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At least 775 records · Page 43Linked to original sources
PubMed2003

Conformation-dependent evolution of copolymer sequences.

A "toy model" of molecular evolution of sequences in copolymers is proposed and implemented using a molecular-dynamics-based algorithm. The model involves coupling of conformation-dependent and sequence-dependent properties. It is shown that this model allows the realization of two main possibilities: ascending and descending branches of evolution (in terms of information content of a sequence), depending on the interaction parameters shaping the conformation of a polymer globule. The problem of adequate description of information complexity of copolymer sequences is studied. It is shown that Shannon's entropy or compressibility of a sequence gives preference to random sequences and therefore cannot be applied for this purpose. On the other hand, the Jensen-Shannon divergence measure turns out to give the description of information complexity which corresponds to our intuitive expectations. In particular, this characteristic can adequately describe two branches of evolution mentioned above, exhibiting a singularity on the boundary of these regimes.

Algorithms↗
PubMed2002

The concerted mechanism of photo-induced biprotonic transfer in 7-azaindole dimers: a model for the secondary evolution of the classic C2h dimer and comparison of four mechanisms.

A mechanism is proposed for the formation in gas phase, during a short time, of the delicately symmetrical coplanar C(2h) classic 7-azaindole (7AI) doubly hydrogen-bonded dimer. Of the five card-pack or otherwise random geometry structures most likely to be formed in the supersonic jet expansion molecular beam, none would be an obvious precursor to the C(2h) dimer. One unstable dimer with dipole-dipole, van der Waals, and plane-to-plane hydrogen bonding is shown to be capable of unhinging about the hydrogen-bond pair as an axis, from 0 degrees to 90 degrees to 180 degrees, yielding a deep minimum for the C(2h) structure with its delicate geometry and symmetry. This relaxation mechanism is feasible in the 3-micros interval between the nozzle escape and the first laser pulse interception of the molecular beam. In the second part of the paper four published mechanisms are compared for concerted vs. two-step biprotonic phototransfer for the 7AI dimers. The dependence of the latter two models on H-atom instead of proton-transfer as an intermediate step negates the mechanism in a singlet (pi,pi*) electronic state by the valency repulsion, in the 3-electron orbital that would be generated. The concerted mechanism for biprotonic phototransfer is reaffirmed by the analysis of the quantum mechanical conditions set on the biprotonic transfer in the photo-excited molecular 7AI pair.

Dimerization↗
PubMed2005

Using the quantitative genetic threshold model for inferences between and within species.

Sewall Wright's threshold model has been used in modelling discrete traits that may have a continuous trait underlying them, but it has proven difficult to make efficient statistical inferences with it. The availability of Markov chain Monte Carlo (MCMC) methods makes possible likelihood and Bayesian inference using this model. This paper discusses prospects for the use of the threshold model in morphological systematics to model the evolution of discrete all-or-none traits. There the threshold model has the advantage over 0/1 Markov process models in that it not only accommodates polymorphism within species, but can also allow for correlated evolution of traits with far fewer parameters that need to be inferred. The MCMC importance sampling methods needed to evaluate likelihood ratios for the threshold model are introduced and described in some detail.

Bayes Theorem↗
PubMed2006

A simple model of linkage disequilibrium and genetic drift in human genomic SNPs: importance of demography and SNP age.

We propose a simple model of evolution at a pair of SNP loci, under mutation, genetic drift and recombination. The developed model allows to consider evolution of SNPs under different demographic scenarios. We applied it to SNP data containing polymorphisms spanning 19 gene regions. We initially matched the linkage disequilibrium (LD) data only, and then we reconciled both LD and heterozygosity data. The imbalance between LD and heterozygosity data, observed for some of the analyzed genomic regions, may be a signature of selection acting in these regions. However, assuming neutrality, we obtain estimates of the age of population expansion of modern humans, which are consistent with the consensus estimates. In addition, we are able to estimate the ages of the polymorphisms observed in different genomic regions and we find that they vary widely with respect to their age. Polymorphisms at loci implicated in human disease, seem to be younger than average. Our results supplement the conclusions originally obtained by Reich and co-workers for the same set of data.

Genetic Drift↗
PubMed2003

A finite element model for ice ball evolution in a multi-probe cryosurgery.

The ice formation in a water body is examined for the computation of temperature field, phase change and a moving ice-water interface whose location is not known á priori. This is classically referred to as the Stefan problem [Rubinstein, L.I. (1971) The Stefan Problem (American Mathematical Society, Providence, Rhode Island 02904]. Based on the Duvaut [Duvaut, G. (1973) "Résolution d'un probléme Stefan" C.R. Acad Sci. Paris 276, 1461-1463] transformation, the governing equations for heat conduction are formulated within a variational principle that is readily amenable to a standard finite element solution without remeshing. Numerical simulation results pertaining to the freezing of tumour tissue in a multi-cryoprobe cryosurgery are presented. These results lend both quantitative and graphical support to the current empirical standards of "effective therapy" in view of refining clinical applications.

Animals↗
PubMed2005

Protein structural influences in rhodopsin evolution.

Incorporating specific structural information can be important for developing a realistic model of evolution for phylogenetic reconstruction of protein-coding genes. We analyzed 62 sequences of vertebrate rhodopsin. The bovine rhodopsin structure was used to label residue sites by surface accessibility, secondary structure, and transmembrane (TM) location. Residue sites with amino acid differences were identified; using maximum parsimony (MP), homoplasious residues were identified. Residues were analyzed for patterns that would indicate correlation of rate with secondary structure, surface accessibility, or position relative to the lipid bilayer. Surface residues, especially those residing in one of the seven TM helices, were significantly correlated with high rates of amino acid substitution. This category of residues, defined solely by protein structural characteristics, potentially defined a class enriched in homoplasious residues. MP analysis using all sites led to a tree with anomalies in the relationships of amphibian, mammalian, bird, and alligator species. Analysis excluding the structurally defined residue class recovered a more accurate phylogeny. A model is presented for including structural influences on rate in phylogenetic inference.

Amino Acid Substitution↗
PubMed1997

Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.

We present a new probabilistic model of evolution of RNA-, DNA-, or protein-like sequences and a tool rose that implements this model. By insertion, deletion and substitution of characters, a family of sequences is created from a common ancestor. During this artificial evolutionary process, the "true" history is logged and the "correct" multiple sequence alignment is created simultaneously. We also allow for varying rates of mutation within the sequences making it possible to establish so-called sequence motifs. The results are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships.

Amino Acid Sequence↗
PubMed2003

Coinfection and superinfection in RNA virus populations: a selection-mutation model.

In this paper, we present a general selection-mutation model of evolution on a one-dimensional continuous fitness space. The formulation of our model includes both the classical diffusion approach to mutation process as well as an alternative approach based on an integral operator with a mutation kernel. We show that both approaches produce fundamentally equivalent results. To illustrate the suitability of our model, we focus its analytical study into its application to recent experimental studies of in vitro viral evolution. More specifically, these experiments were designed to test previous theoretical predictions regarding the effects of multiple infection dynamics (i.e., coinfection and superinfection) on the virulence of evolving viral populations. The results of these experiments, however, did not match with previous theory. By contrast, the model we present here helps to understand the underlying viral dynamics on these experiments and makes new testable predictions about the role of parameters such the time between successive infections and the growth rates of resident and invading populations.

Evolution, Molecular↗
PubMed1997

The foldability landscape of model proteins.

Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to "neutral networks," where the sequence and the interactions can be significantly changed while a constant structure is maintained.

Amino Acid Sequence↗
PubMed1993

How should physicians view heart failure? The philosophical and physiological evolution of three conceptual models of the disease.

During the last 50 years, physicians have developed three distinct conceptual models of heart failure that have provided a rational basis for the treatment of the disease. In the 1940s through the 1960s, physicians regarded heart failure principally as an edematous disorder and formulated a cardiorenal model of the disease in an attempt to explain the sodium retention of these patients. This model led to the widespread use of digitalis and diuretics. In the 1970s and 1980s, physicians viewed heart failure principally as a hemodynamic disorder and formulated a cardiocirculatory model of the disease in an attempt to explain patients' symptoms and disability. This model led to the widespread use of peripheral vasodilators and the development of novel positive inotropic agents. Now, in the 1990s, physicians are beginning to think about heart failure as a neurohormonal disorder in an attempt to explain the progression of the disease and its poor long-term survival. This new conceptual framework has led to the widespread use of converting-enzyme inhibitors and the development of beta blockers for the treatment of heart failure. Which conceptual model most accurately describes the syndrome of heart failure and leads physicians to utilize the most effective treatment? This paper critically reviews the available evidence supporting and refuting the validity of all three models of heart failure. We conclude that, to varying degrees, all three approaches provide useful, but incomplete, insights into this physiologically complex and therapeutically challenging disease.

Cardiac Output, Low↗
PubMed2005

The mammalian alphaD-globin gene lineage and a new model for the molecular evolution of alpha-globin gene clusters at the stem of the mammalian radiation.

We have explored the evolution of the alpha-globin gene family by comparative sequence and phylogenetic analyses of mammalian alpha-globin genes. Our analyses reveal the existence of a new alpha-globin gene lineage in mammals that is related to the alpha(D)-globin genes of birds, squamates and turtles. The gene is located in the middle of the alpha-globin gene cluster of a marsupial, Sminthopsis macroura and of humans. It exists in a wide variety of additional mammals, including pigs, cows, cats, and dogs, but is a pseudogene in American marsupials. Evolutionary analyses suggest that the gene has generally evolved under purifying selection, indicative of a functional gene. The presence of mRNA products in humans, pigs, and cows also suggest that the gene is expressed and likely to be functional. The analyses support the hypothesis that the alpha(D)-globin gene lineage has an ancient evolutionary origin that predates the divergence of amniotes. The structural similarity of alpha-globin gene clusters of marsupials and humans suggest that an eight gene cluster (5'-zeta2-zeta1-alpha(D)-alpha3-alpha2-alpha1-theta-omega-3'), including seven alpha-like genes and one beta-like globin gene (omega-globin) existed in the common ancestor of all marsupial and eutherian mammals. This basic structure has remained relatively stable in marsupials and in the lineage leading to humans, although omega-globin has been lost from the alpha-globin gene cluster of humans.

Animals↗
PubMed2000

AKAP79 and the evolution of the AKAP model.

A molecular explanation for the specificity of the cAMP-dependent protein kinase (PKA) can be provided by its compartmentalization through association with A-kinase-anchoring proteins (AKAPs). Structural and functional studies have led to the development of an anchoring model proposing that AKAPs contain a common PKA binding domain and a unique subcellular targeting domain. The discovery that AKAPs can bind other signaling enzymes led to the addition of a third property, that of scaffolding molecule. Recent research has now expanded the role of AKAPs to members of multiunit complexes containing both upstream activators and downstream targets.

A Kinase Anchor Proteins↗
PubMed2002

The evolution of the hospitalist model in the United States.

Emerging data support the hypothesis that the use of hospital-based physicians can lead to improved efficiency without compromising patient [table: see text] outcomes or satisfaction. Nevertheless, for the foreseeable future, hospital care in the United States will likely remain a highly pluralistic system in which the organization of care is determined by efforts to improve the value of care in the context of local culture, patient populations, and patient and provider preferences. The method of hospital care chosen by each institution and group of physicians should be the one that promotes the best clinical outcomes and highest patient satisfaction at the lowest costs. With these goals in mind, it is likely that hospitalists will play an increasingly important and visible role in many institutions across the country.

Diffusion of Innovation↗
PubMed2004

Role of DNA organisation and environmental scavenging capacity in the evolution of radiobiological damage: models and simulations.

BACKGROUND AND PURPOSE: Theoretical models and Monte Carlo simulations were developed, aimed to investigate the role played by the organisation of interphase DNA and the environmental scavenging capacity conditions in the induction of radiobiological damage. METHODS: The induction of single- and double-strand breaks by gamma rays impinging on different DNA structures (e.g. linear DNA, SV40 minichromosome and cellular DNA) was simulated as a function of the environment scavenging capacity. Furthermore, yields of chromosome aberrations (CA) induced by gamma rays and light ions were simulated with a purposely developed MC code that explicitly takes into account the DNA higher-order organisation as chromosome territories. RESULTS AND CONCLUSIONS: Simulations performed with the PARTRAC code allowed quantification of the dependence of dsb and ssb both on the target structure, and on the scavenging capacity. The results relative to CA showed the importance of DNA damage complexity (nanometre scale) and interphase chromosome domains (micrometre scale) in the process of aberration formation. Very good agreement was found between the model predictions on ssb, dsb and CA and available experimental data.

Animals↗
PubMed1999

The evolution of mass balance models of persistent organic pollutant fate in the environment.

Current approaches to modelling the fate of persistent organic pollutants (POPs) in the environment have evolved in response to four dominant characteristics of these substances; namely: (1) the presence of POPs in virtually all environmental phases and the ease with which they move from one to the other requires multi-compartmental modelling. Describing transport across phase boundaries becomes as, or even more, important as quantifying transport within the phases; (2) POPs may persist in the environment for many decades. For chemicals that 'have time', concepts such as equilibrium partitioning and steady-state become more important than for short-lived substances whose fate is more controlled by the rates of transformation; (3) measuring POPs is difficult and expensive and observed concentrations of POPs are not available in high spatial or temporal resolution. Consequently, high resolution tends not to be a high priority in POP models; and (4) detrimental effects of POPs often manifest themselves in top predators, which has led to a focus on modelling biotic uptake and transfer within food chains. The task of building a POPs model is viewed as combining the four 'building blocks' of partitioning, transport, transformation and source data with the help of the law of the conservation of mass. Process models, evaluative models, models of real local, regional and global fate, as well as biological uptake models are presented and references to numerous examples are provided. An attempt is made to forecast future directions in the field of POPs modelling. It is expected that modelling techniques that do not rely on quantitative emission estimates as well as approaches that take into account spatial, temporal and climatic variability as well as parameter uncertainty will increase in importance. Finally, the relationship between modelling POPs and models of other pollutant issues is addressed, as are potential interactions between POPs and pollutant issues such as eutrophication, acidification and global climate change.

Journal Article↗