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Topic: Quasispecies model

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	BioMed Central \| Full text \| Quasispecies theory in the context of population genetics
		Quasispecies theory is often cited as the theory to describe the evolution of RNA viruses [3], but in recent years several authors have questioned whether quasispecies theory has any relevance for virus evolution [4-7].
		Quasispecies theory has its origin in a seminal paper written by Eigen in 1971 [10], in which he studied the error-prone self-replication of biological macromolecules, primarily with the goal of understanding the origin of life.
		In the previous section, I have established that the quasispecies model is equivalent to the theory of mutation-selection balance in an infinite, haploid, asexual population.
	www.biomedcentral.com /1471-2148/5/44 (5241 words)

	Quasispecies model - Wikipedia, the free encyclopedia
		The quasispecies [kwaa'-zei-spee"-seez] model is a description of the process of the Darwinian evolution of self-replicating entities within the framework of physical chemistry.
		The quasispecies model was put forward by Manfred Eigen and Peter Schuster (see note 1) based on initial work done by Eigen(see note 2).
		In the quasispecies model, mutations occur through errors made in the process of copying already existing sequences.
	en.wikipedia.org /wiki/Quasispecies_model (1145 words)

	Models of molecular-genetic systems origin
		Quasispeciesis a model of a Darwinian evolution of a population of the polynucleotide strings (analogous to RNA), which are supposed to have certain replication abilities.
		The model of quasispecies was analyzed mathematically by a number of authors [1-6], and the particularities, concerning a final sequence distribution, a restriction on the sequence length, and a rate of evolution were quantitatively estimated.
		These models can be used to develop the scenarios of the first cybernetic systems origin, they can be juxtaposed with biochemical data to interpret qualitatively the corresponding experiments, and can be considered as a step for developments of more powerful models.
	pespmc1.vub.ac.be /ORIGIN.html (859 words)

	Untitled Document
		We developed a model within the quasispecies framework that incorporated genetic repair, and computed the equilibrium fraction of mutators as a function of mutation rate and repair efficiency.
		Presumably, the oldest DNA strands are the most accurate templates for daughter strand synthesis, and therefore their retention in the stem cells greatly slows the rate of accumulation of mutations in the stem cell population.
		Our theoretical model established that lesion repair should be completely suppressed in order to optimally preserve the genetic integrity of the stem cell population over the course of a human lifetime.
	www-shakh.harvard.edu /~tannenba (1461 words)

	Quasispecies model
		The quasispecies model was put forward by Manfred Eigen [maan'-fRed ei'-gen] and Peter Schuster [pay'-teR shuu'-steR] (see note 1) based on initial work done by Eigen.
		At equilibrium, removal of slowly replicating sequences due to decay or outflow is balanced by replenishing, so that even relatively slowly replicating sequences can remain present in finite abundance.
		The relative growths of the quasispecies are given by the corresponding eigenvalues.
	publicliterature.org /en/wikipedia/q/qu/quasispecies_model.html (610 words)

	Star Trek Plastic Model
		The model of the Botany Bay vessel was later seen as a target in "The Ultimate Computer" star trek plastic model and was featured in the 25th anniversary "Star Trek" display at the Smithsonian's Air star trek plastic model and Space Museum.
		Our design team pulled molds from one of the original props star trek plastic model and the castings were then given to our factory, to reproduce the same subtle curves star trek plastic model and contours of the originals.
		Quasispecies model - The quasispecies [kwaa'-zei-spee"-seez] model is a description of the process of the Darwinian evolution of self-replicating entities within the framework of physical chemistry.
	www.willieholt.com /startrekplasticmodel.html (1462 words)

	Wikipedia: Evolution
		A pre-programmed task, as in a military maneuver, using this definition, may be termed an "evolution." One can also speak of stellar evolution, chemical evolution, cultural evolution or the evolution of an idea.
		All species, as described by this model, are in a state of transition.
		Altruism has been one of the last (and most deeply embedded) thorns in the side of evolutionary theory, but recent developments in game theory have suggested explanations with an evolutionary context.
	www.factbook.org /wikipedia/en/e/ev/evolution.html (3666 words)

	Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens -- Bergstrom et al. 96 (9): 5095 -- ... (Site not responding. Last check: 2007-10-19)
		In this model, all hosts contribute viral particles, in proportion to their viral titer, to a common pool (e.g., a host carrying twice as many virions as a second host contributes twice as many viral particles to the common pool).
		In the horizontal model, the effective transmission bottleneck size on the entire viral population is nb.
		virulence is unchanged from that at the quasispecies equilibrium,
	www.pnas.org /cgi/content/full/96/9/5095 (4155 words)

	Theoretical Ecology Lab Tea (Site not responding. Last check: 2007-10-19)
		I propose a model for the response of stomata to these factors that is based on the mechanisms of: (1)diffusion across stomata, (3)photosynthesis, and (3)plant water transport.
		The advantage of the model over previous ones is that all the parameters have an explicit physical meaning, potentially allowing independent estimation and model validation using gas exchange measurements.
		Notice that this model is different from the "majority vote" model (when the elector polls his or her neighbors, and chooses the most common opinion), and from the well-known "cow skin" model of Henry Horn.
	www.eeb.princeton.edu /~plotkin/labtea_spring2001.html (2986 words)

	PRONUNCIATION (Site not responding. Last check: 2007-10-19)
		model is a description of the process of the Darwinian evolution of self-replicating entities within the framework of physical chemistry.
		As a consequence, the sequence that replicates fastest may even disappear completely in selection-mutation equilibrium, in favor of more slowly replicating sequences that are part of a quasispecies with a higher average growth rate.
		Mutational clouds as predicted by the quasispecies model have been observed in RNA viruses and in in vitro RNA replication.
	nupedia.8media.org /article/short/The+Quasispecies+model (570 words)

	[No title] (Site not responding. Last check: 2007-10-19)
		In this talk, we present an extension of the quasispecies model to account for the semiconservative nature of DNA replication, whereby each strand serves as the template for the synthesis of its complementary daughter strand.
		This is a necessary first step toward making the quasispecies model a quantitative tool for analyzing the evolutionary dynamics of unicellular organisms.
		From the semiconservative quasispecies equations we are able to show that, at sufficiently high error rates, faster replicating cells die more quickly than slower replicating cells.
	www.math.technion.ac.il /~techm/20040113110020040113tan (99 words)

	BioMed Central \| Full text \| Phenotypic mixing and hiding may contribute to memory in viral quasispecies
		For instance, the standard quasispecies model assumes low multiplicity of infection (m.o.i.), that is, each cell is assumed to be infected by at most one virion.
		We propose that our model may explain some of the quantitative differences observed between theoretical predictions of the quasispecies model and experimental data published in the literature [42-45].
		The research design of the original work [42-45] does not allow us to conclusively accept or reject our model as the correct explanation for their observations, but the values of mutant frequencies predicted by our model are consistent with the experimental data.
	www.biomedcentral.com /1471-2180/3/11 (5861 words)

	[No title]
		These two quasispecies populations differed in their pattern of evolution, with one population accumulating changes in a linear, time-dependent manner, while the other population evolved radially from a common variant.
		Modeling these interactions is somewhat complicated by the inherent flexibility of carbohydrates as well as their relatively large number of functional groups.
		Phylogenetic and cluster analyses suggested that the population of Rev variants was comprised of two distinct quasispecies that co-existed during infection, the populations shifted rapidly during febrile and afebrile periods with as little as 10 days between changes in population dominance of populations.
	www.bcb.iastate.edu /students/BCB-Alums.html (12704 words)

	Philip Dixon
		A better model for the sequence change can be constructed as a Bayesian hierarchical model.
		This combines a model for the mutation process, a model for the abundance of each sequence over time, and a model for the sampling process.
		The approach is illustrated using data from a long term study of the PRRS virus, a recent and devastating viral disease in pigs.
	www.stat.colostate.edu /graybillconference2003/Abstracts/Dixon.html (150 words)

	Evolution - Psychology Wiki - A Wikia wiki
		Following this, the work of population geneticists and zoologists in the 1930s and 1940s was able to create a model of Darwinian evolution compatible with the science of genetics, which became known as the modern evolutionary synthesis.
		In scientific terminology however, a theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation.
		Combining the simple coalescence model of cladogenesis with rare HGT [horizontal gene transfer] events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life.
	psychology.wikia.com /wiki/Evolution (7733 words)

	Quasispecies
		Quasispecies is a model of informational sequences evolution [1,2].
		Using the spin-glass concept (see Spin-glass model of evolution), it is possible to construct a similar model of informational sequences evolution for the case of very large number of the local maxima of a selective value.
		This model can be used to characterize roughly the hypothetical prebiotic polynucleotide sequence evolution and to illustrate mathematically general features of biological evolution.
	pespmc1.vub.ac.be /QUASIS.html (903 words)

	The Fifth Georgia Tech International Conference on Bioinformatics (Site not responding. Last check: 2007-10-19)
		For three types of the models, the sequence of independent identically distributed random variables, the first-order Markov chain and the hidden Markov model (HMM), we derive the lower bound for the rate of convergence in probability of the maximum error in estimating over all parameters of the model.
		We study the quasispecies model with a mutator allele with a view to systematic quantitative understanding of the evolution of mutation rates.
		Since hidden Markov models (HMMs) and generalizations thereof are extensively used to describe biomolecular sequences, the problem of parameter estimation for HMMs is important in the context of bioinformatics modeling methodology.
	opal.biology.gatech.edu /conference/index.cgi?display=posters (10484 words)

	Evidence for the Non-quasispecies Evolution of RNA Viruses -- Jenkins et al. 18 (6): 987 -- Molecular Biology and ...
		it was concluded that VSV was a quasispecies.
		Quasispecies in viral persistence and pathogenesis of hepatitis C virus.
		A codon-based model of nucleotide substitution for protein-coding DNA sequences.
	mbe.oxfordjournals.org /cgi/content/full/18/6/987 (4910 words)

	CiteULike: Replication and mutation on neutral networks. (Site not responding. Last check: 2007-10-19)
		Replication and mutation on neutral networks are modeled by phenomenological rate equations as well as by a stochastic birth-and-death model.
		The error classes of the quasispecies model are replaced by distance classes between the master shape and the other structures.
		Analytical results are derived for single-shape landscapes, in particular, simple expressions are obtained for the mean fraction of master shapes in a population and for phenotypic error thresholds.
	www.citeulike.org /article/210320 (673 words)

	Examining The Theory of Error Catastrophe -- Summers and Litwin 80 (1): 20 -- The Journal of Virology (Site not responding. Last check: 2007-10-19)
		of deleterious and lethal mutations in the quasispecies as a
		Eigen's error threshold and mutational meltdown in a quasispecies model.
		Quasispecies, error catastrophe, and the antiviral activity of ribavirin.
	intl-jvi.asm.org /cgi/content/full/80/1/20 (4269 words)

	Probability of Fixation of an Advantageous Mutant in a Viral Quasispecies -- Wilke 163 (2): 467 -- Genetics
		in a viral quasispecies is investigated in the framework of
		quasispecies is not given by the fitness of the initial mutant,
		of RNA viruses and that the deterministic quasispecies equations
	www.genetics.org /cgi/content/full/163/2/467 (4121 words)

	Artificial Life VII: Workshops and Tutorials
		Especially, the Swarm group is working on standardized models for multi-agent simulations and other software library writers have a big impact on the methodology of computer based science.
		Much of that understanding comes from Eigen's and Schuster's seminal work on the quasispecies model, which can be solved analytically for static fitness landscapes.
		In that case, a simple analytic solution is not at hand, and even such simple concepts as the quasispecies and the error threshold are not well defined in the general case.
	alife7.alife.org /workshops.shtml (4913 words)

	[No title]
		The model grants a quantitative measure of the valorization of this cultural good based on the relative values of the coupling between agents who have watched the movie and the ones who have not.
		For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories traced out by a population can be described in close analogy to record dynamics, with two complications.
		Abstract:As models of generalized conduction or transport, we consider chains of dynamical systems in which transfer of energy is mediated by tracer particles.
	www.math.rutgers.edu /events/smm/abstracts_1218-2005.html (2870 words)

	Life and social physics
		Flicker Noise in a Model of Coevolving Biological Populations
		Extinctions and taxonomy in a trophic model of coevolution
		Soluble Model for the Accumulation of Mutations in Asexual Populations
	www.fzu.cz /~slanina/bookmark_files/bkm4.html (2199 words)

	Virus evolution - Wikipedia, the free encyclopedia
		RNA viruses are also used as a model system to study evolution in the laboratory.
		One of the main theoretical models to study virus evolution is the quasispecies model, as the viral quasispecies.
		Quasispecies and RNA Virus Evolution: Principles and Consequences.
	en.wikipedia.org /wiki/Virus_evolution (214 words)

	Redundancy, antiredundancy, and the robustness of genomes -- Krakauer and Plotkin, 10.1073/pnas.032668599 -- ... (Site not responding. Last check: 2007-10-19)
		We used a mathematical model to examine which general conditions favor the evolution of redundancy and which favor antiredundancy.
		For small population sizes, the deterministic quasispecies equation does not apply.
		We perform quasispecies simulations in which individuals are characterized both by their hamming class k and their individual landscape steepness s.
	www.pnas.org /cgi/content/full/032668599v1 (3016 words)

	MAAA Seminar - abstracts
		Navier--Stokes-alpha model as a closure model to the
		A model is suggested to describe a density of the surface flow and the profile of the free surface of the granular material.
		The performance of a feedback control system depends on the model used for the controller design and upon the degree by which the actual process differs from the model.
	www.wisdom.weizmann.ac.il /mathusers/vered/analsemabs.html (10965 words)

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