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PubMed2004

Predictive modelling of the microbial lag phase: a review.

This paper summarises recent trends in predictive modelling of microbial lag phenomena. The lag phase is approached from both a qualitative and a quantitative point of view. First, a definition of lag and an analysis of the prevailing measuring techniques for the determination of lag time is presented. Furthermore, based on experimental results presented in literature, factors influencing the lag phase are discussed. Major modelling approaches concerning lag phase estimation are critically assessed. In predictive microbiology, a two-step modelling approach is used. Primary models describe the evolution of microbial numbers with time and can be subdivided into deterministic and stochastic models. Primary deterministic models, e.g., Baranyi and Roberts [Int. J. Food Microbiol. 23 (1994) 277], Hills and Wright [J. Theor. Biol. 168 (1994) 31] and McKellar [Int. J. Food Microbiol. 36 (1997) 179], describe the evolution of microorganisms, using one single (deterministic) set of model parameters. In stochastic models, e.g., Buchanan et al. [Food Microbiol. 14 (1997) 313], Baranyi [J. Theor. Biol. 192 (1998) 403] and McKellar [J. Appl. Microbiol. 90 (2001) 407], the model parameters are distributed or random variables. Secondary models describe the relation between primary model parameters and influencing factors (e.g., environmental conditions). This survey mainly focuses on the influence of temperature and culture history on the lag phase during growth of bacteria.

Bacteria↗

PubMed2006

An evolutionary analysis of the relationship between spite and altruism.

We investigate the selective pressures on a social trait when evolution occurs in a population of constant size. We show that any social trait that is spiteful simultaneously qualifies as altruistic. In other words, any trait that reduces the fitness of less related individuals necessarily increases that of related ones. Our analysis demonstrates that the distinction between "Hamiltonian spite" and "Wilsonian spite" is not justified on the basis of fitness effects. We illustrate this general result with an explicit model for the evolution of a social act that reduces the recipient's survival ("harming trait"). This model shows that the evolution of harming is favoured if local demes are of small size and migration is low (philopatry). Further, deme size and migration rate determine whether harming evolves as a selfish strategy by increasing the fitness of the actor, or as a spiteful/altruistic strategy through its positive effect on the fitness of close kin.

Altruism↗

PubMedDate not supplied

[The dynamic trends of biological evolution].

The available data on the thermodynamic stability of supramolecular biological structures and variations in the chemical composition of living organisms have allowed a macrothermodynamic model of biological evolution to be developed experimentally. In this model, the tendency toward a minimum of the specific Gibbs function of the formation of supramolecular structures of living organisms causes variations in the chemical composition and structure of living systems. It is shown that in the course of ontogenesis and phylogenesis, as well as long-lasting stages in the evolution of the organic world, the biosystems (as a result of the thermodynamic direction of evolutionary processes of the formation of supramolecular structures) are enriched with energy-intensive chemical substances, which displace water from these biosystems. The change in the composition and structure of biostructures of an adaptive character is also explained from the angle of macrothermodynamics.

Animals↗

PubMed2003

Evolving protein interaction networks through gene duplication.

The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few edges while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus re-wiring of the newly created genes. The statistical features displayed by the proteome of well-known organisms are reproduced and suggest that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model.

Animals↗

PubMed2000

The Evolution of Plasticity and Nonplastic Spatial and Temporal Adaptations in the Presence of Imperfect Environmental Cues.

A model for the evolution of plasticity is considered in which the phenotype, undergoing stabilizing selection, is modeled as a linear function of an environmental cue correlated with the phenotypic optimum, with the coefficients z0 and z1 evolving according to standard quantitative genetic theory. In contrast to previous theoretical models, as the rate of migration between demes or the rate of cyclic fluctuations in the optimum increases, the amount of plasticity [Formula: see text] at equilibrium is shown to increase gradually, in part accounting for the effect of reduced nonplastic adaptation and reaching a maximum equal to the squared correlation between the environmental cue and the phenotypic optimum. Given that information available to the organism is limited, this bias of the expressed phenotype toward the global optimum is still optimal, however, in a certain decision-theoretic sense. When genetic variation in the plastic component of the trait is small so that spatial or temporal differentiation in plasticity is small, the effect of plasticity on nonplastic adaptation is to reduce the effects of variation in the phenotypic optimum by a factor [Formula: see text] only. Information acquisition costs and joint evolution of sensory systems are discussed.

environmental cues↗

PubMed1994

Analytical expression of the purine/pyrimidine autocorrelation function after and before random mutations.

The mutation process is a classical evolutionary genetic process. The type of mutations studied here is the random substitutions of a purine base R (adenine or guanine) by a pyrimidine base Y (cytosine or thymine) and reciprocally (transversions). The analytical expressions derived allow us to analyze in genes the occurrence probabilities of motifs and d-motifs (two motifs separated by any d bases) on the R/Y alphabet under transversions. These motif probabilities can be obtained after transversions (in the evolutionary sense; from the past to the present) and, unexpectedly, also before transversions (after back transversions, in the inverse evolutionary sense, from the present to the past). This theoretical part in Section 2 is a first generalization of a particular formula recently derived. The application in Section 3 is based on the analytical expression giving the autocorrelation function (the d-motif probabilities) before transversions. It allows us to study primitive genes from actual genes. This approach solves a biological problem. The protein coding genes of chloroplasts and mitochondria have a preferential occurrence of the 6-motif YRY(N)6YRY (maximum of the autocorrelation function for d = 6, N = R or Y) with a periodicity modulo 3. The YRY(N)6YRY preferential occurrence without the periodicity modulo 3 is also observed in the RNA coding genes (ribosomal, transfer, and small nuclear RNA genes) and in the noncoding genes (introns and 5' regions of eukaryotic nuclei). However, there are two exceptions to this YRY(N)6YRY rule: the protein coding genes of eukaryotic nuclei, and prokaryotes, where YRY(N)6YRY has the second highest value after YRY(N)0YRY (YRYYRY) with a periodicity modulo 3. When we go backward in time with the analytical expression, the protein coding genes of both eukaryotic nuclei and prokaryotes retrieve the YRY(N)6YRY preferential occurrence with a periodicity modulo 3 after 0.2 back transversions per base. In other words, the actual protein coding genes of chloroplasts and mitochondria are similar to the primitive protein coding genes of eukaryotic nuclei and prokaryotes. On the other hand, this application represents the first result concerning the mutation process in the model of DNA sequence evolution we recently proposed. According to this model, the actual genes on the R/Y alphabet derive from two successive evolutionary genetic processes: an independent mixing of a few nonrandom types of oligonucleotides leading to genes called primitive followed by a mutation process in these primitive genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗

PubMed1997

Spatially resolved in vitro molecular ecology.

Sensitive CCD-based fluorescence detection has made spatially resolved studies of evolving cell-free molecular systems possible. In recent years our attention has focussed on making the transition to open and interacting spatially-resolved amplification systems using silicon microreactor technology and on providing a hardware platform for individual based simulation of such systems. Significant progress has been achieved in this direction. Open microflow reactors have been realized in zero (well-mixed), one and two dimensions with volumes small enough to allow long-time studies with limited biochemical materials. The primer directed 3SR reaction (amplifying DNA and RNA) has been used as a basis for constructing interacting model systems with both predator-prey and cooperative amplification character. Theoretical work has demonstrated the need for individual based modeling of such systems: a significant fraction of the population consists of distinct sequence polymers in any case. A massively parallel processor-configurable computer NGEN has been designed and constructed which allows the high speed simulation in hardware of relatively large populations of locally interacting individual strings of chosen length (e.g. up to 2000*2000 for 64 bases), in addition to its application as an evolvable hardware machine. Simulations show self-replicating spots to stabilize the cooperative amplification in evolving systems (a mechanism proposed by the author in 1994). Both oscillatory kinetics and pattern formation are expected in the experimental model systems under investigation which profoundly affect the course of evolution. Such in vitro model systems serve both to test current theories of cooperative evolution and provide clues for optimisation strategies in molecular biotechnology.

Biotechnology↗

PubMed2004

A receiver bias in the origin of three-spined stickleback mate choice.

Receiver-bias models of signal evolution predict that male sexually selected traits evolve through prior selection for other functions. Female three-spined sticklebacks (Gasterosteus aculeatus) in many populations show a mating preference for males with a red throat and jaw. It has been proposed that this preference evolved because the choice of males with red coloration confers direct and indirect benefits to females in accordance with the Fisher-Zahavi model of sexual selection. We present indirect evidence that the preference is an effect of a receiver bias in the perceptual or cognitive system of G. aculeatus for the colour red, which may have arisen in the context of foraging. In laboratory trials, male and female three-spined and nine-spined sticklebacks (Pungitius pungitius) responded most strongly to red objects outside a mating context. This result demonstrates a correlation between a sexually selected trait and an intrinsic attraction to red objects, and supports the sensory-exploitation model for the evolution of red nuptial coloration in three-spined sticklebacks.

Analysis of Variance↗

PubMed2002

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes.

Basidiomycota↗

PubMed1989

DNA microenvironments and the molecular clock.

A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compartments, the isochores, defined by their G + C content has been proposed recently. We have found that only homologous gene pairs that are stationary, and belong to the same isochore, can be used consistently for the determination of phylogeny and base substitution rate. In particular, for the rodent-human couple, only about half of the homologous gene pairs are stationary. Stationary genes evolve at the third silent codon position with the same velocity independent of the genes and base composition. By contrast, nonstationary genes display apparent rate values (pseudovelocities) that are significantly higher. Our results cast doubt upon recent claims of a large acceleration in the rate of molecular evolution in rodents.

Biological Evolution↗

PubMed1994

Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.

The neutral theory of molecular evolution asserts that while many mutations are deleterious and rapidly eliminated from populations, those that we observe as polymorphisms within populations are functionally equivalent to each other and thus neutral with respect to fitness. Mitochondrial DNA (mtDNA) is widely used as a genetic marker in evolutionary studies and is generally assumed to evolve according to a strictly neutral model of molecular evolution. One prediction of the neutral theory is that the ratio of replacement (nonsynonymous) to silent (synonymous) nucleotide substitutions will be the same within and between species. We tested this prediction by measuring DNA sequence variation at the mitochondrially encoded NADH dehydrogenase subunit 3 (ND3) gene among 56 individual house mice, Mus domesticus. We also compared ND3 sequence from M. domesticus to ND3 sequence from Mus musculus and Mus spretus. A significantly greater number of replacement polymorphisms were observed within M. domesticus than expected based on comparisons to either M. musculus or M. spretus. This result challenges the conventional view that mtDNA evolves according to a strictly neutral model. However, this result is consistent with a nearly neutral model of molecular evolution and suggests that most amino acid polymorphisms at this gene may be slightly deleterious.

Amino Acid Sequence↗

PubMed1998

Modeling INR data to predict maintenance fluindione dosage.

This study was designed to construct a pharmacokinetic/pharmacodynamic model describing the evolution of International Normalized Ratio (INR) under oral anticoagulation treatment by fluindione in patients and to develop a method for individualization of fluindione dosage. Three indirect response models describing the concentration-INR relationship were tested using a nonparametric estimation method. INR was modelled as a quantity being produced and eliminated. According to a log-likelihood ratio test, the evolution of INR was best modelled as an inhibition of its elimination by fluindione. The selected model was evaluated in 24 additional patients with INR measurements (after 2, 3, 4, 6, and 10 doses). Using a Bayesian method with data until day 4, INR was correctly predicted for days 6 and 10. The population characteristics of fluindione were estimated, pooling the two groups of patients. A Bayesian method for individualization of dosage regimen was developed, based on a risk function for INR at steady state. Prescription rules for fluindione were derived using this method retrospectively on the 73 patients in this study.

Anticoagulants↗

PubMed1985

Evolution of mating preference and sexual dimorphism.

A quantitative genetic model of the joint evolution of female mating preferences and sexual dimorphism in homologous characters of the sexes is described for polygamous species with no male parental effort, such that mating preferences are selectively neutral and evolve only by indirect selection on genetically correlated characters. The male character and the homologous female character are each under stabilizing natural selection toward an optimum phenotype. At an evolutionary equilibrium the female character under natural selection is at its optimum, whereas there is a line of possible equilibria between female mating preferences and the male character. The line of equilibria may be stable or unstable, depending on the intensity of natural selection, the type of mating preferences, and the inheritance of the characters. Various mechanisms for maladaptive evolution of mating preferences and sexual dimorphism are discussed.

Animals↗

PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗

PubMed2004

A general mathematical framework to model generation structure in a population of asynchronously dividing cells.

In otherwise homogeneous cell populations, individual cells undergo asynchronous cell cycles. In recent years, interest in this fundamental observation has been boosted by the wide usage of CFSE, a fluorescent dye that allows the precise estimation by flow cytometry of the number of divisions performed by different cells in a population, and thus the generation structure. In this work, we propose two general mathematical frameworks to model the time evolution of generation structure in a cell population. The first modeling framework is more descriptive and assumes that cell division time is distributed in the cell population, due to intrinsic noise in the molecular machinery in individual cells; while the second framework assumes that asynchrony in cell division stems from randomness in the interactions individual cells make with environmental agents. We reduce these formalisms to recover two preexistent models, which build on each of the hypotheses. When confronted to kinetics data on CFSE labeled cells taken from literature, these models can fit precursor frequency distributions at each measured time point. However, they fail to fit the whole kinetics of precursor frequency distributions. In contrast, two extensions of those models, derived also from our general formalisms, fit equally well both the whole kinetics and individual profiles at each time point, providing a biologically reasonable estimation of parameters. We prove that the distribution of cell division times is not Gaussian, as previously proposed, but is better described by an asymmetric distribution such as the Gamma distribution. We show also that the observed cell asynchrony could be explained by the existence of a single transitional event during cell division. Based on these results, we suggest new ways of combining theoretical and experimental work to assess how much of noise in internal machinery of the cell and interactions with the environmental agents contribute to the asynchrony in cell division.

CD4-Positive T-Lymphocytes↗

PubMed2002

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition. Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design. Assuming conservation of specificity among orthologs and different specificity of paralogs, we identify residues that correlate with this grouping by specificity. The method is taking advantage of complete genomes to find multiple orthologs and paralogs. The central part of this method is a procedure to compute statistical significance of the predictions. The procedure is based on a simple statistical model of protein evolution. When applied to a large family of bacterial transcription factors, our method identified 12 residues that are presumed to determine the protein-DNA and protein-ligand recognition specificity. Structural analysis of the proteins and available experimental results strongly support our predictions. Our results suggest new experiments aimed at rational re-design of specificity in bacterial transcription factors by a minimal number of mutations.

Bacteria↗

PubMed2001

Mitochondrial genomics flies high.

A new pair of papers reports the complete coding sequences for 28 mitochondrial DNAs in Drosophila. By examining the patterns of polymorphism and divergence among functionally distinct classes of synonymous and nonsynonymous nucleotide sites, Bill Ballard provides a comprehensive whole-genome picture of how mtDNA sequence evolution can depart from the strictly neutral and nearly neutral models of molecular evolution.

Journal Article↗

PubMed2000

Redundant and non-functional guide RNA genes in Trypanosoma brucei are a consequence of multiple genes per minicircle.

The mitochondrial mRNA of the parasitic protozoa Trypanosoma brucei is extensively edited by the insertion, and occasional deletion, of uridine residues. The editing is mediated by over 200 guide RNAs (gRNAs) that are encoded in circular DNA molecules called minicircles. There are some 250 different types of minicircle, called classes, with each encoding several gRNAs. Sequencing of gRNAs and minicircles has revealed a surprising amount of both redundancy, where gRNAs from different minicircle classes edit exactly the same part of an mRNA, and non-functionality, where partial or no complementarity is found between gRNA and mRNA. How does this redundancy and non-functionality arise and persist? We propose the following. Minicircle classes that contain several functional gRNA genes can be lost from the population via drift and replaced by more minicircle classes that contain fewer functional gRNA genes, on the condition that the cells keep a full complement of functional gRNAs. We demonstrate this hypothesis in a computer simulation of a model of minicircle evolution. We show that this process leads to an increasing number of minicircle classes and inevitably to only one functional gRNA per minicircle. Moreover, we show that the genome contains more minicircle classes than is actually necessary for cell survival. We also analyse the available minicircle sequence data and conclude that T. brucei is at a transient stage in this process. In addition, ten new putative gRNAs have been discovered.

Animals↗