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PubMed1986

A model for DNA sequence evolution within transposable element families.

A quantitative model is proposed for the expected degree of relationship between copies of a family of transposable elements in a finite population of hosts. Special cases of the model (in which the process of homogenization of element copies either is or is not limited by transposition rate) are presented and illustrated, using data on mobile sequences from different species. It is shown that transposition will be expected, in large populations, to result in only a rather distant relationship between transposable elements at different genomic sites. Possible inadequacies of the model are suggested and quantified.

Animals↗
PubMed2000

Molecular markers predictive of response and prognosis in the patient with advanced squamous cell carcinoma of the head and neck: evolution of a model beyond TNM staging.

Advanced head and neck cancer is a disease with poor prognosis. TNM staging is an inadequate prognostic indicator of individual response to evolving multimodal therapies. New markers have been studied in progressively more refined analyses. Even though their role in predicting response and prognosis of head and neck cancer is still under evolution, it is becoming clear that individual markers are inadequate in constructing a prognostically meaningful tumor profile for each patient. Rather the combined study of a number of well-characterized markers acting in unrelated cellular pathways may be much more successful in defining prognostic patient categories of greater utility than traditional TNM staging. Special attention should also be paid to the expression pattern and location of tumor markers within the biopsy specimen as these parameters also appear to influence prognostic significance.

Biomarkers, Tumor↗
PubMed2006

Using hidden Markov models and observed evolution to annotate viral genomes.

MOTIVATION: ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. RESULTS: The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.

Algorithms↗
PubMed1994

Mutational bias provides a model for the evolution of Huntington's disease and predicts a general increase in disease prevalence.

Huntington's disease (HD) correlates with abnormal expansion in a block of CAG repeats in the Huntington's disease gene. We have investigated HD evolution by typing CAG alleles in several human populations and in a variety of primates. We find that human alleles have expanded from a shorter ancestral state and exhibit unusual asymmetric length distributions. Computer simulations are used to show that the human state can be derived readily from a primate ancestor, without the need to invoke natural selection. The key element is a simple length-dependent mutational bias towards longer alleles. Our model can explain a number of empirical observations, and predicts an ever-increasing incidence of HD.

Alleles↗
PubMed2000

Dosage, deletions and dominance: simple models of the evolution of gene expression.

Dominance of the wild-type allele over spontaneous null mutations, such as deletions, can be explained in terms of the effects of changes in enzyme dose on the flux of metabolic pathways. If ever increasing levels of enzyme activity have ever decreasing effects on the flux of the biochemical pathway, then halving of dosage will always have a lesser effect on flux than half the effect of complete removal of gene activity. Furthermore, if gene expression rates are high, then halving of dose can have a negligible effect on flux and dominance will be strong. Given that strong dominance appears to be common, this leaves open the issue of why enzyme activity levels are so high that a halving of expression rates is of minimal effect. Why produce so much surplus enzyme? One explanation, suggested by Haldane, is that selection favoured high expression levels as a defence against mutation. We model this scenario formally and show that protection from mutation is an extremely weak force determining expression levels. The selective coefficients are only of the order of the mutation rate. However, if we suppose a linear mapping of flux with fitness and a monotonic cost to increased gene expression, it follows simply that here exists an optimal level of gene expression. By contrast to the mutational model, doubling of gene expression rates when the system is distant from the optimum is associated with extremely high selective coefficients (orders of magnitude higher than the mutation rate). When the cost of gene expression is slight the optimal rate of expression is such that strong dominance will follow.

Animals↗
PubMed1996

A model of complete random molecular evolution by recurrent mutation.

A model for random molecular evolution based on recurrent mutation is proposed. Recurrent mutation replaces completely any original base in a nucleotidic site. This occurs if more than four times the number of reproductive cycles equal to the reciprocal of the mutation rate happen; no matter the population size, the number of nucleotides a genome has, or the taxa at which it belongs. The main results are: i) the expected distribution of DNA bases in a site is an isotetranomial distribution, where Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) occur with probability equal to 0.25; ii) the distribution of bases in a site is independent from the distribution of bases in other sites. Several expected consequences that can be contrasted with actual data are generated. Species or operational taxonomic units (OTUs) that evolved in big populations should present distances equal to zero and similarities equal to one. OTUs evolving in small populations should present distances equal to 3/4 and similarities equal to 1/4. Thus, random molecular evolution by recurrent mutation cannot yield a tree at all. The only possible tree is that produced by random fluctuations of distances according to their variances (stochastic tree). Some consequences of the model on the expected primary structure of proteins are also analyzed. There are sufficient generations for any DNA segment evolving apart during the last four hundred million years, to reach those expected base distributions.

Chymotrypsinogen↗
PubMed1998

Model scenarios for evolution of the eukaryotic cell cycle.

Progress through the division cycle of present day eukaryotic cells is controlled by a complex network consisting of (i) cyclin-dependent kinases (CDKs) and their associated cyclins, (ii) kinases and phosphatases that regulate CDK activity, and (iii) stoichiometric inhibitors that sequester cyclin-CDK dimers. Presumably regulation of cell division in the earliest ancestors of eukaryotes was a considerably simpler affair. Nasmyth (1995) recently proposed a mechanism for control of a putative, primordial, eukaryotic cell cycle, based on antagonistic interactions between a cyclin-CDK and the anaphase promoting complex (APC) that labels the cyclin subunit for proteolysis. We recast this idea in mathematical form and show that the model exhibits hysteretic behaviour between alternative steady states: a Gl-like state (APC on, CDK activity low, DNA unreplicated and replication complexes assembled) and an S/M-like state (APC off, CDK activity high, DNA replicated and replication complexes disassembled). In our model, the transition from G1 to S/M ('Start') is driven by cell growth, and the reverse transition ('Finish') is driven by completion of DNA synthesis and proper alignment of chromosomes on the metaphase plate. This simple and effective mechanism for coupling growth and division and for accurately copying and partitioning a genome consisting of numerous chromosomes, each with multiple origins of replication, could represent the core of the eukaryotic cell cycle. Furthermore, we show how other controls could be added to this core and speculate on the reasons why stoichiometric inhibitors and CDK inhibitory phosphorylation might have been appended to the primitive alternation between cyclin accumulation and degradation.

Animals↗
PubMed2004

Relations between cuticular hydrocarbon (HC) polymorphism, resistance against desiccation and breeding temperature; a model for HC evolution in D. melanogaster and D. simulans.

D. simulans and D. melanogaster present two types of polymorphism in their cuticular hydrocarbon (HC) composition. Especially both sexes of D. simulans, and D. melanogaster males display 7-tricosene (7T) as the major compound type [7T]s and [7T]m, or 7-pentacosene (7P) [7P]s and [7P]m. D. melanogaster females display 7,11-heptacosadiene (7,11HD) as the major compound: [7,11HD]m, or 5,9-heptacosadiene (5,9HD): [5,9HD]m. The [7P]s, [7P]m and [5,9HD]m are mainly present in central Africa. A significant correlation was found between latitude and the proportion of compounds with 23 and 25 carbon atoms, especially 7T and 7P in both sexes of D. melanogaster. [7P]m type of D. melanogaster, characterized with an excess of C25 compounds, presents a higher resistance against desiccation than [7T]m type, where C23 compounds are more abundant. These differences can be correlated with calculated HC fusion temperatures. Moreover, increasing the breeding temperature from 18 to 29 degrees C induces in D. melanogaster males an increase in 25C compounds and a decrease in 23C compounds, but the opposite effect in D. simulans. A mathematical model of biosynthesis, based on kinetics of elongation and decarboxylation enzymes, suggests that a simple variation of the efficiency of an elongation enzyme may account for the differences observed between the [7T]m and [7P]m types of D. melanogaster and [7T]s and [7P]s types D. simulans. Finally on the basis of the geographical distribution of the HC types of both Drosophila species, an evolutionary dispersal pathway is proposed and discussed in relation to the environment and reproductive behavior.

Africa↗
PubMed1996

Natural repressors of P-induced hybrid dysgenesis in Drosophila melanogaster: a model for repressor evolution.

Type I repressors control P element transposition and comprise full length elements and elements with small 3' deletions in the final exon. Using a sensitive assay for measuring the strength of repression of P element transposition in somatic and germline tissues, we have isolated and characterized a naturally occurring type I repressor element from a Q population of Drosophila melanogaster. We demonstrate that the almost complete repression of transposition in this population is a mixture of KP elements with intermediate levels of repression, and the strong contribution of a single 2.6 kb P element deletion derivative, which we call SR (Strong Repressor). A deletion in the final intron of SR allows for the constitutive production of a putative 75 kDa repressor protein in germline tissues in addition to the production of the 66 kDa repressor in the soma, which would result in a biparental mode of inheritance of repression. Based on the four observed classes of natural Q populations, we propose a model in which populations containing SR-like elements, capable of producing strong type I repressor constitutively, have a selective advantage over populations which rely either on maternally transmitted P cytotype or on KP-induced weak levels of repression. Such populations may subsequently spread and constitute an evolutionary stable strategy for the repression of hybrid dysgenesis in Drosophila melanogaster.

Amino Acid Sequence↗
PubMed2005

Modelling the thermal evolution of enzyme-created bubbles in DNA.

The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach, we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that, in fact, from certain local structural distortions, there originate oscillating localized patterns, that is, radial and torsional breathers, which are associated with localized H-bond deformations, reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim, the underlying nonlinear oscillator network of the DNA duplex is brought into contact with a heat bath using the Nosé-Hoover method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for non-zero temperature, the H-bond breathers move coherently along the double chain, whereas at T=0 standing radial and torsional breathers result.

DNA↗
PubMed1987

Selection by differential molecular survival: a possible mechanism of early chemical evolution.

A model is proposed to account for selective chemical evolution, progressing from a relatively simple initial set of abiotic synthetic phenomena up to the elaborately sophisticated processes that are almost certainly required to produce the complex molecules, such as replicatable RNA-like oligonucleotides, needed for a Darwinian form of selection to start operating. The model makes the following assumptions: (i) that a small number of micromolecular substances were present at high concentration; (ii) that a random assembly mechanism combined these molecules into a variety of multimeric compounds comprising a wide repertoire of rudimentary catalytic activities; and (iii) that a lytic system capable of breaking down the assembled products existed. The model assumes further that catalysts supplied with substrates were significantly protected against breakdown. It is shown that, by granting these assumptions, an increasingly complex network of metabolic pathways would progressively be established. At the same time, the catalysts concerned would accumulate selectively to become choice substrates for elongation and other modifications that could enhance their efficiency, as well as their survival. Chemical evolution would thus proceed by a dual process of metabolic extension and catalytic innovation. Such a process should be largely deterministic and predictable from initial conditions.

Biochemical Phenomena↗
PubMed1984

Composite human VK genes and a model of their evolution.

A phage library and two cosmid libraries were screened for human VK genes. Two recombinant phage and four cosmid clones were analysed in detail by restriction mapping and sequencing. Each one contained a single VKI sequence. Two of these six sequences are potentially functional VK genes and four are pseudogenes. Two pseudogenes derived from different genomic DNAs are highly homologous and are therefore either allelic variants or the products of a recent duplication event. Comparisons of our sequences with all fully determined human VKI amino acid and DNA sequences reveal identical segments which at first sight appear like minigenes. But these segments do not coincide with the subregions and some of the segments include both, framework and complementarity determining regions (FR, CDR, ref. 2). The findings may be explained by an evolutionary model generating composite genes by gene conversion and selection.

Alleles↗
PubMed2006

The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution.

Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral L-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a D-enantiomeric excess of >80% with L-Val-L-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life.

Catalysis↗
PubMed1994

The evolution of a rat model of chronic spontaneous limbic seizures.

The evolution of untreated partial epilepsy is unknown. This study uses a newly developed model of chronic limbic epilepsy to determine whether seizures inexorably worsen in duration, frequency and behavioral accompaniment. The seizures begin following an episode of limbic status epilepticus induced by continuous electrical stimulation of the hippocampus, and they persist for more than a year (longest duration followed). We monitored 10 rats continuously with combined EEG and closed circuit television for 24 weeks following the first recorded spontaneous seizure. Seizure duration, behavioral accompaniment and frequency all intensified during the early stages, but the last 12-16 weeks of the study were characterized by a plateau for all measures. The results showed significant increases that occurred over the first 12 weeks only (P < 0.01 for duration and behavioral accompaniment, P < 0.05 for seizure frequency). These findings suggest that untreated epilepsy will undergo an early maturation process, but that once the seizures mature they remain stable over a prolonged period. It was also noted that 67% (P < 0.00001) of the seizures occurred during the day, suggesting that the sleep-wake cycle has a strong influence on the occurrence of seizures in this model of limbic epilepsy.

Analysis of Variance↗
PubMed2002

Modeling of a possible evolutional process from a ribozyme to a catalytic RNP.

A model process for molecular evolution from an RNA enzyme to a catalytic RNA-protein complex (RNP) is proposed. In the model, one RNA-RNA interaction in the enzyme is replaced by an RNA-protein interaction via an intermediary state where the original RNA-RNA and newly introduced RNA-protein interaction co-exist. To test the model, a catalytic RNP was designed and examined by employing the Tetrahymena ribozyme.

Animals↗
PubMedDate not supplied

Stochastic model of the evolution of viral hepatitis morbidity.

Starting from the elementary epidemiological processes, the authors develop an evolution equation of the function generating the probability distribution of the number of viral hepatitis (VH) patients and susceptible subjects. Evolution equations for moments of order 1 and 2 - resulting from the equation of the generating function-are also discussed on the ground of certain simplifying hypotheses. The formulae are applied to the analysis of VH morbidity evolution in several children communities. The data on the evolution of the different moments and of the probability distributions are used from the specification of epidemiological transmissibility and susceptibility parameters.

Epidemiologic Methods↗