single mtHsp70, Ssc1. We propose that an Hsp70 having a role limited to Fe-S cluster biogenesis arose twice during evolution. In the fungal lineage, the gene encoding multifunctional mtHsp70, Ssc1, was duplicated, giving rise to specialized Ssq1. Therefore, Ssq1 is not orthologous to the specialized Hsp70 from E. coli (HscA), but shares a striking level of convergence at the biochemical level. Thus, in the vast majority of eukaryotes, Jac1 and Isu function with the single, multifunctional mtHsp70 in Fe-S cluster biogenesis.

Computational Biology↗
PubMed2006

The octopus: a model for a comparative analysis of the evolution of learning and memory mechanisms.

Comparative analysis of brain function in invertebrates with sophisticated behaviors, such as the octopus, may advance our understanding of the evolution of the neural processes that mediate complex behaviors. Until the last few years, this approach was infeasible due to the lack of neurophysiological tools for testing the neural circuits mediating learning and memory in the brains of octopus and other cephalopods. Now, for the first time, the adaptation of modern neurophysiological methods to the study of the central nervous system of the octopus allows this avenue of research. The emerging results suggest that a convergent evolutionary process has led to the selection of vertebrate-like neural organization and activity-dependent long-term synaptic plasticity. As octopuses and vertebrates are very remote phylogenetically, this convergence suggests the importance of the shared properties for the mediation of learning and memory.

Action Potentials↗
PubMed1982

[Origin and evolution of the genetic code].

We propose a quantitative model which suggests that the present genetic code appeared under the influence of mutations, while optimizing its own resistance against their effects. Its evolution was realized by successive steps in which the number of translated codons grew, whereas the number of terminators decreased. The main constraint of this model is selection against nonsense mutations: the competition among many primitive codes gives advantage to those which resist best to the occurrence of nonsense mutations. The structures of the selected systems converge towards that of the present genetic code. This one appears then as built so as to resist to errors, information noise, mutations.

Biological Evolution↗
PubMedDate not supplied

Structure, function, and evolution of the oviducts of squamate reptiles, with special reference to viviparity and placentation.

In lizards and snakes, the oviducts function in fertilization, sperm storage, egg transport, eggshell deposition, maintenance of the early embryo, and expulsion of the egg or fetus. In viviparous forms they also contribute to placentae responsible for gas exchange and nutrient provision to the fetus. Dissections of species of 30 genera coupled with data from the literature indicate that squamate oviducts vary interspecifically in seven macroscopic features, including the extent and nature of regional differentiation, vascular supply, topographic asymmetry, number of oviducts, vaginal pouches, and relationship to the cloaca. The uterus, infundibulum, and vagina differ histologically in their epithelia, glands, and myometrial layers. Season cyclicity occurs in all three oviductal regions, most prominently in the uterus, and is under endocrinological control. Regional and cytological specializations reflect the diverse functions performed by the oviduct. Definitive evidence for oviductal albumen production and egg resorption is lacking. In viviparous squamates, three uterine specializations may facilitate maternal-fetal gas exchange: an attenuated epithelium, reduced uterine glands (and a reduced shell membrane), and increased vascularization. Contrary to previous reports, pregnant uteri show no epithelial erosion or capillary exposure. Specializations for nutrient provision to the fetus include mucosal hypertrophy, enlarged glandular epithelia, and multicellular glands whose secretions are absorbed by the chorioallantois. Comparisons with other amniotes indicate that squamates inherited the oviduct as an organ with capabilities for egg uptake and transport, fertilization, eggshell deposition, and oviposition. Other features have evolved convergently among squamates: infundibular sperm receptacles, unilateral oviduct loss, uterine gestation, placentation, and specializations for placentotrophy. Cladistic analysis indicates that oviductal features associated with deposition of tertiary egg investments in reptiles reflect evolutionary convergence as well as secondary simplification, rather than a unidirectional trend towards increased specialization.

Animals↗
PubMed2005

Optimization via intermittency with a self-organizing neural network.

One of the major obstacles in using neural networks to solve combinatorial optimization problems is the convergence toward one of the many local minima instead of the global minima. In this letter, we propose a technique that enables a self-organizing neural network to escape from local minima by virtue of the intermittency phenomenon. It gives rise to novel search dynamics that allow the system to visit multiple global minima as meta-stable states. Numerical experiments performed suggest that the phenomenon is a combined effect of Kohonen-type competitive learning and the iterated softmax function operating near bifurcation. The resultant intermittent search exhibits fractal characteristics when the optimization performance is at its peak in the form of 1/f signals in the time evolution of the cost, as well as power law distributions in the meta-stable solution states. TheN-Queens problem is used as an example to illustrate the meta-stable convergence process that sequentially generates, in a single run, 92 solutions to the 8-Queens problem and 4024 solutions to the 17-Queens problem.

Algorithms↗