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Results for “Evolutionary coordination”

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PubMed2004

Structural and functional characterization of the unusual triheme cytochrome bound to the reaction center of Rhodovulum sulfidophilum.

The cytochrome bound to the photosynthetic reaction center of Rhodovulum sulfidophilum presents two unusual characteristics with respect to the well characterized tetraheme cytochromes. This cytochrome contains only three hemes because it lacks the peptide motif CXXCH, which binds the most distal fourth heme. In addition, we show that the sixth axial ligand of the third heme is a cysteine (Cys-148) instead of the usual methionine ligand. This ligand exchange results in a very low midpoint potential (-160 +/- 10 mV). The influence of the unusual cysteine ligand on the midpoint potential of this distal heme was further investigated by site-directed mutagenesis. The midpoint potential of this heme is upshifted to +310 mV when cysteine 148 is replaced by methionine, in agreement with the typical redox properties of a His/Met coordinated heme. Because of the large increase in the midpoint potential of the distal heme in the mutant, both the native and modified high potential hemes are photooxidized at a redox poise where only the former is photooxidizable in the wild type. The relative orientation of the three hemes, determined by EPR measurements, is shown different from tetraheme cytochromes. The evolutionary basis of the concomitant loss of the fourth heme and the down-conversion of the third heme is discussed in light of phylogenetic relationships of the Rhodovulum species triheme cytochromes to other reaction center-associated tetraheme cytochromes.

Amino Acid Motifs↗
PubMed1999

An emergence of coordinated communication in populations of agents.

The purpose of this article is to demonstrate that coordinated communication spontaneously emerges in a population composed of agents that are capable of specific cognitive activities. Internal states of agents are characterized by meaning vectors. Simple neural networks composed of one layer of hidden neurons perform cognitive activities of agents. An elementary communication act consists of the following: (a) two agents are selected, where one of them is declared the speaker and the other the listener; (b) the speaker codes a selected meaning vector onto a sequence of symbols and sends it to the listener as a message; and finally, (c) the listener decodes this message into a meaning vector and adapts his or her neural network such that the differences between speaker and listener meaning vectors are decreased. A Darwinian evolution enlarged by ideas from the Baldwin effect and Dawkins' memes is simulated by a simple version of an evolutionary algorithm without crossover. The agent fitness is determined by success of the mutual pairwise communications. It is demonstrated that agents in the course of evolution gradually do a better job of decoding received messages (they are closer to meaning vectors of speakers) and all agents gradually start to use the same vocabulary for the common communication. Moreover, if agent meaning vectors contain regularities, then these regularities are manifested also in messages created by agent speakers, that is, similar parts of meaning vectors are coded by similar symbol substrings. This observation is considered a manifestation of the emergence of a grammar system in the common coordinated communication.

Algorithms↗
PubMed2005

Hormone signaling in evolution and development: a non-model system approach.

Cooption and modularity are informative concepts in evolutionary developmental biology. Genes function within complex networks that act as modules in development. These modules can then be coopted in various functional and evolutionary contexts. Hormonal signaling, the main focus of this review, has a modular character. By regulating the activities of genes, proteins and other cellular molecules, a hormonal signal can have major effects on physiological and ontogenetic processes within and across tissues over a wide spatial and temporal scale. Because of this property, we argue that hormones are frequently involved in the coordination of life history transitions (LHTs) and their evolution (LHE). Finally, we promote the usefulness of a comparative, non-model system approach towards understanding how hormones function and guide development and evolution, highlighting thyroid hormone function in echinoids as an example.

Animals↗
PubMed2001

The evolution of inefficiency in a simulated stag hunt.

We used genetic algorithms to evolve populations of reinforcement learning (Q-learning) agents to play a repeated two-player symmetric coordination game under different risk conditions and found that evolution steered our simulated populations to the Pareto inefficient equilibrium under high-risk conditions and to the Pareto efficient equilibrium under low-risk conditions. Greater degrees of forgiveness and temporal discounting of future returns emerged in populations playing the low-risk game. Results demonstrate the utility of simulation to evolutionary psychology.

Algorithms↗
PubMed2004

Group performance and decision making.

Theory and research on small group performance and decision making is reviewed. Recent trends in group performance research have found that process gains as well as losses are possible, and both are frequently explained by situational and procedural contexts that differentially affect motivation and resource coordination. Research has continued on classic topics (e.g., brainstorming, group goal setting, stress, and group performance) and relatively new areas (e.g., collective induction). Group decision making research has focused on preference combination for continuous response distributions and group information processing. New approaches (e.g., group-level signal detection) and traditional topics (e.g., groupthink) are discussed. New directions, such as nonlinear dynamic systems, evolutionary adaptation, and technological advances, should keep small group research vigorous well into the future.

Cognition↗
PubMed2005

Evolutionary computation applied to the reconstruction of 3-D surface topography in the SEM.

A genetic algorithm has been applied to the line profile reconstruction from the signals of the standard secondary electron (SE) and/or backscattered electron detectors in a scanning electron microscope. This method solves the topographical surface reconstruction problem as one of combinatorial optimization. To extend this optimization approach for three-dimensional (3-D) surface topography, this paper considers the use of a string coding where a 3-D surface topography is represented by a set of coordinates of vertices. We introduce the Delaunay triangulation, which attains the minimum roughness for any set of height data to capture the fundamental features of the surface being probed by an electron beam. With this coding, the strings are processed with a class of hybrid optimization algorithms that combine genetic algorithms and simulated annealing algorithms. Experimental results on SE images are presented.

Journal Article↗
PubMed1993

A coordinate-free approach to the analysis of growth patterns: models and theoretical considerations.

Developmental biology holds keys to our understanding of morphological pattern formation whether these patterns are expressed in the fossil record or among extant species. Though much is known about osseous growth at the cellular level (e.g. Hall, 1991), we have minimal understanding of the coordinated processes that combine to produce a complex, three-dimensional form. We have proposed a framework for the coordinate-free representation of form, a statistical method for comparing and modelling growth trajectories for complex morphologies, and a means for the eventual elucidation of the role of growth in the evolution of morphology. Our method uses the coordinate locations of biological landmarks to represent form as a matrix of all possible linear distances between landmarks, the form matrix. When two forms are expressed in this way, comparison of these forms is accomplished by computing the ratios of like linear distances, the form difference matrix. When the forms being compared are from a growth series, the matrix of ratios is called a growth matrix. Patterns of growth for two groups can be compared by computing the growth difference matrix. We applied growth difference matrix analysis to the study of sexual dimorphism of ontogeny in the M. fascicularis craniofacial skeleton. Growth matrices describing growth in male and female M. fascicularis were presented along with the growth difference matrix that describes sexual dimorphism of growth to underscore the detailed information available from this analytical technique. The method is quite general and can be applied to two- or three-dimensional data sets of landmark coordinates (cross-sectional or longitudinal) collected from almost any developing structure. The methods that we propose enable us to go beyond a mathematical summary of the comparison of forms and the comparison of growth patterns. We provide examples of how growth patterns might be used in the study of phylogenetic relationships. Our plans for use of this method in the study of evolutionary change assumes that morphological change in the craniofacial skeleton results from evolutionary change in developmental units (as defined by Atchley & Hall, 1991) that underlie morphological structure. We believe we have the basic tools to ultimately propose informed phylogenies based solely on developmental data. This task requires the identification of 'growth features' and the polarization of these features as primitive or derived. It is also advisable to determine a set of primitive growth features for the groups of interest. This will necessitate the inclusion of outgroups in our growth analysis.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1999

The genetics and evolution of the mariner transposable element in Drosophila simulans: worldwide distribution and experimental population dynamics.

We have studied both the frequency and biogeographical distribution of the transposable DNA element mariner in natural populations of Drosophila simulans and the short-term evolutionary characteristics of mariner in experimental populations. The mariner element has been identified in natural populations of D. simulans from Africa, Europe, the Middle East, Japan, Australia, several Pacific islands, North America, and South America. Only four lines out of 296 were devoid of active mariner elements, as measured by the presence of functional mariner transposase. A slight correlation was found between the latitudinal coordinate of the collection sites and the level of mariner activity in the populations; this correlation became highly significant in Australia where a cline in mariner activity was observed along the eastern coast of the continent. We also observed that wild-type laboratory strains kept for several years as small populations might lose mariner activity over time. Using experimental populations, we modeled what might happen when naturally occurring populations exhibiting high and low levels of mariner activity encounter one another. We found that active mariner elements either will tend to lose their activity over time and gradually become inactive or possibly will be lost from the population; in either case, this will lead to the pattern seen in this experiment of a significant loss of mariner activity over time.

Animals↗
PubMed1978

[The evolutionary historical (phylogenetic) background of the wisdom-tooth problem].

The almost ubiquitous wisdom tooth problem of modern man is in the present paper made the object of an analysis and evaluation on a comprehensive biological basis. It is pointed out that a number of fundamental traits of human cranio-facial evolution have implied developmental trends which have ultimately placed them at the bottom of the later wisdom tooth problem. These aspects are particularly associated with the discrepancy between the size of the jaws and the dental apparatus, arising by failing coordination in the tempo of regression of the separate masticatory elements during the phylogenetic process. The wisdom tooth problem, however, has not become manifest and acute until the present age, with the marked reduction of masticatory function which has taken place.

Animals↗
PubMed2005

A zinc(II)/lead(II)/cadmium(II)-inducible operon from the Cyanobacterium anabaena is regulated by AztR, an alpha3N ArsR/SmtB metalloregulator.

A novel Zn(II)/Pb(II)/Cd(II)-responsive operon that consists of genes encoding a Zn(II)/Pb(II) CPx-ATPase efflux pump (aztA) and a Zn(II)/Cd(II)/Pb(II)-specific SmtB/ArsR family repressor (aztR) has been identified and characterized from the cyanobacterium Anabaena PCC 7120. In vivo real time quantitative RT-PCR assays reveal that both aztR and aztA expression are induced by divalent metal ions Zn(II), Cd(II), and Pb(II) but not by other divalent [Co(II), Ni(II)] or monovalent metal ions [Cu(I) and Ag(I)]. The introduction of a plasmid containing the azt operon into a Zn(II)/Cd(II)-hypersensitive Escherichia coli strain GG48 functionally restores Zn(II) and Pb(II) resistance with a limited effect on Cd(II) resistance. Gel mobility shift assays and aztR O/P-lacZ induction experiments confirm that AztR is the metal-regulated repressor of this operon. In vitro biochemical and mutagenesis studies indicate that AztR contains a sole metal-binding site, designated the alpha3N site, that binds Zn(II), Cd(II), and Pb(II) with a high affinity. Optical absorption spectra of Co(II)- and Cd(II)-substituted AztR and (113)Cd NMR spectroscopy of (113)Cd(II)-substituted AztR reveal that the sole alpha3N site in AztR is a CadC-like distorted tetrahedral S(3)(N,O) metal site. The first metal-coordination shell in the AztR alpha3N site differs from other alpha3N family members that sense Cd(II)/Pb(II) and those alpha5 repressors that sense Zn(II)/Co(II). Our results reveal that the alpha3N site in AztR mediates derepression of the azt operon in the presence of Zn(II), as well as Cd(II) and Pb(II); this might have provided Anabaena with an evolutionary advantage to adapt to heavy-metal-rich environments, while maintaining homeostasis of an essential metal ion, Zn(II).

Amino Acid Sequence↗
PubMed2002

The usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizards.

Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the application of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining principal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration.

Animals↗
PubMed2006

Role of Na+ and K+ in enzyme function.

Metal complexation is a key mediator or modifier of enzyme structure and function. In addition to divalent and polyvalent metals, group IA metals Na+ and K+ play important and specific roles that assist function of biological macromolecules. We examine the diversity of monovalent cation (M+)-activated enzymes by first comparing coordination in small molecules followed by a discussion of theoretical and practical aspects. Select examples of enzymes that utilize M+ as a cofactor (type I) or allosteric effector (type II) illustrate the structural basis of activation by Na+ and K+, along with unexpected connections with ion transporters. Kinetic expressions are derived for the analysis of type I and type II activation. In conclusion, we address evolutionary implications of Na+ binding in the trypsin-like proteases of vertebrate blood coagulation. From this analysis, M+ complexation has the potential to be an efficient regulator of enzyme catalysis and stability and offers novel strategies for protein engineering to improve enzyme function.

Animals↗
PubMed1992

Neural mechanisms of emotion.

When viewed from an evolutionary perspective, the neural mechanisms of emotion can be seen to be distributed across the brainstem, limbic, paralimbic, and neocortical regions. Descending and ascending connections among these levels are discussed in relation to three types of emotional processes: peripheral effects on patterned bodily responses, central effects on cognitive processing, and subjective emotional experience. Descending influences from the higher to the lower levels allow for an increasing coordination and flexibility of emotional responses, culminating in patterned activity across the peripheral endocrine, autonomic, and motor systems. Ascending influences from lower to higher levels provide preparatory modulation of cortical pathways, thus enabling perceptual and cognitive processing that is adaptive given the current emotional state. The bodily feelings of emotion are a function of cortical interoceptive sensory fields, activated by centrally generated signals or peripheral inputs from the body.

Adult↗
PubMed2000

Manipulation of the phenolic chemistry of willows by gall-inducing sawflies.

The ability to induce galls on plants has evolved independently in many insect orders, but the adaptive significance and evolutionary consequences of gall induction are still largely unknown. We studied these questions by analyzing the concentrations of various plant defense compounds in willow leaves and sawfly galls. We found that the galls are probably nutritionally beneficial for the sawfly larvae, because the concentrations of most defensive phenolics are substantially lower in gall interiors than in leaves. More importantly, changes in chemistry occur in a similar coordinated pattern in all studied willow species, which suggests that the insects control the phenolic biosynthesis in their hosts. The resulting convergence of the chemical properties of the galls both within and between host species indicates that the role of plant chemistry in the evolution of host shifts may be fundamentally less significant in gallers than in other phytophagous insects.

Animals↗
PubMedDate not supplied

Heterarchy of cognition: the depths and the highs of a framework for memory research.

To celebrate the levels-of-processing approach, I describe a multilevel evolutionary architecture for human behaviour and cognition. New experimental data on human eye movements are presented that demonstrate a possibility of splitting visual perceptual activity at least on two hierarchical but closely interrelated levels of processing. Furthermore, data from behavioural studies of human memory and neuroimaging testify that within the domain of cognition proper two higher levels can be differentiated. I call them "conceptual structures" and "metacognitive coordinations" and provide evidence that the latter may residue in the phylogenetically new structures of prefrontal and particularly right prefrontal cortices. From this point of few, the most natural framework for an analysis of the levels-of-processing effects on human memory is to consider them as interactions within the main gradients of evolution and development of the corresponding neurophysiological mechanisms. Finally, several new, still unanswered questions for the future research are formulated.

Biological Evolution↗
PubMed1997

The evolution of eyes.

Eyes are the preeminent source of sensory information for the brain in most species, and many features of eyes reflect evolutionary solutions to particular selective pressures, both from the nonbiological environment and from other animals. As a result, the evolution of eyes, among all the sense organs, has attracted considerable attention from scientists. Paired eyes in the three major phyla, vertebrates, arthropods and mollusks, have long been considered to be classic examples of evolutionary convergence. At the macroscopic level, this must be true since they arise from different tissues and have evolved radically different solutions to the common problem of collecting and focusing light. However, opsin, the light-absorbing receptor protein, has a significant amount of shared DNA sequence homology across the phyla, and recently it has been discovered that some part of ocular development in different phyla is coordinated by a homologous, gene, Pax-6. So, although eyes from diverse phyla are clearly not homologous, neither can they be viewed as resulting solely from convergence. Instead, this shows that homology at the molecular level of organization does not predict homology at the organ or organismic level. The presence of homologous constituent molecules in nonhomologous structures reminds us that molecules are not eyes.

Animals↗
PubMed2026

Cultivar-dependent regulation of cytokinin biosynthesis in wheat: developmental expression of TaIPT genes and hormonal crosstalk during reproductive development.

BACKGROUND: Cytokinins are key regulators of plant growth, reproductive development, and yield formation. In cereals, cytokinin biosynthesis is catalyzed by isopentenyltransferase (IPT) enzymes, yet the genomic organization and developmental regulation of IPT genes in polyploid wheat remain incompletely understood, especially at the cultivar level. RESULTS: Here, we present an integrated genomic, transcriptional, and hormonal analysis of the TaIPT gene family during vegetative and reproductive development in two wheat cultivars, awnless Kontesa and awned Ostka. Genome-wide analysis identified nine core TaIPT genes represented by 25 homoeologs distributed across the A, B, and D subgenomes, for which a unified nomenclature was established. Phylogenetic analysis resolved TaIPTs into conserved evolutionary clades corresponding to ATP/ADP-dependent and tRNA-dependent IPT groups. Expression profiling revealed distinct spatial and temporal patterns of TaIPT transcription across roots, leaves, inflorescences, and developing spikes. Several TaIPT genes showed enhanced expression during early reproductive stages, coinciding with dynamic changes in cytokinin concentrations. Comparative analyses revealed cultivar-specific expression and co-variation patterns, with Kontesa displaying more compartmentalized TaIPT expression and Ostka showing coordinated activation of multiple TaIPT genes during early grain development. Hormone profiling further indicated stage-dependent associations between TaIPT expression, cytokinin metabolism, and the balance between cytokinins and abscisic acid. These relationships are interpreted as correlative and provide a framework for future functional testing rather than direct evidence of causality. CONCLUSIONS: Together, these results provide a cultivar-focused framework for understanding the organization and regulation of cytokinin biosynthesis genes in wheat. The data highlight cultivar-dependent TaIPT expression patterns and their association with cytokinin dynamics during reproductive development, while also identifying the need for homoeolog-specific and functional validation. This study establishes a foundation for future research on cytokinin-mediated regulation of wheat growth and grain development.

Triticum↗
PubMed2005

Mitochondrial hexokinases: guardians of the mitochondria.

There is accumulating evidence that cell survival and energy metabolism are inexorably linked. As a major mediator of both the metabolic and anti-apoptotic effects of growth factors, the serine/threonine kinase Akt (also known as protein kinase B or PKB) is particularly well-suited to coordinate the regulation of these interrelated processes. Recent demonstrations that growth factors and Akt require glucose (Glc) to prevent apoptosis and promote cell survival are compatible with this contention, as is a positive correlation between Akt-regulated mitochondrial hexokinase (mtHK) association and apoptotic resistance. From a phylogenetic perspective, the ability of Akt to regulate cellular energy metabolism apparently preceded the capacity to control cell survival, suggesting an evolutionary basis for the Glc dependent anti-apoptotic effects of Akt. We speculate that, somewhere in the course of evolution, the metabolic regulatory function of Akt evolved into an adaptive sensing system involving mtHK that ensures mitochondrial homeostasis, thereby coupling metabolism to cell survival. We also propose that this "guardian" function of mtHK may be specifically exploited for therapeutic purposes.

Animals↗