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Evolving gene regulatory networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19917456 [PubMed - in process] (Source: Biosystems)
Source: Biosystems - November 18, 2009 Category: Biotechnology Authors: Jin Y, Hallinan J Tags: Biosystems Source Type: journals

NIK and IKK interdependence in NF-B signalling - Flux analysis of regulation through metabolites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Activation of the transcription factor NF-kappaB is central to control of immune and inflammatory responses. Cytokine induced activation through the classical or canonical pathway relies on degradation of the inhibitor, IkappaBalpha and regulation by the IKKbeta kinase. In addition, the NF-kappaB is activated through the NF-kappaB-inducing kinase, NIK. Analysis of the IKK/NIK inter-relationship and its impact on NF-kappaB control, were analysed by mathematical modelling, using matrix formalism and stoichiometrically balanced reactions. The analysis considered a range of bio-reactions and core metabolites and their role...
Source: Biosystems - November 9, 2009 Category: Biotechnology Authors: Kim HB, Evans I, Smallwood R, Holcombe M, Qwarnstrom EE Tags: Biosystems Source Type: journals

Bose-Einstein Condensates Form in Heuristics Learned by; Ciliates Deciding to Signal 'Social' Commitments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study, inspired by the discovery that preferential attachment rules computed by complex technological networks obey Bose-Einstein statistics, is the first rigorous attempt to examine whether analogues of Bose-Einstein condensation precipitate learned decision making in live biological systems as bioenergetics optimization predicts. By exploiting the ciliate Spirostomum ambiguum's capacity to learn and store behavioral strategies advertising mating availability into heuristics of topologically invariant computational networks, three distinct phases of strategy use were found to map onto statistical distributions descri...
Source: Biosystems - October 30, 2009 Category: Biotechnology Authors: Clark KB Tags: Biosystems Source Type: journals

Evolutionary classification of toxin mediated interactions in microorganisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A trade-off between the parameters of Lotka-Volterra systems is used to give verifica-tions of known relations between intrinsic growth rate and limiting capacity and the stability type of the resulting dynamical system. The well known rock-paper-scissors game serves as a template for toxin mediated interactions, which is best represented by the bacteriocin producing E.coli bacteria. There, we have three strains of the same species. The producer produces a toxin lethal to the sensitive, while the resistant is able to protect itself from that toxin. Due to the fact that there are costs for production and for resistance,...
Source: Biosystems - October 30, 2009 Category: Biotechnology Authors: Neumann GF Tags: Biosystems Source Type: journals

The evolution of senescence in multi-component systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Actuarial senescence is characterized by an increase in mortality rate with increasing chronological age. The reliability theory of senescence proposes that organisms' vital functions can be modelled as a suite of damageable, irreplaceable elements (typically genes or their products) that protect their bearer from condition-dependent death so long as at least one of the elements remains intact. Current incarnations of the reliability theory of senescence are continuous-time models with no explicit evolutionary component. Here, we use elementary probability theory and evolutionary dynamics analysis to derive a discrete-...
Source: Biosystems - October 28, 2009 Category: Biotechnology Authors: Laird RA, Sherratt TN Tags: Biosystems Source Type: journals

Selection Advantage of Metabolic Over Non-Metabolic Replicators: A Kinetic Analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A kinetic analysis and simulation of the replication reactions of two competing replicators - one non-metabolic (thermodynamic), the other metabolic, is presented. Our analysis indicates that in a rich resource environment the non-metabolic replicator is likely to be kinetically selected for over the metabolic replicator. However, in the more typical resource-poor environment it will be the metabolic replicator that is the kinetically more stable entity, and the one that will be kinetically selected for. Accordingly, a causal relationship between the emergence of a simple replicator and the emergence of a metabolic sys...
Source: Biosystems - October 26, 2009 Category: Biotechnology Authors: Wagner N, Pross A, Tannenbaumy E Tags: Biosystems Source Type: journals

A Multi-Objective Di_erential Evolutionary Approach Toward More Stable Gene Regulatory Networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study we use random Boolean networks (RBNs) as an abstract model of gene regulatory systems. By applying Di_erential Evolution (DE), an evolution-based optimization technique, we produce networks with increased stability. DE requires relatively few user-specified parameters, has fast convergence and does not rely on initial conditions to find the global minima within multi-dimensional search spaces. The stability of networks is evaluated by taking parameters such as their network sensitivity, attractor cycle length and number of attractor basins into account. In this study we present an evolutionary approach to pro...
Source: Biosystems - October 20, 2009 Category: Biotechnology Authors: Esmaeili A, Jacob C Tags: Biosystems Source Type: journals

Coevolutionary games - a mini review.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Prevalence of cooperation within groups of selfish individuals is puzzling in that it contradicts with the basic premise of natural selection. Favoring players with higher fitness, the latter is key for understanding the challenges faced by cooperators when competing with defectors. Evolutionary game theory provides a competent theoretical framework for addressing the subtleties of cooperation in such situations, which are known as social dilemmas. Recent advances point towards the fact that the evolution of strategies alone may be insufficient to fully exploit the benefits offered by cooperative behavior. Indeed, whil...
Source: Biosystems - October 14, 2009 Category: Biotechnology Authors: Perc M, Szolnoki A Tags: Biosystems Source Type: journals

Spatio-temporal dynamics of glycolysis in cell layers. A mathematical model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Glycolytic oscillations occur in many cell types and have been intensively studied in yeast. Recent experimental and theoretical research has been focussed on the oscillatory dynamics and the synchronisation mechanism in stirred yeast cell suspensions. Here we are interested in the spatio-temporal organisation of glycolysis in cell layers. To this end we study a grid of a few thousand compartments each containing a cell. The intracellular dynamics is described by a core model of glycolysis. The compartments can exchange metabolites via diffusion. The conditions for oscillatory dynamics in a single compartment are inves...
Source: Biosystems - October 14, 2009 Category: Biotechnology Authors: Schütze J, Wolf J Tags: Biosystems Source Type: journals

ModuleMaster: a new tool to decipher transcriptional regulatory networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the programincludes all necessary data and algorithms to performevery step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job...
Source: Biosystems - October 7, 2009 Category: Biotechnology Authors: Clemenswrzodek , Schr̈oder A, Dr̈ager A, Dierkwanke , Berendzen K, Kronfeld M, Harter K, Zell A Tags: Biosystems Source Type: journals

On Prokaryotic Inteligence: Strategies For Sensing The Environment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussions on the nature of cellular intelligence, however, have not systematically pursued yet the question of whether there is a fundamental way of sensing the environment, which may characterize prokaryotic cells, or not. The molecular systems found in bacterial signaling are extremely diverse, ranging from very simple transcription regulators (single proteins comprising just two domains) to the multi-component, multi-pathway signaling cascades that regulate crucial stages of the cell cycle, such as sporulation, biofilm formation, dormancy, pathogenesis or flagellar biosynthesis. The combined complexity of the environm...
Source: Biosystems - September 21, 2009 Category: Biotechnology Authors: Marijuán PC, Navarro J, Del Moral R Tags: Biosystems Source Type: journals

Mitochondrial tRNAs as light strand replication origins: Similarity between Anticodon Loops and the Loop of the Light Strand Replication Origin predicts initiation of DNA replication.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Stem-loop hairpins formed by mitochondrial light strand replication origins (OL) and by heavy strand DNA coding for tRNAs that form OL-like structures initiate mitochondrial replication. The loops are recognized by one of the two active sites of the vertebrate mitochondrial gamma polymerase, which are homologuous to the active sites of class II amino-acyl tRNA synthetases. Therefore, the polymerase site recognizing the OL loop could recognize tRNA anticodon loops and sequence similarity between anticodon and OL loops should predict initiation of DNA replication at tRNAs. Strengths of genome-wide deamination gradients s...
Source: Biosystems - September 11, 2009 Category: Biotechnology Authors: Seligmann H Tags: Biosystems Source Type: journals

Reproducibility and Usability of Chronic Virus Infection Model Using Agent-based Simulation; Comparing with a Mathematical Model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We created agent-based models that visually simulate conditions of chronic viral infections using two software. The results from two models were consistent, when they have same parameters during the actual simulation. The simulation results comprise a transient phase and an equilibrium phase, and unlike the mathematical model, virus count transit smoothly to the equilibrium phase without overshooting which correlates with actual biology in vivo of certain viruses. We investigated the effects caused by varying all the parameters included in concept; increasing virus lifespan, uninfected cell lifespan, uninfected cell re...
Source: Biosystems - September 10, 2009 Category: Biotechnology Authors: Itakura J, Kurosaki M, Itakura Y, Maekawa S, Asahina Y, Izumi N, Enomoto N Tags: Biosystems Source Type: journals

Coupling oscillations and switches in genetic networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Switches (bistability) and oscillations (limit cycle) are omnipresent in genetic networks. Synthetic genetic networks producing bistability and oscillations have been designed and constructed experimentally. However, in real biological systems, regulatory circuits are usually interconnected and the dynamics of those complex networks is often richer than the dynamics of simple modules. Here we coupled the genetic Toggle switch and the Repressilator, two prototypic systems exhibiting bistability and oscillations, respectively. We studied two types of coupling. In the first type, the bistable switch is under the control o...
Source: Biosystems - September 3, 2009 Category: Biotechnology Authors: Gonze D Tags: Biosystems Source Type: journals

Mutual Trust and Cooperation in the Evolutionary Hawks-Doves Game.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Using a new dynamical network model of society in which pairwise interactions are weighted according to mutual satisfaction, we show that cooperation is the norm in the Hawks-Doves game when individuals are allowed to break ties with undesirable neighbors and to make new acquaintances in their extended neighborhood. Moreover, cooperation is robust with respect to rather strong strategy perturbations. We also discuss the empirical structure of the emerging networks, and the reasons that allow cooperators to thrive in the population. Given the metaphorical importance of this game for social interaction, this is an encour...
Source: Biosystems - September 2, 2009 Category: Biotechnology Authors: Tomassini M, Pestelacci E, Luthi L Tags: Biosystems Source Type: journals

Scaling and Fractal Behaviour Underlying Meiotic Recombination.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper we investigate some of the mathematical properties of mei-otic recombination. Working within the framework of a genetic model with n loci, where a alleles are possible at each locus, we find that the proportion of all possible diploid parental genotypes that can produce a particular haploid gamete is exp [-n log [alpha(2)/2alpha-1])]. We show that this proportion connects recombination with a fractal geometry of dimension log(2alpha-1)/ log(alpha). The fractal dimension of a geometric object manifests itself when it is measured at increasingly smaller length scales. Decreasing the length scale of a geomet...
Source: Biosystems - August 23, 2009 Category: Biotechnology Authors: Waxman D, Stoletzki N Tags: Biosystems Source Type: journals

Similarity measures, non synonymous substitutions and degeneracy in the genetic code.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The first symmetry by base substitutions of degeneracy in the genetic code was described by Rumer (1966) and the other symmetries were identified later by Lehmann (2000), Jestin and Soulé (2006, 2007). Here, a rationale accounting for these symmetries is reported. The number of non-synonymous substitutions over the replicated coding sequence is written as a function of the substitution matrix, whose elements are the number of substitutions from any codon to any other codon. The p-adic distance used as a similarity measure and applied to this matrix is shown to be biologically relevant. The rationale indicates that...
Source: Biosystems - August 18, 2009 Category: Biotechnology Authors: Jestin JL Tags: Biosystems Source Type: journals

Embryoid bodies from mouse stem cells express oxytocin receptor, Oct-4 and DAZL.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Oxytocin is a nine amino acid peptide involved in a wide spectrum of physiological functions; predominantly those concerning reproduction and differentiation are of interest. Oxytocin receptors are expressed at early developmental stages of mammals, suggesting that oxytocin might be involved in the determination of the germ stem cell line, at the very early stages of mammalian development. In this respect, the proximate aim of the present study was to confirm and further analyze the existence of oxytocin receptors at a very early level of cell commitment, that is, the determination of germ cells derived from embryoid b...
Source: Biosystems - August 16, 2009 Category: Biotechnology Authors: Stefanidis K, Loutradis D, Anastasiadou V, Beretsos P, Bletsa R, Dinopoulou V, Lekka K, Elenis E, Kiapekou E, Koussoulakos S, Fotinos A, Antsaklis A Tags: Biosystems Source Type: journals

Escherichia coli autoinducer-2 uptake network does not display hysteretic behavior but AI-2 synthesis rate controls transient bifurcation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Analysis of different architectures of quorum sensing networks has been the center of attention in recent times. The approach employs mathematical models to uncover the factors behind the dynamics. Quorum sensing networks mostly display autoregulation such as Pseudomonas aeruginosa and Vibrio cholerae. However, Es cherichia coli autoinducer 2 (AI-2) synthesis does not display autoinduction (i.e. autoregulation). This and other features have raised questions about the actual function of AI-2 inside the cell. In this paper we propose a model for lsr operon regulation which explains or at least is consistent with AI-2 upt...
Source: Biosystems - August 16, 2009 Category: Biotechnology Authors: Barrios AF, Achenie LE Tags: Biosystems Source Type: journals

Origins of Learned Reciprocity in Solitary Ciliates Searching Grouped 'Courting' Assurances at Quantum Efficiencies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Learning to reciprocate socially valued actions, such as cheating and cooperation, marks evolutionary advances in animal intelligence thought unequalled by even colonial microbes known to secure respective individual or group fitness tradeoffs through genetic and epigenetic processes. However, solitary ciliates, unique among microbes for their emulation of simple Hebbian-like learning contingent upon feedback between behavioral output and vibration-activated mechanosensitive Ca(2+) channels, might be the best candidates to learn to reciprocate necessary preconjugant touches perceived during complex 'courtship rituals'....
Source: Biosystems - August 13, 2009 Category: Biotechnology Authors: Clark KB Tags: Biosystems Source Type: journals

Evaluation of dynamic behavior forecasting parameters in the process of transition rule induction of unidimensional cellular automata.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The simulation of the dynamics of a cellular systems based on cellular automata (CA) can be computationally expensive. This is particularly true when such simulation is part of a procedure of rule induction to find suitable transition rules for the CA. Several efforts have been described in the literature to make this problem more treatable. This work presents a study about the efficiency of dynamic behavior forecasting parameters (DBFPs) used for the induction of transition rules of CA for a specific problem: the classification by the majority rule. A total of 8 DBFPs were analyzed for the 31 best-performing rules fou...
Source: Biosystems - August 13, 2009 Category: Biotechnology Authors: Rodrigoweinert W, Lopes HS Tags: Biosystems Source Type: journals

Synchrony of spatial populations induced by colored environmental noise and dispersal.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we develop a spatially struc-tured population model, which is described by coupled-map lattices and incorporates both dispersal and colored environmental noise. A method for generating time series with desired spatial correlation and color is introduced. Then, we use these generated time series to analyze the in fl uence of noise color on synchrony in population dynamics. The noise color refers to the temporal correlation in the time series data of the noise, and is expressed as the degree of ( fi rst-order) autocorrelation for autoregressive noise. Patterns of spatial synchrony are considered for stable, pe...
Source: Biosystems - August 10, 2009 Category: Biotechnology Authors: Liu Z, Gao M, Zhang F, Li Z Tags: Biosystems Source Type: journals

An Evolutionary System using Development and Artificial Genetic Regulatory Networks for Electronic Circuit Design.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biology presents incomparable, but desirable, characteristics compared to engineered systems. Inspired by biological development, we have devised a multi-layered design architecture that attempts to capture the favourable characteristics of biological mechanisms for application to design problems. We have identified and implemented essential features of Genetic Regulatory Networks (GRNs) and cell signalling which lead to self-organization and cell differentiation. We have applied this to electronic circuit design. PMID: 19679161 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - August 9, 2009 Category: Biotechnology Authors: Zhan S, Miller JF, Tyrrell AM Tags: Biosystems Source Type: journals

A declarative constraint-based method for analyzing discrete gene regulation networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a four-step method for the systematic construction and analysis of discrete models of GRNs by means of a declarative approach. Instead of in-stantiating the models as in classical modeling approaches, the biological knowledge on the network structure and its dynamics is formulated in the form of constraints. The compatibility of the network structure with the constraints is queried and in case of inconsistencies, some constraints are relaxed. Common properties of the consistent models are then analyzed by means of dedicated languages. Two such languages are introduced in the paper. Removing ques-tionable constra...
Source: Biosystems - August 3, 2009 Category: Biotechnology Authors: Corblin F, Tripodi S, Fanchon E, Ropers D, Trilling L Tags: Biosystems Source Type: journals

The fourfold way of the genetic code.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé (2007), and the rearrangements of the table by Delarue (2007) and Rodin and Rodin (2008), respectively. PMID: 19643160 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - July 26, 2009 Category: Biotechnology Authors: Jiménez-Montaño MA Tags: Biosystems Source Type: journals

The Selectivity of noise and coupling for coherence biresonance and array-enhanced coherence biresonance in Coupled Neural Systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The selectivity of noise and coupling for coherence biresonance(CBR) and array-enhanced coherence biresonance(AECBR) in coupled neural systems has been investigated. It is shown that, depending on the coupling strength and noise intensity, various coherence behaviors and phenomena are exhibited, including CBR, coherence resonance without tuning, AECBR and undamped signal transmission. There exist optimal coupling and noise regions for occurrence of CBR and AECBR in the transmission of noise-induced oscillations(NIO). PMID: 19615426 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - July 13, 2009 Category: Biotechnology Authors: Shi J, Dong ML Tags: Biosystems Source Type: journals

Construction of a DNA Nano-Object Directly Demonstrates Computation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report an experiment in which three-vertex colorability for a 6-vertex graph with 9 edges is solved by constructing a DNA molecule representing the colored graph itself. Our findings show that computation based on "shape processing" is a viable alternative to symbol processing when computing by molecular self- assembly. PMID: 19607875 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - July 12, 2009 Category: Biotechnology Authors: Wu G, Jonoska N, Seeman NC Tags: Biosystems Source Type: journals

An Efficient Method for Stochastic Simulation of Biological Populations in Continuous Time.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present an efficient algorithm for individual-based, stochastic simulation of biological populations in continuous time. A simple method for its implementation is given and it is compared to Gillespie's commonly-used Direct Method. These two methods are proven to be exactly equivalent and, using a basic evolutionary model, it is demonstrated that the new algorithm can run thousands of times faster. Furthermore, while computational cost per event increases linearly with population size under the Direct Method, this cost is independent of population size under the new algorithm. We argue that this gain in efficiency opens...
Source: Biosystems - July 12, 2009 Category: Biotechnology Authors: Allen GE, Dytham C Tags: Biosystems Source Type: journals

Cellular "bauplans": Evolving unicellular forms by means of Julia sets and Pickover biomorphs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e., the "bauplan" discussion. Thirty years ago, however, Lynn and Tucker studied the biological mechanisms responsible for defining organelles position inside cells. The fact that differentiated structures performing a specific function within the eukaryotic cell (i.e. mitochondrion, vacuole, or chloroplas...
Source: Biosystems - July 9, 2009 Category: Biotechnology Authors: Mojica NS, Navarro J, Marijuán PC, Lahoz-Beltra R Tags: Biosystems Source Type: journals

Entropy decrease associated to solute compartmentalization in the cell.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have deduced equations to quantify the entropy associated to the compartmentalization of components in eukaryotic cells as a function of cell and compartment volumes, and of the concentration of solutes. On the basis of known and plausible values of volume and solute concentrations and the deduced equations, we estimate that the contribution of compartmentalization to the decrease of entropy is approximately -14.4x10(-14) JK(-1)cell(-1) (-0.7 JK(-1)L(-1)) in the case of Saccharomyces cerevisiae, a typical eukaryotic cell, and approximately -49.6x10(-14) JK(-1)cell(-1) (-1.0 JK(-1)L(-1)) in the more complex Chlamydom...
Source: Biosystems - July 8, 2009 Category: Biotechnology Authors: Marín D, Martín M, Sabater B Tags: Biosystems Source Type: journals

Species extinction and permanence of an impulsively controlled two-prey one-predator system with seasonal effects.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently, the population dynamic systems with impulsive controls have been researched by many authors. However, most of them are reluctant to study the seasonal effects on prey. Thus, in this paper, an impulsively controlled two-prey one-predator system with the Beddington-De Angelis type functional response and seasonal effects is investigated. By using the Floquet theory, the sufficient conditions for the existence of a globally asymptotically stable two-prey-free periodic solution are established. Further, it is proven that this system is permanent under some conditions via a comparison method involving multiple Lya...
Source: Biosystems - July 6, 2009 Category: Biotechnology Authors: Baek H Tags: Biosystems Source Type: journals

Predicting protein subnuclear localization using GO-amino-acid composition features.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study obtains homologies of query proteins with known accession numbers using BLAST to retrieve GO terms for sequence-based subnuclear localization prediction. A prediction method PGAC, which involves mining informative GO terms associated with amino-acid composition features, is proposed to design a support vector machine-based classifier. PGAC yields 55 informative GO terms with training and test accuracies of 85.7% and 76.3%, respectively, using a data set SNL_35 (561 proteins in 9 localizations) with 35% sequence identity. Upon comparison with Nuc-PLoc, which combines amphiphilic pseudo amino acid composition of a...
Source: Biosystems - July 3, 2009 Category: Biotechnology Authors: Huang WL, Tung CW, Huang HL, Ho SY Tags: Biosystems Source Type: journals

A possible mechanism of processive nucleotide and repeat additions by the telomerase.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Telomerase is a specialized cellular ribonucleoprotein complex that can synthesize long stretches of a DNA primer by using an intrinsic RNA template sequence. This requires that the telomerase must be able to carry out both nucleotide and repeat additions. Here, based on available structures and experimental data, a model is presented to describe these two addition activities. In the model, the forward movement of the polymerase active site along the template during the processive nucleotide addition is rectified through the incorporation of a matched base, via the Brownian ratchet mechanism. The unpairing of the DNA:R...
Source: Biosystems - July 2, 2009 Category: Biotechnology Authors: Xie P Tags: Biosystems Source Type: journals

Di-codon usage for classification of genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genes are often classified into biologically-related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying genes by using di-codon usage as features. The method is illustrated on 1,841 HLA sequences which are classified into two major classes, HLA-I and HLA-II, and further classified into the subclasses of major classes. By using both...
Source: Biosystems - July 1, 2009 Category: Biotechnology Authors: Nguyen MN, Ma J, Fogel GB, Rajapakse JC Tags: Biosystems Source Type: journals

On the Evolution of Scale-Free Topologies with a Gene Regulatory Network Model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A novel approach to generating scale-free network topologies is introduced, based on an existing artificial Gene Regulatory Network model. From this model, different interaction networks can be extracted, based on an activation threshold. By using an evolutionary computation approach, the model is allowed to evolve, in order to reach specific network statistical measures. The results obtained show that, when the model uses a duplication and divergence initialisation, such as seen in nature, the resulting regulation networks not only are closer in topology to scale-free networks, but also require only a few evolutionary...
Source: Biosystems - July 1, 2009 Category: Biotechnology Authors: Nicolau M, Schoenauer M Tags: Biosystems Source Type: journals

Neural model of frog ventilatory rhythmogenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the adult frog respiratory system, periods of rhythmic movements of the buccal floor are interspersed by lung ventilation episodes. The ventilatory activity results from the interaction of two hypothesized oscillators in the brainstem. Here, we model these oscillators with two coupled neural networks, whose co-activation results in the emergence of new dynamics. One of the networks is built with "loop chains" of excitatory and inhibitory neurones producing periodic activities. We define two groups of excitatory neurones whose oscillatory antiphasic sums of activities represent output signals as possible motor comman...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Horcholle-Bossavit G, Quenet B Tags: Biosystems Source Type: journals

A Condition-Enumeration Tree method for mining biclusters from DNA microarray data sets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biclustering, which performs simultaneous clustering of rows (e.g., genes) and columns (e.g., conditions), has proved of great value for finding interesting patterns from microarray data. To find biclusters, a model called pCluster was proposed. A pCluster consists of a set of genes and a set of conditions, where the expression levels of these genes have a similar variation under these conditions. Based on this model, most of the previous methods need to compute MDSs (maximum dimension sets) for every two genes in the microarray data. Since the number of genes is far larger than the number of conditions, this step is i...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Chen JR, Chang YI Tags: Biosystems Source Type: journals

Energy efficiency of information transmission by electrically coupled neurons.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The generation of spikes by neurons is energetically a costly process. This paper studies the consumption of energy and the information entropy in the signalling activity of a model neuron both when it is supposed isolated and when it is coupled to another neuron by an electrical synapse. The neuron has been modelled by a four-dimensional Hindmarsh-Rose type kinetic model for which an energy function has been deduced. For the isolated neuron values of energy consumption and information entropy at different signalling regimes have been computed. For two neurons coupled by a gap junction we have analyzed the roles of the...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Torrealdea FJ, Sarasola C, d'Anjou A, Moujahid A, de Mendizábal NV Tags: Biosystems Source Type: journals

Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Both direct and indirect experimental evidence has shown signaling, communication and conductivity in microtubules (MTs). Theoretical models have predicted that MTs can be potentially used for both classical and quantum information processing although controversies arose in regard to physiological temperature effects on these capabilities. In this paper, MTs have been studied using well-established principles of classical statistical physics as applied to information processing, information storage and signal propagation. To investigate the existence of information processing in MTs we used cellular automata (CA) model...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Craddock TJ, Beauchemin C, Tuszynski JA Tags: Biosystems Source Type: journals

On the robustness of update schedules in Boolean networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Deterministic Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states are to be updated. We study the robustness of the dynamical behavior of a Boolean network with respect to different update schedules (synchronous, block-sequential, sequential), which can provide modelers with a better understanding of the consequences of changes in this aspect of the model. For a given Boolean network, we define equivalence classes of update schedules with the same dynamical behavior, introducing a la...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Aracena J, Goles E, Moreira A, Salinas L Tags: Biosystems Source Type: journals

Nonlinear electronic circuit with neuron like bursting and spiking dynamics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is difficult to design electronic nonlinear devices capable of reproducing complex oscillations because of the lack of general constructive rules, and because of stability problems related to the dynamical robustness of the circuits. This is particularly true for current analog electronic circuits that implement mathematical models of bursting and spiking neurons. Here we describe a novel, four-dimensional and dynamically robust nonlinear analog electronic circuit that is intrinsic excitable, and that displays frequency adaptation bursting and spiking oscillations. Despite differences from the classical Hodgkin-Huxl...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Savino GV, Formigli CM Tags: Biosystems Source Type: journals

Hidden pattern discovery on event related potential EEG signals.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
EEG signals are important to capture brain disorders. They are useful for analyzing the cognitive activity of the brain and diagnosing types of seizure and potential mental health problems. The Event Related Potential can be measured through the EEG signal. However, it is always difficult to interpret due to its low amplitude and sensitivity to changes of the mental activity. In this paper, we propose a novel approach to incrementally detect the pattern of this kind of EEG signal. This approach successfully summarizes the whole stream of the EEG signal by finding the correlations across the electrodes and discriminates...
Source: Biosystems - June 13, 2009 Category: Biotechnology Authors: Ng KS, Yang HJ, Kim SH Tags: Biosystems Source Type: journals

Nonlinearities in mating sounds of American crocodiles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We use nonlinear time series analysis methods to analyze the dynamics of the sound-producing apparatus of the American crocodile (Crocodylus acutus). We capture its dynamics by analyzing a recording of the singing activity during mating time. First, we reconstruct the phase space from the sound recording and thereby reveal that the attractor needs no less than five degrees of freedom to fully evolve in the embedding space, which suggests that a rather complex nonlinear dynamics underlies its existence. Prior to investigating the dynamics more precisely, we test whether the reconstructed attractor satisfies the notions ...
Source: Biosystems - June 5, 2009 Category: Biotechnology Authors: Benko TP, Perc M Tags: Biosystems Source Type: journals

Predict prokaryotic proteins through detecting N-formymethionine residues in protein sequences using support vector machine.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Identifying prokaryotes in silico is commonly based on DNA sequences. In experiments where DNA sequences may not be immediately available, we need to have a different approach to detect prokaryotes based on RNA or protein sequences. N-formylmetheonine (fMet) is known as a typical characteristic of prokaryotes. A web tool has been implemented here for predicting prokaryotes through detecting the N-formylmethionine residues in protein sequences. The predictor is constructed using support vector machine. An online predictor has been implemented using Python. The implemented predictor is able to achieve the total predictio...
Source: Biosystems - June 5, 2009 Category: Biotechnology Authors: Yang ZR Tags: Biosystems Source Type: journals

A Novel Generalized Design Methodology and Realization of Boolean operations using DNA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The biological Deoxyribonucleic acid (DNA) strand has been increasingly seen as a promising computing unit. A new algorithm is formulated in this paper to design any DNA-Boolean-operator with molecular beacons (MB) as its input. Boolean operators realized using the proposed design methodology is presented. The developed operators adopt a uniform representation for logical 0 and 1 for any Boolean operator. The Boolean operators designed in this work employ only a hybridization operation at each stage. Further, this paper for the first time brings out the realization of a binary adder and subtractor using Molecular Beaco...
Source: Biosystems - June 5, 2009 Category: Biotechnology Authors: Zoraida BS, Arock M, Ronald BS, Ponalagusamy R Tags: Biosystems Source Type: journals

Variable Wavelength Surface Plasmon Resonance (SPR) in Biosensing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we fabricated a novel variable wavelength surface plasmon resonance (SPR) sensor, which detects resonance conditions such as a maximum attenuation wavelength, measuring change of microscopic refractive index. Such a change was measured to detect a salmonella antigen-antibody reaction and a penicillinase-penicillin reaction. Our experiments were performed after immobilizing a salmonella antibody on the sensor chip. We measured the shift in resonant wavelength during the antigen-antibody reaction for 30min by injecting 5x10(7) cells/ml concentration of salmonella antigen solution into the sample chamber. Also,...
Source: Biosystems - May 29, 2009 Category: Biotechnology Authors: Eum NS, Kim DE, Yeom SH, Kang BH, Kim KJ, Park CS, Kang SW Tags: Biosystems Source Type: journals

Intracellular viral kinetics limited by the supply of amino acids for synthesis of viral proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A minimal model proposed by the author [Zhdanov, V.P., 2004. Stochastic kinetics of reproduction of virions inside a cell. Biosystems 77, 143-150] to describe intracellular viral kinetics includes genome replication, mRNA and protein synthesis and degradation, capsid assembly, and virion release from a cell. Here, this model is complemented by the terms describing the balance of the amino acid determining the rate of the synthesis of viral capsid protein. If the effect of virions on this balance is negligible, the model predicts either a steady state or unlimited growth of the virion population. In the latter case, the...
Source: Biosystems - May 21, 2009 Category: Biotechnology Authors: Zhdanov VP Tags: Biosystems Source Type: journals

Optimal treatment of an SIR epidemic model with time delay.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper the optimal control strategies of an SIR (susceptible-infected-recovered) epidemic model with time delay are introduced. In order to do this, we consider an optimally controlled SIR epidemic model with time delay where a control means treatment for infectious hosts. We use optimal control approach to minimize the probability that the infected individuals spread and to maximize the total number of susceptible and recovered individuals. We first derive the basic reproduction number and investigate the dynamical behavior of the controlled SIR epidemic model. We also show the existence of an optimal control f...
Source: Biosystems - May 21, 2009 Category: Biotechnology Authors: Zaman G, Kang YH, Jung IH Tags: Biosystems Source Type: journals

A simulation model of the conventional kinesin based on the Driven-by-Detachment mechanism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Kinesins are molecular motors that unidirectionally move along microtubules using the chemical energy of ATP. Although the core structure of kinesins is similar to that of myosins, the lever-arm hypothesis, which is widely accepted as a plausible mechanism to explain the behaviors of myosins, cannot be directly applied to kinesins. Masuda has proposed a mechanochemical process called the 'Driven-by-Detachment (DbD)' mechanism to explain the characteristic behaviors of myosins, including the backward movement of myosin VI and the loose coupling phenomenon of myosin II. The DbD mechanism assumes that the energy of ATP is...
Source: Biosystems - May 21, 2009 Category: Biotechnology Authors: Masuda T Tags: Biosystems Source Type: journals

Harvesting on a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the natural world, there are many species whose individual members have a life history that they take them with two distinct stages: immaturity and maturity. In particular, we have in mind mammalian populations and some amphibious animals. We improve the assumption of a single population as a whole. It is assumed that the immature individuals and mature individuals are divided by a fixed period. This paper concentrates on the study of a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin at fixed moments. Furthermore, the mature individual...
Source: Biosystems - May 19, 2009 Category: Biotechnology Authors: Jiao J, Yang X, Chen L Tags: Biosystems Source Type: journals