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101 records returned

Diploidy and the selective advantage for sexual reproduction in unicellular organisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. The asexual and sexual life cycles are based on the asexual and sexual life cycles in Saccharomyces cerevisiae, Baker's yeast, which normally reproduces by asexual budding, but switches to sexual reproduction when stressed. The mathematical models consider three reproduction pathways: (1) Asexual reproduction, (2) self-fertilization, and (3) sexual reproduction. We also consider two forms of genome organization. In the first case, we assume that the genome c...
Source: Theory in Biosciences - November 10, 2009 Category: Biology Authors: Kleiman M, Tannenbaum E Tags: Theory Biosci Source Type: journals

What makes some species of milk snakes more attractive to humans than others?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, humans showed a surprising ability to classify milk snake patterns; they repeatedly formed the same distinct groups of species, thus completing a process that resembles unsupervised categorization. PMID: 19890672 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - November 5, 2009 Category: Biology Authors: Marešová J, Landová E, Frynta D Tags: Theory Biosci Source Type: journals

From molecules to the biosphere: Nikolai V. Timoféeff-Ressovsky's (1900-1981) research program within a totalitarian landscape.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
From molecules to the biosphere: Nikolai V. Timoféeff-Ressovsky's (1900-1981) research program within a totalitarian landscape. Theory Biosci. 2009 Oct 16; Authors: Levit GS, Hoßfeld U Nikolai Vladimirovich Timoféeff-Ressovsky was one of the key figures in the Synthetic Theory of Evolution. Living and researching under what was arguably the two most powerful and cruel totalitarian regimes in human history, the Third Reich and the Soviet Union, Timoféeff-Ressovsky succeeded in developing an ambitious research program aiming to explain evolution on all major levels, from the molecular-genetic,...
Source: Theory in Biosciences - October 15, 2009 Category: Biology Authors: Levit GS, Hoßfeld U Tags: Theory Biosci Source Type: journals

Response to commentaries on our paper gene and genon concept: coding versus regulation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19784686 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - September 25, 2009 Category: Biology Authors: Scherrer K, Jost J Tags: Theory Biosci Source Type: journals

Comments on "Gene and genon concept" by K. Scherrer and J. Jost.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19779755 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - September 24, 2009 Category: Biology Authors: Billeter MA Tags: Theory Biosci Source Type: journals

On quantitative effects of RNA shape abstraction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over the last few decades, much effort has been taken to develop approaches for identifying good predictions of RNA secondary structure. This is due to the fact that most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native folding among all these possible secondary structures. Using the abstract shapes approach as introduced by Giegerich et al. (Nucleic Acids Res 32(16):4843-4851, 2004), each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives...
Source: Theory in Biosciences - September 14, 2009 Category: Biology Authors: Nebel ME, Scheid A Tags: Theory Biosci Source Type: journals

Comments on the paper by K. Scherrer and J. Jost "Gene and genon" concept: coding versus regulation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19730918 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - September 2, 2009 Category: Biology Authors: Gros F Tags: Theory Biosci Source Type: journals

Editorial.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19707809 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - August 25, 2009 Category: Biology Authors: Breidbach O Tags: Theory Biosci Source Type: journals

Commentary on Scherrer and Jost (2007) Gene and genon concept: coding versus regulation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19697074 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - August 20, 2009 Category: Biology Authors: Noble D Tags: Theory Biosci Source Type: journals

Scherrer and Jost's symposium: the gene concept in 2008.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Reconsideration of the term "gene" should take into account (a) the potential clash between hierarchical levels of information discussed in the 1970s by Gregory Bateson, (b) the contrast between conventional and genome phenotypes discussed in the 1980s by Richard Grantham, and (c) the emergence in the 1990s of a new science-Evolutionary Bioinformatics-that views genomes as channels conveying multiple forms of information through the generations. From this perspective, there is conceptual continuity between the functional "gene" of Mendel and today's GenBank sequences. If the function attributed to a gene can change spe...
Source: Theory in Biosciences - August 20, 2009 Category: Biology Authors: Forsdyke DR Tags: Theory Biosci Source Type: journals

Defining genes: a computational framework.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous work, we proposed an approach for constructing gene concepts that combines genomic heritability with elements of function. Here, we introduce a definition of the gene within a computational framework of cellular interactions. The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology. PMID: 19557452 [PubMed -...
Source: Theory in Biosciences - June 25, 2009 Category: Biology Authors: Stadler PF, Prohaska SJ, Forst CV, Krakauer DC Tags: Theory Biosci Source Type: journals

Culture-area relation in Axelrod's model for culture dissemination.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Axelrod's model for culture dissemination offers a nontrivial answer to the question of why there is cultural diversity given that people's beliefs have a tendency to become more similar to each other's as they interact repeatedly. The answer depends on the two control parameters of the model, namely, the number F of cultural features that characterize each agent, and the number q of traits that each feature can take on, as well as on the size A of the territory or, equivalently, on the number of interacting agents. Here, we investigate the dependence of the number C of distinct coexisting cultures on the area A in Axe...
Source: Theory in Biosciences - May 7, 2009 Category: Biology Authors: Barbosa LA, Fontanari JF Tags: Theory Biosci Source Type: journals

Symbiogenesis, natural selection, and the dynamic Earth.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One century ago, Constantin S. Mereschkowsky introduced the symbiogenesis theory for the origin of chloroplasts from ancient cyanobacteria which was later supplemented by Ivan E. Wallin's proposal that mitochondria evolved from once free-living bacteria. Today, this Mereschkowsky-Wallin principle of symbiogenesis, which is also known as the serial primary endosymbiosis theory, explains the evolutionary origin of eukaryotic cells and hence the emergence of all eukaryotes (protists, fungi, animals and plants). In 1858, the concept of natural selection was described independently by Charles Darwin and Alfred R. Wallace. I...
Source: Theory in Biosciences - April 27, 2009 Category: Biology Authors: Kutschera U Tags: Theory Biosci Source Type: journals

Distribution of variation over populations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, the association approach to an analysis of the distribution of trait variation over populations resolves problems that are frequently encountered with the apportionment perspective and its commonly applied measures in both population genetics and ecology, suggesting new and more comprehensive methods of analysis that include patterns of differentiation and apportionment. PMID: 19381704 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - April 17, 2009 Category: Biology Authors: Gregorius HR Tags: Theory Biosci Source Type: journals

Realistic threshold policy with hysteresis to control predator-prey continuous dynamics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper introduces a threshold policy with hysteresis (TPH) for the control of one-predator one-prey models. The models studied are the Lotka-Volterra and Rosenzweig-MacArthur two species density-dependent predator-prey models and the Arditi-Ginzburg nondimensional ratio-dependent model. The proposed policy (TPH) changes the dynamics of the system in such a way that a bounded oscillation is achieved confined to a region that does not allow extinction of either species. The policy can be designed by a suitable choice of so called virtual equilibrium points in a simple and intuitive manner. PMID: 19290561 [PubMed ...
Source: Theory in Biosciences - March 17, 2009 Category: Biology Authors: Mendoza Meza ME, Bhaya A Tags: Theory Biosci Source Type: journals

Evolution of gametophytic apomixis in flowering plants: an alternative model from Maloid Rosaceae.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gametophytic apomixis, asexual reproduction involving megagametophytes, occurs in many flowering-plant families and as several variant mechanisms. Developmental destabilization of sexual reproduction as a result of hybridization and/or polyploidy appears to be a general trigger for its evolution, but the evidence is complicated by ploidy-level changes and hybridization occurring with facultative apomixis. The repeated origins of polyploid apomictic complexes in the palaeopolyploid Maloid Rosaceae suggest a new model of evolutionary transitions that may have wider applicability. Two conjectures are fundamental to this m...
Source: Theory in Biosciences - March 5, 2009 Category: Biology Authors: Talent N Tags: Theory Biosci Source Type: journals

Marine invertebrates, model organisms, and the modern synthesis: epistemic values, evo-devo, and exclusion.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the ...
Source: Theory in Biosciences - February 25, 2009 Category: Biology Authors: Love AC Tags: Theory Biosci Source Type: journals

Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Large-scale-even genome-wide-duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a "fish-specific genome duplication" (FSGD) that is shared by most ray-finned fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richn...
Source: Theory in Biosciences - February 19, 2009 Category: Biology Authors: Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH Tags: Theory Biosci Source Type: journals

Saltational evolution: hopeful monsters are here to stay.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion I argue that the complete dismissal of saltational evolution is a major historical error of evolutionary biology tracing back to Darwin that needs to be rectified. PMID: 19224263 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - February 18, 2009 Category: Biology Authors: Theißen G Tags: Theory Biosci Source Type: journals

On some historical and theoretical foundations of the concept of chordates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The concept of chordates arose from the alliance between embryology and evolution in the second half of the nineteenth century, as a result of a theoretical elaboration on Kowalevsky's discoveries about some fundamental similarities between the ontogeny of the lancelet, a putative primitive fish, and that of ascidians, then classified as molluscs. Carrying out his embryological studies in the light of Darwin's theory and von Baer's account of the germ layers, Kowalevsky was influenced by the German tradition of idealistic morphology that was concerned with transformations driven by laws of form, rather than with a grad...
Source: Theory in Biosciences - February 17, 2009 Category: Biology Authors: Raineri M Tags: Theory Biosci Source Type: journals

Embryos in evolution: evo-devo at the Naples Zoological Station in 1874.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Eighteen seventy-four was a high point in evolutionary embryology. Thanks to Charles Darwin, the theory of evolution by natural selection provided a revolutionary new way of viewing the relationships and origins of organisms on Earth. Thanks to Ernst Haeckel, embryos were the way to study evolution (Haeckel in Generelle morphologie der organismen, vols 1, 2. Verlag Georg Reimer, Berlin, 1866)-it really was embryos in evolution-and recapitulation was in the air. Thanks to Anton Dohrn, a new research facility was on the ground, designed, located and structured to facilitate the study of embryos in evolution. Anton Dohrn ...
Source: Theory in Biosciences - February 13, 2009 Category: Biology Authors: Hall BK Tags: Theory Biosci Source Type: journals

Preface. Between Ernst Haeckel and the homeobox: the role of developmental biology in explaining evolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19214615 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - February 12, 2009 Category: Biology Authors: Olsson L, Hoßfeld U, Breidbach O Tags: Theory Biosci Source Type: journals

A theoretical framework for beta-glucan degradation during barley malting.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
During malting, barley germinates and produces hydrolytic enzymes that de-structure the endosperm, making the grains soft and friable. This process starts close to the embryo and spreads throughout the whole grain. It is leaded by the degradation of cell walls, which are mainly constituted of beta-glucans. Fast and extended breakdown of beta-glucans occurs by means of an expanding reaction front driven by beta-glucanase, and appears to follow pseudo-first-order kinetics. Endosperm permeabilization to macromolecules is closely linked to the dismantling of cell walls, thus that access to beta-glucans by beta-glucanase it...
Source: Theory in Biosciences - January 8, 2009 Category: Biology Authors: Gianinetti A Tags: Theory Biosci Source Type: journals

Longevity of orders is related to the longevity of their constituent genera rather than genus richness.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime (Van Valen in Evol Theory 1:1-30, 1973). Using the fossil marine animal genera database (Sepkoski in Bull Am Paleontol 363, pp 563, 2002) we here examine the relationship between longevity of a higher taxonomic group (orders) and the longevity of its lower taxonomic groups (genera). We find insignificant correlation between the size of an order and its longevity, whereas we observe large correlation be...
Source: Theory in Biosciences - December 20, 2008 Category: Biology Authors: Bornholdt S, Sneppen K, Westphal H Tags: Theory Biosci Source Type: journals

Selective advantage for sexual reproduction with random haploid fusion.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article develops a simplified set of models describing asexual and sexual replication in unicellular diploid organisms. The models assume organisms whose genomes consist of two chromosomes, where each chromosome is assumed to be functional if it is equal to some master sequence sigma(0), and non-functional otherwise. We review the previously studied case of selective mating, where it is assumed that only haploids with functional chromosomes can fuse, and also consider the case of random haploid fusion. When the cost for sex is small, as measured by the ratio of the characteristic haploid fusion time to the characteris...
Source: Theory in Biosciences - December 5, 2008 Category: Biology Authors: Tannenbaum E Tags: Theory Biosci Source Type: journals

Evolution in biological and nonbiological systems under different mechanisms of generation and inheritance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article presents the thesis that this conception is too restrictive and that evolution can occur in systems in which there is no copy of information between generations. For that purpose, this article introduces a new set of concepts and a theoretical framework that is designed to be equally applicable to the study of the evolution of biological and nonbiological systems. In contrast to some theoretical approaches in evolution, like neo-Darwinism, the approach presented here is not focused on the transmission and change of hereditary information that can be copied (like in the case of DNA). Instead, multiple mechanism...
Source: Theory in Biosciences - October 23, 2008 Category: Biology Authors: Salazar-Ciudad I Tags: Theory Biosci Source Type: journals

Stability of the analytical solution of Penna model of biological aging.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There are some analytical solutions of the Penna model of biological aging; here, we discuss the approach by Coe et al. (Phys. Rev. Lett. 89, 288103, 2002), based on the concept of self-consistent solution of a master equation representing the Penna model. The equation describes transition of the population distribution at time t to next time step (t + 1). For the steady state, the population n(a, l, t) at age a and for given genome length l becomes time-independent. In this paper we discuss the stability of the analytical solution at various ranges of the model parameters-the birth rate b or mutation rate m. The map f...
Source: Theory in Biosciences - October 22, 2008 Category: Biology Authors: Magdoń-Maksymowicz MS Tags: Theory Biosci Source Type: journals

The need for sperm selection may explain why termite colonies have kings and queens, whereas those of ants, wasps and bees have only queens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hymenoptera have haploid males, which produce sperm by cloning. Sperm selection theory predicts that because termites have diploid males that produce genetically diverse sperm, they may profit from a high sperm surplus (large K), whereas Hymenoptera (ants, bees and wasps) should produce few sperm per fertilization (low Kappa). Male reproductive "kings", which continuously provide spermatozoa during the whole life of the queen, allow for a large K. Available empirical evidence confirms the existence of a large difference in K between diploid insects, especially Blattodea (Isoptera) (K > 1,000), and haplo-diploids suc...
Source: Theory in Biosciences - September 13, 2008 Category: Biology Authors: Jaffe K Tags: Theory Biosci Source Type: journals

A comparison of sexual and asexual replication strategies in a simplified model based on the yeast life cycle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper develops simplified mathematical models describing the mutation-selection balance for the asexual and sexual replication pathways in Saccharomyces cerevisiae, or Baker's yeast. The simplified models are based on the single-fitness-peak approximation in quasispecies theory. We assume diploid genomes consisting of two chromosomes, and we assume that each chromosome is functional if and only if its base sequence is identical to some master sequence. The growth and replication of the yeast cells is modeled as a first-order process, with first-order growth rate constants that are determined by whether a given gen...
Source: Theory in Biosciences - August 21, 2008 Category: Biology Authors: Tannenbaum E Tags: Theory Biosci Source Type: journals

Psychoontogeny and psychophylogeny: Bernhard Rensch's (1900-1990) selectionist turn through the prism of panpsychistic identism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Toward the end of the 1930s, Bernhard Rensch (1900-1990) turned from Lamarckism and orthogenesis to selectionism and became one of the key figures in the making of the Synthetic Theory of Evolution (STE). He contributed to the Darwinization of biological systematics, the criticism of various anti-Darwinian movements in the German lands, but more importantly founded a macroevolutionary theory based on Darwinian gradualism. In the course of time, Rensch's version of the STE developed into an all-embracing metaphysical conception based on a kind of Spinozism. Here we approach Rensch's "selectionist turn" by outlining its ...
Source: Theory in Biosciences - August 13, 2008 Category: Biology Authors: Levit GS, Simunek M, Hoßfeld U Tags: Theory Biosci Source Type: journals

American precursors of evo-devo: ecology, cell lineage, and pastimes unworthy of the Deity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The American precursors of evo-devo have numerous phenotypes. Fritz Müller, a German émigré living in Brazil, was one of the first post-Darwin evolutionary biologists to look seriously at the roles of larvae in constraining and permitting evolutionary change. His book, Für Darwin, contains the germs of numerous ideas concerning recapitulation, larval ecology, punctuated equilibrium, and canalization. William Keith Brooks was interested in larval ecology and the mechanisms that promoted selectable variation. One of his students, E. B. Wilson, followed one of Mülller's paths and brought the notio...
Source: Theory in Biosciences - July 3, 2008 Category: Biology Authors: Gilbert SF Tags: Theory Biosci Source Type: journals

Macroevolution via secondary endosymbiosis: a Neo-Goldschmidtian view of unicellular hopeful monsters and Darwin's primordial intermediate form.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called "hopeful monsters". Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called "secondary endosymbiosis" (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic hos...
Source: Theory in Biosciences - June 26, 2008 Category: Biology Authors: Kutschera U, Niklas KJ Tags: Theory Biosci Source Type: journals

Importance of scaling exponents and other parameters in growth mechanism: an analytical approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The growth process of a living organism is studied with the help of a mathematical model where a part of the surplus power is assumed to be used for growth. In the present study, the basic mathematical framework of the growth process is based on a pioneering theory proposed by von Bertalanffy and his work is the main intellectual driving force behind the present analysis. Considering the existence of an optimum size for which the surplus power becomes maximum, it has been found that the scaling exponent for the intake rate must be smaller than the exponent for the metabolic cost. A relationship among the empirical cons...
Source: Theory in Biosciences - June 19, 2008 Category: Biology Authors: Biswas D, Das SK, Roy S Tags: Theory Biosci Source Type: journals

Proceedings of the annual European Conference on Complex Systems. 2007. Dresden, Germany.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: PMID: 18561366 [PubMed - indexed for MEDLINE] (Source: Theory in Biosciences)
Source: Theory in Biosciences - June 1, 2008 Category: Biology Tags: Theory Biosci Source Type: journals

A self-referential model for the formation of the genetic code.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A model for the formation of the genetic code is presented where protein synthesis is directed initially by tRNA dimers. Proteins that are resistant to degradation and efficient RNA-binders protect the RNAs. Replication becomes elongational producing poly-tRNAs from which the mRNAs and ribosomes are derived. Attributions are successively fixed to tRNAs paired through the perfect palindromic anticodons, with the same bases at the extremities (5'ANA: UNU 3'; GNG: CNC; principal dinucleotides, pDiN). The 5' degeneracy is then developed. The first pairs to be encoded correspond to the hydropathy correlation outliers (Gly-C...
Source: Theory in Biosciences - May 21, 2008 Category: Biology Authors: Guimarães RC, Moreira CH, de Farias ST Tags: Theory Biosci Source Type: journals

Information transfer in moving animal groups.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Moving animal groups provide some of the most intriguing and difficult to characterise examples of collective behaviour. We review some recent (and not so recent) empirical research on the motion of animal groups, including fish, locusts and homing pigeons. An important concept which unifies our understanding of these groups is that of transfer of directional information. Individuals which change their direction of travel in response to the direction taken by their near neighbours can quickly transfer information about the presence of a predatory threat or food source. We show that such information transfer is optimise...
Source: Theory in Biosciences - May 6, 2008 Category: Biology Authors: Sumpter D, Buhl J, Biro D, Couzin I Tags: Theory Biosci Source Type: journals

Topology-based abstraction of complex biological systems: application to the Golgi apparatus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Many complex cellular processes involve major changes in topology and geometry. We have developed a method using topology-based geometric modelling in which the edge labels of an n-dimensional generalized map (a subclass of graphs) represent the relations between neighbouring biological compartments. We illustrate our method using two topological models of the Golgi apparatus. These models can be animated using transformation rules, which depend on geometric and/or biochemical data and which modify both these data and the topology. Both models constitute plausible topological representations of the Golgi apparatus, but...
Source: Theory in Biosciences - May 6, 2008 Category: Biology Authors: Poudret M, Arnould A, Comet JP, Le Gall P, Meseure P, Képès F Tags: Theory Biosci Source Type: journals

Random perturbations of spiking activity in a pair of coupled neurons.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We examine the effects of stochastic input currents on the firing behaviour of two coupled Type 1 or Type 2 neurons. In Hodgkin-Huxley model neurons with standard parameters, which are Type 2, in the bistable regime, synaptic transmission can initiate oscillatory joint spiking, but white noise can terminate it. In Type 1 cells (models), typified by a quadratic integrate and fire model, synaptic coupling can cause oscillatory behaviour in excitatory cells, but Gaussian white noise can again terminate it. We locally determine an approximate basin of attraction, [Formula: see text] of the periodic orbit and explain the fi...
Source: Theory in Biosciences - May 1, 2008 Category: Biology Authors: Gutkin B, Jost J, Tuckwell HC Tags: Theory Biosci Source Type: journals

Multiscale analysis of reaction networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the different abilities to form bonds between different types of atoms and molecules create much of the properties we experience in our everyday life, especially in all biological activity. There are essentially two types of processes related to biochemical reaction networks, the interactions among molecules and interactions involving their conformational changes, so in a sense, their internal s...
Source: Theory in Biosciences - April 30, 2008 Category: Biology Authors: Sbano L, Kirkilionis M Tags: Theory Biosci Source Type: journals

Editorial.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 18443838 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - April 29, 2008 Category: Biology Authors: Jost J, Helbing D, Lörincz A, Middendorf M Tags: Theory Biosci Source Type: journals

Stability and performance of ant queue inspired task partitioning methods.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we consider computing systems that have autonomous helper components which fulfill support functions and that possess reconfigurable hardware so that they can specialize to different types of service tasks. Several self-organized task partitioning methods are proposed that can be used by the helper components to decide how to reconfigure and which service tasks to execute. The proposed task partitioning methods are inspired by the so-called ant queue system that can be found in real ants for partitioning tasks between the individuals. The aim of this study is to investigate basic properties of the task p...
Source: Theory in Biosciences - April 29, 2008 Category: Biology Authors: Scheidler A, Merkle D, Middendorf M Tags: Theory Biosci Source Type: journals

Genes, information and sense: complexity and knowledge retrieval.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Information capacity of nucleotide sequences measures the unexpectedness of a continuation of a given string of nucleotides, thus having a sound relation to a variety of biological issues. A continuation is defined in a way maximizing the entropy of the ensemble of such continuations. The capacity is defined as a mutual entropy of real frequency dictionary of a sequence with respect to the one bearing the most expected continuations; it does not depend on the length of strings contained in a dictionary. Various genomes exhibit a multi-minima pattern of the dependence of information capacity on the string length, thus r...
Source: Theory in Biosciences - April 29, 2008 Category: Biology Authors: Sadovsky MG, Putintseva JA, Shchepanovsky AS Tags: Theory Biosci Source Type: journals

3D Multi-agent models for protein release from PLGA spherical particles with complex inner morphologies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In order to better understand and predict the release of proteins from bioerodible microspheres or nanospheres, it is important to know the influences of different initial factors on the release mechanisms, though often it is difficult to assess what exactly is at the origin of a certain dissolution profile. We propose here a new class of fine-grained multi-agent models built to incorporate increasing complexity, permitting the exploration of the role of different parameters, especially that of the internal morphology of the spheres, in the exhibited release profile. This approach, based on Monte Carlo (MC) and cellula...
Source: Theory in Biosciences - April 26, 2008 Category: Biology Authors: Barat A, Ruskin HJ, Crane M Tags: Theory Biosci Source Type: journals

Hierarchical analysis of piecewise affine models of gene regulatory networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected co...
Source: Theory in Biosciences - April 25, 2008 Category: Biology Authors: Tournier L, Gouzé JL Tags: Theory Biosci Source Type: journals

A model for the neuronal substrate of dead reckoning and memory in arthropods: a comparative computational and behavioral study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Returning to the point of departure after exploring the environment is a key capability for most animals. In the absence of landmarks, this task will be solved by integrating direction and distance traveled over time. This is referred to as path integration or dead reckoning. An important question is how the nervous systems of navigating animals such as the 1 mm(3) brain of ants can integrate local information in order to make global decision. In this article we propose a neurobiologically plausible system of storing and retrieving direction and distance information. The path memory of our model builds on the well esta...
Source: Theory in Biosciences - April 22, 2008 Category: Biology Authors: Bernardet U, Bermúdez I Badia S, Verschure PF Tags: Theory Biosci Source Type: journals

Consistency principle in biological dynamical systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are derived and confirmed experimentally. They include a power law distribution of gene expressions, a lognormal distribution of cellular chemical abundances over cells, and embedding of the power law into the network connectivity distribution. Second, given a consistency between genotype and phenotype, a general relationship between phenotype fluctuations by genetic variation and isogenic phe...
Source: Theory in Biosciences - April 22, 2008 Category: Biology Authors: Kaneko K, Furusawa C Tags: Theory Biosci Source Type: journals

Metagenomics and the niche concept.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to ...
Source: Theory in Biosciences - April 18, 2008 Category: Biology Authors: Marco D Tags: Theory Biosci Source Type: journals

Flow-network adaptation in Physarum amoebae.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study examined how Physarum amoebae compute these solutions. The mechanism involves the adaptation of the tubular body, which appears to be similar to a network, based on cell dynamics. Our model describes how the network of tubes expands and contracts depending on the flux of protoplasmic streaming, and reproduces experimental observations of the behavior of the organism. The proposed algorithm based on Physarum is simple and powerful. PMID: 18415133 [PubMed - as supplied by publisher] (Source: Theory in Biosciences)
Source: Theory in Biosciences - April 16, 2008 Category: Biology Authors: Tero A, Yumiki K, Kobayashi R, Saigusa T, Nakagaki T Tags: Theory Biosci Source Type: journals

Neuroevolution and complexifying genetic architectures for memory and control tasks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The way genes are interpreted biases an artificial evolutionary system towards some phenotypes. When evolving artificial neural networks, methods using direct encoding have genes representing neurons and synapses, while methods employing artificial ontogeny interpret genomes as recipes for the construction of phenotypes. Here, a neuroevolution system (neuroevolution with ontogeny or NEON) is presented that can emulate a well-known neuroevolution method using direct encoding (neuroevolution of augmenting topologies or NEAT), and therefore, can solve the same kinds of tasks. Performance on challenging control and memory ...
Source: Theory in Biosciences - April 16, 2008 Category: Biology Authors: Inden B Tags: Theory Biosci Source Type: journals

Evolution of a multi-agent system in a cyclical environment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The synchronisation phenomena in biological systems is a current and recurring subject of scientific study. This topic, namely that of circadian clocks, served as inspiration to develop an agent-based simulation that serves the main purpose of being a proof-of-concept of the model used in the BitBang framework, that implements a modern autonomous agent model. Despite having been extensively studied, circadian clocks still have much to be investigated. Rather than wanting to learn more about the internals of this biological process, we look to study the emergence of this kind of adaptation to a daily cycle. To that end ...
Source: Theory in Biosciences - April 15, 2008 Category: Biology Authors: Baptista T, Costa E Tags: Theory Biosci Source Type: journals