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PubMed1983

Evolutionary changes in the information content of polypeptides.

Thermal proteins arising from the self-sequencing of amino acids satisfy the necessary conditions required for them to become a candidate of the evolutionary precursors of contemporary proteins. The source matrix of information or, equivalently, the statistical ensemble of polypeptides, in reference to which the information content of each amino acid residue can be defined and determined, changes with time endogenously through the production of and the change in the mechanism of production of polypeptides. The change proceeds in the direction along which the order of autocatalysis, the number of autocatalytic polymers needed for synthesizing one such polymer, increases. The underlying dynamics is material flow equilibration working in any material aggregate open to material flow, saying that any open system changes its interaction with the exterior endogenously and successively so as to maintain the continuity of material flow there. The self-sequencing and the autocatalytic polymerization of amino acids are the forms of producing polypeptides. The change in the mechanism of producing polypeptides results from the incorporation of polynucleotides into the polypeptide synthesis. The earlier polymeric information translation proceeds from polypeptide to polynucleotide. The direction of translation is reversed at a later stage of evolution. All these evolutionary events are consistent with viewing thermal proteins produced by self-sequencing of amino acids as an evolutionary precursor of contemporary proteins.

Amino Acid Sequence↗
PubMed2005

Niche construction through phenological plasticity: life history dynamics and ecological consequences.

The ability of an organism to alter the environment that it experiences has been termed 'niche construction'. Plants have several ways whereby they can determine the environment to which they are exposed at different life stages. This paper discusses three of these: plasticity in dispersal, flowering timing and germination timing. It reviews pathways through which niche construction alters evolutionary and ecological trajectories by altering the selective environment to which organisms are exposed, the phenotypic expression of plastic characters, and the expression of genetic variation. It provides examples whereby niche construction creates positive or negative feedbacks between phenotypes and environments, which in turn cause novel evolutionary constraints and novel life-history expression.

Biological Evolution↗
PubMed2000

Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data.

Renal cell carcinoma is characterized by an accumulation of complex chromosomal alterations during tumor progression. Chromosome 3p deletions are known to occur early in the carcinogenesis, but the nature of subsequent events, their interrelationships, and their sequence is poorly understood, as one usually only obtains a single "view" of the dynamic process of tumor development in a particular cancer patient. To address this limitation, we used comparative genomic hybridization analysis in combination with a distance-based and a branching-tree method to search for tree models of the oncogenesis process of 116 conventional (clear cell) renal carcinomas. This provides a means to analyze and model cancer development processes based on a more dynamic model, including the presence of multiple pathways, as compared with the fixed linear model first proposed by Vogelstein et al. (N. Engl. J. Med., 319: 525-532, 1988) for colorectal cancer. The most common DNA losses involved 3p (61%), 4q (50%), 6q (40%), 9p (35%), 13q (37%), and Xq (21%). The most common gains were seen at chromosome 17p and 17q (20%). The tree model derived from the distance-based method is consistent with the established theory that -3p is an important early event in conventional (clear cell) renal cancer and supports the prediction made from the branching tree that -4q is another important early event. Both tree models suggest that there may be two groups of clear cell renal cancers: one characterized by -6q, +17q, and + 17p, and another by -9p, -13q, and -18q. Putative prognostic parameters were -9p and -13q. The distance-based tree clarifies that -8p (present in 12% of tumors) is a late event, largely independent of other events. In summary, tree modeling of comparative genomic hybridization data provided new information on the interrelationships of genetic changes in renal cancer and their possible order, as well as a clustering of these events. Using tree analysis, one can derive a more in-depth understanding of the renal cancer development process than is possible by simply focusing on the frequencies of genetic events in a given cancer type.

Carcinoma, Renal Cell↗
PubMed2006

Lifetime reproductive success and density-dependent, multi-variable resource selection.

Individuals are predicted to maximize lifetime reproductive success (LRS) through selective use of resources; however, a wide range of ecological and social processes may prevent individuals from always using the highest-quality resources available. Resource selection functions (RSFs) estimate the relative amount of time an individual spends using a resource as a function of the proportional availability of that resource. We quantified the association between LRS and coefficients of individual-based RSFs describing lifetime resource selection for 267 female red deer (Cervus elaphus) of the Isle of Rum, Scotland, from 1970 to 2001. LRS was significantly related to first- and second-order effects of selection for Agrostis/Festuca grassland and proximity to the sea coast (quality of forage within Agrostis/Festuca grassland was highest nearest the coast (ratio of short:long grassland)). The benefits of selecting for quality in Agrostis/Festuca grassland, however, traded-off with increases in LRS gained by avoiding conspecific density. LRS was inversely associated with local density, which was highest along the coast, and reproductive benefits of selecting Agrostis/Festuca grassland diminished with increasing density. We discuss the relevance of these results to our understanding of the spatial distribution of red deer abundance, and potential applications of our approach to evolutionary and applied ecology.

Agrostis↗
PubMed2006

Frequency and dynamics of recombination within different species of human enteroviruses.

Enteroviruses are members of the family Picornaviridae that cause widespread infections in human and other mammalian populations. Enteroviruses are genetically and antigenically highly variable, and recombination within and between serotypes contributes to their genetic diversity. To investigate the dynamics of the recombination process, sequence phylogenies between three regions of the genome (VP4, VP1, and 3Dpol) were compared among species A and B enterovirus variants detected in a human population-based survey in Scotland between 2000 and 2001, along with contemporary virus isolates collected in the same geographical region. This analysis used novel bioinformatic methods to quantify phylogenetic compatibility and correlations with serotype assignments of evolutionary trees constructed for different regions of the enterovirus genome. Species B enteroviruses showed much more frequent, time-correlated recombination events than those found for species A, despite the equivalence in population sampling, concordant with a linkage analysis of previously characterized enterovirus sequences obtained over longer collection periods. An analysis of recombination among complete genome sequences by computation of a phylogenetic compatibility matrix (PCM) demonstrated sharply defined boundaries between the VP2/VP3/VP1 block and sequences to either side in phylogenetic compatibility. The PCM also revealed equivalent or frequently greater degrees of incompatibility between different parts within the nonstructural region (2A-3D), indicating the occurrence of extensive recombination events in the past evolution of this part of the genome. Together, these findings provide new insights into the dynamics of species A and B enterovirus recombination and evolution and into the contribution of structured sampling to documenting reservoirs, emergence, and spread of novel recombinant forms in human populations.

Capsid Proteins↗
PubMed2006

The cenH3 histone variant defines centromeres in Giardia intestinalis.

Histone H3 variants play critical roles in the functional specialization of chromatin by epigenetically marking centromeric chromatin and transcriptionally active or silent genes. Specifically, the cenH3 histone variant acts as the primary epigenetic determinant of the site of kinetochore assembly at centromeres. Although the function of histone variants is well studied in plants, animals, and fungi, there is little knowledge of the evolutionary conservation of histone variants and their function in most protists. We find that Giardia intestinalis--a diplomonad parasite with two equivalent nuclei--has two phylogenetically distinct histone H3 variants with N-terminal extensions and nonconserved promoters. To determine their role in chromatin dynamics, conventional H3 and the two H3 variants were GFP-tagged, and their subcellular location was monitored during interphase and mitosis. We demonstrate that one cenH3-like variant has a conserved function in epigenetically marking centromeres. The other H3 variant (H3B) has a punctate distribution on chromosomes, but does not colocalize with active transcriptional regions as indicated by H3K4 methylation. We suggest that H3B could instead mark noncentromeric heterochromatin. Giardia is a member of the Diplomonads and represents an ancient divergence from metazoans and fungi. We confirm the ancient role of histone H3 variants in modulating chromatin architecture, and suggest that monocentric chromosomes represent an ancestral chromosome morphology.

Amino Acid Sequence↗
PubMed2004

Evolution of the digital revolution: a radiologist perspective.

The transformation from film-based to filmless operation has become more and more challenging, as imaging studies expand in size and complexity. To adapt to these changes, radiologists must proactively develop new workflow strategies to compensate for increasing work demands and the existing workforce shortage. This article addresses the evolutionary changes underway in the radiology interpretation process and reviews changes that have occurred in the past decade. These include a number of developments in soft-copy interpretation, which is migrating from a relatively static process, duplicating film-based interpretation, to a dynamic process, using multi-planar reconstructions, volumetric navigation, and electronic decision support tools. The result is optimization of the human-computer interface with improved productivity, diagnostic confidence, and interpretation accuracy.

Humans↗
PubMed2001

Alzheimer's disease as a disorder of mechanisms underlying structural brain self-organization.

Mental function has as its cerebral basis a specific dynamic structure. In particular, cortical and limbic areas involved in "higher brain functions" such as learning, memory, perception, self-awareness and consciousness continuously need to be self-adjusted even after development is completed. By this lifelong self-optimization process, the cognitive, behavioural and emotional reactivity of an individual is stepwise remodelled to meet the environmental demands. While the presence of rigid synaptic connections ensures the stability of the principal characteristics of function, the variable configuration of the flexible synaptic connections determines the unique, non-repeatable character of an experienced mental act. With the increasing need during evolution to organize brain structures of increasing complexity, this process of selective dynamic stabilization and destabilization of synaptic connections becomes more and more important. These mechanisms of structural stabilization and labilization underlying a lifelong synaptic remodelling according to experience, are accompanied, however, by increasing inherent possibilities of failure and may, thus, not only allow for the evolutionary acquisition of "higher brain function" but at the same time provide the basis for a variety of neuropsychiatric disorders. It is the objective of the present paper to outline the hypothesis that it might be the disturbance of structural brain self-organization which, based on both genetic and epigenetic information, constantly "creates" and "re-creates" the brain throughout life, that is the defect that underlies Alzheimer's disease (AD). This hypothesis is, in particular, based on the following lines of evidence. (1) AD is a synaptic disorder. (2) AD is associated with aberrant sprouting at both the presynaptic (axonal) and postsynaptic (dendritic) site. (3) The spatial and temporal distribution of AD pathology follows the pattern of structural neuroplasticity in adulthood, which is a developmental pattern. (4) AD pathology preferentially involves molecules critical for the regulation of modifications of synaptic connections, i.e. "morphoregulatory" molecules that are developmentally controlled, such as growth-inducing and growth-associated molecules, synaptic molecules, adhesion molecules, molecules involved in membrane turnover, cytoskeletal proteins, etc. (5) Life events that place an additional burden on the plastic capacity of the brain or that require a particularly high plastic capacity of the brain might trigger the onset of the disease or might stimulate a more rapid progression of the disease. In other words, they might increase the risk for AD in the sense that they determine when, not whether, one gets AD. (6) AD is associated with a reactivation of developmental programmes that are incompatible with a differentiated cellular background and, therefore, lead to neuronal death. From this hypothesis, it can be predicted that a therapeutic intervention into these pathogenetic mechanisms is a particular challenge as it potentially interferes with those mechanisms that at the same time provide the basis for "higher brain function".

Alzheimer Disease↗
PubMed2006

Biological applications of the theory of birth-and-death processes.

In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.

Animals↗
PubMed2006

On the logical relationship between natural selection and self-organization.

Most evolutionary biologists cherish Darwin's theory of natural selection (NS) as the process of adaptive evolution more than 140 years after publication of his first book on the subject. However, in the past few decades the study of self-organization (SO) in complex dynamical systems has suggested that adaptation may occur through intrinsic reorganization without NS. In this study, we attempt to describe the logical framework that relates the general process of SO to the specific process of NS. We describe NS as a mechanism that coordinates the coevolution of species in an ecosystem to effectively capture, process and dissipate solar energy into the earth's shadow. Finally, we conclude that NS is an emergent process founded on the same thermodynamic imperatives that are thought to underlie all SO. This perspective suggests that the theory of self-organizing systems offers a broader physical context in which to understand the process of NS, rather than contesting it. It even suggests the possibility that there may be a physical basis for understanding the origin of the process of NS. Rather than being merely a fluke of nature, the origin of NS that may be driven by energy flows across gradients.

Adaptation, Biological↗
PubMed2002

Genetic algorithms for the application of Activated Sludge Model No. 1.

The genetic algorithm (GA) has been integrated into the IWA ASM No. 1 to calibrate important stoichiometric and kinetic parameters. The evolutionary feature of GA was used to configure the multiple local optima as well as the global optimum. The objective function of optimization was designed to minimize the difference between estimated and measured effluent concentrations at the activated sludge system. Both steady state and dynamic data of the simulation benchmark were used for calibration using denitrification layout. Depending upon the confidence intervals and objective functions, the proposed method provided distributions of parameter space. Field data have been collected and applied to validate calibration capacity of GA. Dynamic calibration was suggested to capture periodic variations of inflow concentrations. Also, in order to verify this proposed method in real wastewater treatment plant, measured data sets for substrate concentrations were obtained from Haeundae wastewater treatment plant and used to estimate parameters in the dynamic system. The simulation results with calibrated parameters matched well with the observed concentrations of effluent COD.

Algorithms↗
PubMed1995

Consumer power as the major evolutionary force.

Each trophic level in evolving ecosystems can behave as either a supplier toward the downstream of trophic energy flow or a consumer toward the upstream, or an arbitrary mixture of the two. We show that each trophic level behaves almost completely as a consumer in evolutionarily sustainable ecosystems. The present prevalence of consumers in evolving ecosystems derives from a model trophic dynamics minimizing the artificial constraints to be applied arbitrarily.

Animals↗
PubMed2006

Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes.

Reductive evolution in mitochondria and obligate intracellular microbes has led to a significant reduction in their genome size and guanine plus cytosine content (GC). We show that genome shrinkage during reductive evolution in prokaryotes follows an exponential decay pattern and provide a method to predict the extent of this decay on an evolutionary timescale. We validated predictions by comparison with estimated extents of genome reduction known to have occurred in mitochondria and Buchnera aphidicola, through comparative genomics and by drawing on available fossil evidences. The model shows how the mitochondrial ancestor would have quickly shed most of its genome, shortly after its incorporation into the protoeukaryotic cell and prior to codivergence subsequent to the split of eukaryotic lineages. It also predicts that the primary rickettsial parasitic event would have occurred between 180 and 425 million years ago (MYA), an event of relatively recent evolutionary origin considering the fact that Rickettsia and mitochondria evolved from a common alphaproteobacterial ancestor. This suggests that the symbiotic events of Rickettsia and mitochondria originated at different time points. Moreover, our model results predict that the ancestor of Wigglesworthia glossinidia brevipalpis, dated around the time of origin of its symbiotic association with the tsetse fly (50-100 MYA), was likely to have been an endosymbiont itself, thus supporting an earlier proposition that Wigglesworthia, which is currently a maternally inherited primary endosymbiont, evolved from a secondary endosymbiont.

Base Composition↗
PubMed2004

Detecting Traces of Prehistoric Human Migrations by Geographic Synthetic Maps of Polyomavirus JC.

The polyomavirus JC (JCV) is a double-stranded DNA virus that is ubiquitous in human populations and is excreted in urine by a large percentage of individuals (20-70%). The strong genetic stability, combined with a mechanism of transmission mainly within the family, makes JCV a good marker of human migrations. In this study, the coevolution of JCV with its human host is investigated by using over a thousand nucleotide sequences deposited in the EMBL database; they correspond to the IG region, which is the genomic region with the highest rate of variation. The pattern of genetic diversity in JCV is evaluated by the principal coordinates analysis and the construction of synthetic maps. The first principal coordinate supports the existence of two distinct virus lineages, both arising from the ancestral African type. The first synthetic map suggests a two-migration model of the human dispersal out of Africa, thus implying a more complex picture than that known from human genes. The second principal coordinate points out the distinctiveness of strains coming from Asian/Amerind populations. The picture yielded by the second synthetic map appears to be more consistent with that known from human genes. In fact, it provides evidence of a deep split of the Asian lineage of JCV into two main branches: one diffusing in Japan and Americas, the other in Southeast Asia. The view that JCV, with its peculiar feature of a dual early emergence from Africa, can provide new information about the evolutionary history of our ancestors is discussed.

Databases, Nucleic Acid↗
PubMed2005

The hitchhiker's guide to avian malaria.

The ecological mechanisms underlying the dispersal of parasites are poorly understood, which is of particular concern in view of currently emerging infectious diseases. In a new study, Pérez-Tris and Bensch examined the distribution and prevalence of avian malaria in a migratory bird across Western Europe. They concluded that repeated independent evolution of year-round transmission has enabled some avian malaria lineages to become more widespread, and more prevalent, than lineages that are transmitted only during the summer. This study blurs the boundaries of evolutionary ecology, epidemiology and macroecology with great potential for cross-disciplinary research.

Animals↗
PubMed2005

Alzheimer's disease as a disorder of dynamic brain self-organization.

Mental function is based on the dynamic organization of neuronal networks. In particular, phylogenetically young brain areas (e.g., cortical associative circuits), involved in the realization of "higher brain functions" such as learning, memory, perception, self-awareness, and consciousness, are continuously re-adjusted even after development is completed. By this life-long self-optimization process, epigenetic information remodels the cognitive, behavioral and emotional reactivity of an individual to meet the environmental demands. To organize brain structures of increasing complexity during evolution, the process of selective dynamic stabilization and destabilization of synaptic connections becomes more and more important. The mechanisms of structural stabilization and labilization underlying a lifelong synaptic remodeling according to experience, are accompanied, however, by an increasing inherent potential of failure and may, thus, not only allow for the evolutionary acquisition of "higher brain function" but at the same time may provide the basis for selective neuronal vulnerability. The mechanisms of synaptic plasticity, i.e., of modifiable interneuronal connectivity, are largely based on external morphoregulatory cues and internal signaling pathways that nonneuronal cells have phylogenetically acquired to sense their relationship to the local neighborhood and to control proliferation and differentiation in the process of tissue repair and regeneration after development is completed. Differentiated neurons that have withdrawn from the cell cycle use these molecular machinery alternatively to control synaptic plasticity. The existence of these alternative effector pathways within a neuron puts it on the risk to erroneously convert signals derived from plastic synaptic changes into positional cues that will activate the cell cycle. This cell cycle activation potentially links synaptic plasticity to cell death. Preventing cell cycle activation by locking neurons in a differentiated but still highly plastic phenotype will, thus, be crucial to prevent neurodegeneration.

Alzheimer Disease↗
PubMed1996

Structure and dynamics of a CheY-binding domain of the chemotaxis kinase CheA determined by nuclear magnetic resonance spectroscopy.

The Escherichia coli histidine autokinase CheA plays an important role in coupling signals received from membrane-bound receptors to changes in the swimming behavior of the cells in order to respond appropriately to environmental signals. Here we describe the structure of the 14 kDa fragment of the chemotaxis kinase CheA, residues 124--257, which binds to the downstream targets of phosphorylation, the response regulators CheY and CheB. This protein fragment contains the CheY-binding domain flanked on each side by regions that correspond to domain linkers in the intact protein. The structure of the domain was determined from 1429 restraints derived from heteronuclear multidimensional NMR experiments. Hybrid distance geometry--dynamical simulated annealing methods were used to calculate a family of structures that satisfy the experimental distance restraints and torsion angle restraints. The root mean square deviation of the 69 ordered residues in the domain is 0.52 A for the backbone heavy atoms and 0.99 A for all heavy atoms. The residues that have been implicated as important for CheY binding form a face consisting of several partially buried hydrophobic residues, framed by charged residues. The dynamic properties of this protein fragment were measured and analyzed using both isotropic and anisotropic models of molecular motion. The linker regions are very flexible and disordered, as evidenced by the very dynamics properties as compared to the CheY-binding domain. The CheY-binding domain of CheA is structurally similar to the histidine-containing phosphocarrier, HPr, which is a protein involved in the phosphoenolpyruvate:sugar phosphotransferase (PTS) pathway. This structural similarity suggests a possible evolutionary relationship of the PTS and chemotaxis pathways.

Amino Acid Sequence↗
PubMed1981

Sex ratio evolution in a variable environment.

We develop a natural selection model for sex ratio control in a spatially variable environment. Predictions of sex ratio alteration as a function of environmental change are tested in laboratory experiments with two parasitic wasps. Field data from a variety of other organisms also support the model. Finally, we discuss possibilities and difficulties for testing this type of evolutionary model.

Animals↗