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PubMed2004

Primate models for human immunodeficiency virus infection. Evolution of receptor use during pathogenesis.

Animal models greatly facilitate understanding of transmission, pathogenesis and immune responses in HIV and SIV infection and provide models for studies on the effect of candidate drugs or vaccines. However, there are several aspects that one should consider when drawing conclusions from results obtained from animal models. First, the genetic relationship of primate lentiviruses cannot be disregarded because it is known that HIV-1 is more closely related to SIV of chimpanzee origin (SIVcpz) than to SIV from sooty mangabey (SIVsm) origin. Nevertheless, SIVsm and SIVmac are the ones most often used as model systems. Second, there are differences in the biological properties, like CXCR4 use and CD4-independent coreceptor use, of HIV and SIV. These differences might be relevant in virus transmission, pathogenesis and in evoking immune responses. Third, in vivo and in vitro selection may influence the results. Neutralizing antibodies may play a role in selection of variant viruses since neutralization sensitive, CD4-independent SIVsm variants seemed to be suppressed in animals that mounted a neutralizing antibody response. It is tempting to speculate that neutralizing antibodies shape the SIV/HIV infection by selecting variants with a more "closed" envelope conformation with consequences for both receptor binding and neutralization sensitivity. The SIV/monkey model, although it has important advantages, may not answer all questions asked about HIV-1 infection in human.

Animals↗

PubMed1992

Quantitative analysis of mutation and selection in self-replicating RNA.

Mutation and selection as principles of Darwinian evolution have contributed a wealth to qualitative insight and understanding of complex biological organizations. However, for quantitative measurements of Darwinian evolution, only model systems are sufficiently simple to allow calculation of values for the relevant evolution parameters. The model system used for our study comprises short-chained RNA species whose self-replication is catalyzed by Q beta replicase. In this system, phenotypic expression of a genotype is reduced to its efficiency in directing its own synthesis. The mechanism of single-stranded RNA reproduction is well understood: RNA synthesis profiles can be described by compact equations. The selection behaviour of competing RNA species can be precisely predicted, using these equations, from kinetic parameters of the species: at low concentrations, RNA species are selected for overall growth rate (fecundity), at higher concentrations, for rapid binding of replicase (selection for competition), and at still higher concentrations, for minimizing losses caused by formation of inactive double strands. Finally, an ecosystem may be established where the different species coexist, their relative concentrations being functions of their kinetic parameters. The analysis of competition and selection can be extended to mutants of a species. Experimental conditions can be found where quantitative measurement of mutation rates and selective values of mutants is possible. The interplay of mutation and selection results in establishing a quasispecies distribution where mutants are represented according to their rates of mutational formation and their selective values. Replicating RNA clones, when amplified, rapidly build up quasispecies distributions containing pronounced "hot spots", produced predominantly by error propagation of nearly neutral mutants. The primitive model system shows the same complex Darwinian behaviour as observed in evolution of biological systems. In the absence of extraneously added template, Q beta replicase synthesizes after long lag times self-replicating RNA de novo. In a first step, nucleoside triphosphates are condensed randomly; self-replicating templates produced by chance are amplified and optimized.

Allolevivirus↗

PubMed2002

The use of a neural network to forecast daily grass pollen concentration in a Mediterranean region: the southern part of the Iberian Peninsula.

BACKGROUND: Pollen allergy is a common disease causing hayfever in 15% of the population in Europe. Medical studies report that a prior knowledge of pollen content in the air can be useful in the management of pollen-related diseases. OBJECTIVES: The aim of this work was to forecast daily Poaceae pollen concentrations in the air by using meteorological data and pollen counts from previous days as independent variables. METHODS: Linear regression models and co-evolutive neural network models were used for this study. Pollen was monitored by a Hirst-type spore trap using standard techniques. The data were obtained from the Spanish Aerobiology Network database, University of Cordoba Monitoring Unit. The set of data includes a series of 20 years, from 1982 to 2001. A classification of the years according to their allergenic potential was made using a K-mean cluster analysis with pollen and meteorological parameters. Statistical analysis was applied to all the years of each class with the exception of the most recent year, which was used for model validation. RESULTS: It was observed that cumulative variables and pollen values from previous days are the most important factors in the models. In general, neural network equations produce better results than linear regression equations. CONCLUSION: Co-evolutive neural network models, which obtain the best forecasts (an almost 90% "good" classification), make it possible to predict daily airborne Poaceae pollen concentrations. This new system based on neural network models is a step toward the automation of the pollen forecast process.

Environmental Pollution↗

PubMed2005

Hox clusters as models for vertebrate genome evolution.

The surprising variation in the number of Hox clusters and the genomic architecture within vertebrate lineages, especially within the ray-finned fish, reflects a history of duplications and subsequent lineage-specific gene loss. Recent research on the evolution of conserved non-coding sequences (CNS) in Hox clusters promises to reveal interesting results for functional and phenotypic diversification.

Animals↗

PubMed2006

Spatial evolutions of Co and Ni atoms during single-walled carbon nanotubes formation: measurements and modeling.

Spatial investigations of nickel and cobalt atoms and of C2 and C3 radicals are performed by laser induced fluorescence (LIF) in a continuous CO2 laser-vaporization reactor during the synthesis of single-walled carbon nanotubes. The chemical composition of the gas vaporized from bimetallic Ni/Co catalysts-carbon targets is determined using a chemical kinetic model. In this model, the evolution of Ni and Co atoms is driven by kinetics of condensation/evaporation process of pure metal clusters. Metal-carbon clusters are assumed to form from soot particles (C80) and 128-atom metal clusters. Spatial profiles of Ni and Co atoms obtained by LIF are compared with the calculations to validate the modeling and to adjust the input data. The value of the initial molar fraction of carbon-metal mixture diluted in helium is determined through a parametric study. Good agreement is found between the measured and the calculated evolution of Ni for a molar fraction of the helium diluent ranging from 10 to 15%. To fit the spatial profile of Co, the activation energy is adjusted in the evaporation rate, changing the cobalt dimer bond energy. The latter is found to be largely uncertain; and three values are tested: 167, 208, and 230 kJ x mol(-1). From comparison, the activation energy is found to be 208 kJ x mol(-1). However, the C2 LIF profiles show that the depletion of C2 is accelerated when cobalt is present. The observed Co evolutions suggest that small Co-C clusters are easier and/or faster to form compared to Ni-C clusters.

Carbon↗

PubMed2004

The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics.

We model the evolution of reaction norms focusing on three aspects: frequency-dependent selection arising from resource competition, maintenance and production costs of phenotypic plasticity, and three characteristics of environmental heterogeneity (frequency of environments, their intrinsic carrying capacity and the sensitivity to phenotypic maladaptation in these environments). We show that (i) reaction norms evolve so as to trade adaptation for acquiring resources against cost avoidance; (ii) maintenance costs cause reaction norms to better adapt to frequent rather than to infrequent environments, whereas production costs do not; and (iii) evolved reaction norms confer better adaptation to environments with low rather than with high intrinsic carrying capacity. The two previous findings contradict earlier theoretical results and originate from two previously unexplored features that are included in our model. First, production costs of phenotypic plasticity are only incurred when a given phenotype is actually produced. Therefore, they are proportional to the frequency of environments, and these frequencies thus affect the selection pressure to avoid costs just as much as the selection pressure to improve adaptation. This prevents the frequency of environments from affecting the evolving reaction norm. Secondly, our model describes the evolution of plasticity for a phenotype determining an individual's capability to acquire resources, and thus its realized carrying capacity. When individuals are distributed randomly across environments, they cannot avoid experiencing environments with intrinsically low carrying capacity. As selection pressures arising from the need to improve adaptation are stronger under such extreme conditions than under mild ones, better adaptation to environments with low rather than with high intrinsic carrying capacity results.

Adaptation, Physiological↗

PubMed2006

Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes.

Evolutionists widely acknowledge that regulatory genetic changes are of paramount importance for morphological and genomic evolution. Nevertheless, mechanistic complexity and a paucity of data from nonmodel organisms have prevented testing and quantifying universal hypotheses about the macroevolution of gene regulatory mechanisms. Here, we use a phylogenetic approach to provide a quantitative demonstration of a previously hypothesized trend, whereby the evolutionary rate of repression or loss of gene expression regions is significantly higher than the rate of activation or gain. Such a trend is expected based on case studies in regulatory evolution and under models of molecular evolution where duplicated genes lose duplicated expression patterns in a complementary fashion. The trend is important because repression of gene expression is a hypothesized mechanism for the origin of evolutionarily novel morphologies through specialization.

Animals↗

PubMed2002

Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution.

We study the phylogeny of the placental mammals using molecular data from all mitochondrial tRNAs and rRNAs of 54 species. We use probabilistic substitution models specific to evolution in base paired regions of RNA. A number of these models have been implemented in a new phylogenetic inference software package for carrying out maximum likelihood and Bayesian phylogenetic inferences. We describe our Bayesian phylogenetic method which uses a Markov chain Monte Carlo algorithm to provide samples from the posterior distribution of tree topologies. Our results show support for four primary mammalian clades, in agreement with recent studies of much larger data sets mainly comprising nuclear DNA. We discuss some issues arising when using Bayesian techniques on RNA sequence data.

Animals↗

PubMed1998

Enigma of Y chromosome degeneration: neo-Y and neo-X chromosomes of Drosophila miranda a model for sex chromosome evolution.

Y chromosome degeneration is characterized by structural changes in the chromosome architecture and expansion of genetic inertness along the Y chromosome. It is generally assumed that the heteromorphic sex chromosome pair has developed from a pair of homologues. Several models have been suggested. We use the unique situation of the secondary sex chromosome pair, neo-Y and neo-X (X2), in Drosophila miranda to analyze molecular mechanisms involved in the evolutionary processes of Y chromosome degeneration. Due to the fusion of one of the autosomes to the Y chromosome (about 2 Mya), a neo-Y chromosome and a neo-X chromosome, designated X2, were formed. Thus, formerly autosomal genes are inherited now on a pair of sex chromosomes in D. miranda. Analyzing DNA sequences from the X2 and neo-Y region, we observed a massive accumulation of DNA insertions on the neo-Y chromosome. From the analysis of several insertion elements, we present compelling evidence that the first step in Y chromosome degeneration is driven by the accumulation of transposable elements, especially retrotransposons. An enrichment of these elements along an evolving Y chromosome could account for the switch from a euchromatic into a heterochromatic chromatin structure.

Animals↗

PubMed1999

Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models.

We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition-transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.

Base Sequence↗

PubMed1999

Complex patterns predicted in an in vitro experimental model system for the evolution of molecular cooperation.

An isothermal biochemical in vitro amplification system with two trans-cooperatively coupled amplifying DNA molecules was investigated homogeneously using a hierarchy of kinetic models and as a simplified reaction-diffusion system. In our model of this recently developed experimental system, no reaction mechanism higher than second order occurs, yet numerical simulations show a variety of complex spatiotemporal patterns which arise in response to finite amplitude perturbations in a flow reactor. In a certain domain of the kinetic parameters the system shows self-replicating spots. These spots can stabilize the cooperative amplification in such evolving systems against emerging parasites. The results are of high relevance for experimental studies on these functional in vitro ecosystems in spatially resolved microstructured reactors.

Journal Article↗

PubMed1998

Increased accuracy in analytical molecular distance estimation.

Analytical molecular distance estimates can be inaccurate and biased estimates of the total number of substitutions not only when the model of evolution they are based on is incorrect, but also when the method of estimating the total is too simple. This comes about because when there are different types of substitutions occurring simultaneously, it can become extremely difficult to estimate the number of the more quickly evolving type, and the variance of this larger number can overwhelm the total estimate. In this paper, in an extension of earlier work with a simple two-parameter model of evolution, more accurate analytical distances are derived for models appropriate to a variety of known DNA types using generalized least squares principles of noise reduction. It is shown that the new estimates can be applied to achieve more accurate results for site-to-site rate variation, regions with biased nucleotide frequencies, and synonymous sites in protein-coding regions. This study also includes a methodology to obtain accurate distance estimates for large numbers of sequence regions evolving in different manners.

Animals↗

PubMed2001

A mathematical model for experimental gene evolution.

The purpose of this paper is to determine the optimal mutation rate for random mutagenesis procedures used to make mutant libraries for subsequent screening. When the mutation rate is low, the probability of achieving a rare beneficial mutation is low. When the mutation rate is high, the probability of producing lethal mutations which result in loss of function is also high. We demonstrate that between these two extremes, an optimal mutation rate exists for experimental gene improvement. This rate depends strongly on the number of simultaneous mutations required for a beneficial change of the gene, but only weakly on the number of possible lethal mutations. This model predicts that when mutagenesis is performed at the optimum mutation rate, at least 63% (1--e(-1)) of the cloned genes in a mutant library will be non-functional.

Animals↗

PubMed2004

The evolution of paternal care with overlapping broods.

Most attempts to model the evolution of parental care assume that caring and mating are mutually exclusive activities (i.e., individuals acquire and guard broods "sequentially"). However, in most fish and certain insects, males can keep mating and collecting additional eggs while continuing to guard broods obtained earlier (i.e., males guard "overlapping" broods). We present a model of parental care with overlapping broods in which males can mate and guard simultaneously, even though there is a trade-off between these two activities. Within this framework, we show that male care is favored by short female processing times and high population densities, which minimize the mating cost of care. Relatively low mortality while guarding is also important for the stability of male care. Female care, on the other hand, is favored by long female processing times and low populations densities, which lead to longer intermating intervals. Biparental care is stable only when the cost to benefit ratio of care was not biased toward either sex. We derive quantitative estimates of fitness for different strategies for two species of assassin bugs with male and female uniparental care and show that the model predicts the correct form of care for both species. We believe our model might help explain the prevalence of male uniparental care in certain taxa, such as fish.

Animals↗

PubMed2006

Dependence among sites in RNA evolution.

Although probabilistic models of genotype (e.g., DNA sequence) evolution have been greatly elaborated, less attention has been paid to the effect of phenotype on the evolution of the genotype. Here we propose an evolutionary model and a Bayesian inference procedure that are aimed at filling this gap. In the model, RNA secondary structure links genotype and phenotype by treating the approximate free energy of a sequence folded into a secondary structure as a surrogate for fitness. The underlying idea is that a nucleotide substitution resulting in a more stable secondary structure should have a higher rate than a substitution that yields a less stable secondary structure. This free energy approach incorporates evolutionary dependencies among sequence positions beyond those that are reflected simply by jointly modeling change at paired positions in an RNA helix. Although there is not a formal requirement with this approach that secondary structure be known and nearly invariant over evolutionary time, computational considerations make these assumptions attractive and they have been adopted in a software program that permits statistical analysis of multiple homologous sequences that are related via a known phylogenetic tree topology. Analyses of 5S ribosomal RNA sequences are presented to illustrate and quantify the strong impact that RNA secondary structure has on substitution rates. Analyses on simulated sequences show that the new inference procedure has reasonable statistical properties. Potential applications of this procedure, including improved ancestral sequence inference and location of functionally interesting sites, are discussed.

Animals↗

PubMed2003

Partition functions and metropolis-type evolution rules for surface growth models with constraints.

We study dynamical scaling properties of the surface growth model with the Metropolis-type evolution rule from a partition function Z= sum ([h(r)])II (h(max))(h=h(min))1/2(1+z(n(h))), where z is a fugacity-like quantity and n(h) is the number of sites with height h in a surface configuration [h(r)]. The partition function describes a 2-particle correlated growth model when z=-1 and a self-flattening growth model when z=0. For one-dimensional equilibrium surfaces, the scaling properties for z>or=-1 except z=1 are all one phase with roughness exponent alpha=1/3 and growth exponent beta approximately equal 0.22. For the growing (eroding) surfaces, there exists a phase transition at z=0 from the grooved phase (alpha=1) for -1 0.

Journal Article↗

PubMed1994

Models of driving behavior: a review of their evolution.

This paper reviews models that emphasize the cognitive components of driving behavior. Studies of individual differences have sought predictors of accident histories. Typically low correlations and reliance on post hoc explanations reflect theoretical deficiencies and problems with the use of accident measures. Motivational models emphasize transient, situation-specific factors rather than stable, individual predictors. However, neither testable hypotheses nor suitable methods have been developed to study situational factors and motives that influence driving. More recent models have incorporated a hierarchical control structure, which assumes concurrent activity at strategic, maneuvering, and operational levels of control. At the same time, automaticity has emerged as a central construct in cognitive psychology. All activities are assumed to combine fast, automatic components with slower, more deliberate, controlled processing. It is argued that identifying the situational factors that increase drivers' uncertainty and thus trigger a shift in attention from automatic to controlled processing will help integrate concepts of automaticity and motivational models. Finally, recent theorizing has suggested that errors associated with the inherent variability of human behavior may be more important to roadway crash causation than systematic errors, which are attributable to the known limits of the human information-processing system. Drivers' abilities to recover from errors may also be important to crash causation. It is concluded that the hierarchical control structure and theories of automaticity and errors provide the potential tools for defining alternative criterion measures, such as safety margins, and developing testable theories of driving behavior and crash causation. Two examples of models that integrate information-processing mechanisms within a motivational framework are described.

Attention↗

PubMed1997

The evolution of genomic imprinting: two modifier-locus models.

We present two autosomal two-locus models in which the primary locus, A, may be imprinted according to the alleles present at the second, modifier locus, M. In the first model, the modifier is cis-acting, which assumes that imprinting occurs late in gametogenesis: whether or not A is imprinted depends only on the M allele in the (unfertilized) egg. We examine three cases in which polymorphism at A is maintained by a mutation-selection balance or heterozygote advantage. We show that a newly arising modifier allele without direct fitness effects can increase at a rate only of the order of the mutation rate at the A locus. This result mirrors that found in two-locus models of the evolution of dominance modifiers. Modifiers that also alter fitnesses, however, may spread quickly. In the second model, a monomorphic primary locus, A, is imprinted according to the mother's genotype at the second, diallelic modifier locus, M. The model is therefore trans-acting, which assumes imprinting occurs early in gametogenesis: whether or not A is imprinted depends on both of the mother's M genes. We show that a newly arising modifier will increase in frequency via selection if either imprinting is advantageous and the modifier increases the proportion of imprinted gametes or imprinting is disadvantageous and the proportion is decreased. Both of these factors-the selective effect of imprinting and the proportion of gametes imprinted-affect the rate of modifier evolution. Selectively maintained polymorphism at the modifier locus is unlikely unless the alleles interact in a nonadditive fashion.

Biological Evolution↗