MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Biosystems' source. Mon, 06 Feb 2012 18:10:48 +0100 http://www.medworm.com/index.php?rid=5620983&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22261639%26dopt%3DAbstract Authors: Manca V, Marchetti L Abstract MP (Metabolic P) systems are a class of P systems introduced for modelling metabolic processes. We refer to the dynamical inverse problem as the problem of identifying (discrete) mathematical models exhibiting an observed dynamics. In this paper, we complete the definition of the algorithm LGSS (Log-gain Stoichiometric Stepwise regression) introduced in Manca and Marchetti (2011) for solving a general class of dynamical inverse problems. To this aim, we develop a reformulation of the classical stepwise regression in the context of MP systems. We conclude with a short review of two applications of LGSS for discovering the internal regulation logic of two phenomena relevant in systems biology. PMID: 22261639 [PubMed - as supplied by publishe... Biosystems journals http://www.medworm.com/rss/comments.php?id=5620983 Thu, 12 Jan 2012 05:00:00 +0100 5620983 http://www.medworm.com/index.php?rid=5620982&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22261640%26dopt%3DAbstract Authors: Adamatzky A, Holley J, Dittrich P, Gorecki J, De Lacy Costello B, Zauner KP, Bull L Abstract When lipid vesicles filled with Belousov-Zhabotinsky (BZ) excitable chemical medium are packed in tight assembles, waves of excitation may travel between the vesicles. When several waves meet in a vesicle some fragments may deflect, others can annihilate or continue their travel undisturbed. By interpreting waves as Boolean values we can construct logical gates and assemble them in large circuits. In numerical modelling we show two architectures of one-bit half-adders implemented in BZ-vesicles. PMID: 22261640 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=5620982 Thu, 12 Jan 2012 05:00:00 +0100 5620982 http://www.medworm.com/index.php?rid=5620981&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22261641%26dopt%3DAbstract Authors: Stano P, Rampioni G, Carrara P, Damiano L, Leoni L, Luisi PL Abstract Biological systems evolved with the ability to communicate with their biotic surroundings through chemical signalling. Production, perception and decoding of the information carried by signal molecules allow individuals of a community to interact, cooperate, and coordinate their activities, establishing complex social behaviours. In this paper we speculate about the opportunity to use semi synthetic minimal cells (SSMCs) as artificial entities able to communicate, by processing biochemical information, with natural systems. SSMCs are liposome-based cell-like molecular assemblies designed for displaying minimal cellular functions, like gene transcription and translation. The technological advancements in ... Biosystems journals http://www.medworm.com/rss/comments.php?id=5620981 Thu, 12 Jan 2012 05:00:00 +0100 5620981 http://www.medworm.com/index.php?rid=5620984&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245315%26dopt%3DAbstract Authors: Nakajima T Abstract Epistatic interactions between genes in the genome constrain the accessible evolutionary paths of lineages. Two factors involving epistasis that can affect the evolutionary path and fate of lineages were investigated. The first factor concerns the impact of competition with another species lineage that has different epistatic constraints. Five enteric bacterial populations were evolved by point mutation in medium containing a single limiting resource. Single-species and two-species cultures were used to determine whether different asexual lineages have different capacities for producing variants due to epistatic constraints, and whether their survival is determined by local inter-lineage competition with different species. Local inter-lineage competitio... Biosystems journals http://www.medworm.com/rss/comments.php?id=5620984 Mon, 09 Jan 2012 05:00:00 +0100 5620984 http://www.medworm.com/index.php?rid=5620985&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22240019%26dopt%3DAbstract Authors: Chaplin JC, Russell NA, Krasnogor N Abstract In this paper we detail experimental methods to implement registers, logic gates and logic circuits using populations of photochromic molecules exposed to sequences of light pulses. Photochromic molecules are molecules with two or more stable states that can be switched reversibly between states by illuminating with appropriate wavelengths of radiation. Registers are implemented by using the concentration of molecules in each state in a given sample to represent an integer value. The register's value can then be read using the intensity of a fluorescence signal from the sample. Logic gates have been implemented using a register with inputs in the form of light pulses to implement 1-input/1-output and 2-input/1-output logic gates... Biosystems journals http://www.medworm.com/rss/comments.php?id=5620985 Thu, 05 Jan 2012 05:00:00 +0100 5620985 http://www.medworm.com/index.php?rid=5578034&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22212352%26dopt%3DAbstract Authors: Kostromins A, Mozga I, Stalidzans E Abstract Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochastic properties and the convergence of the objective function to the global optimum is hardly predictable. Determination of suitable optimization method and necessary duration of optimization becomes critical in case of evaluation of high number of combinations of adjustable parameters or in case of large dynamic models. This task is complex due to variety of optimization methods, softwa... Biosystems journals http://www.medworm.com/rss/comments.php?id=5578034 Thu, 29 Dec 2011 05:00:00 +0100 5578034 http://www.medworm.com/index.php?rid=5578035&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22212351%26dopt%3DAbstract Authors: Kochi N, Matache MT Abstract In this paper we provide a mean-field Boolean network model for a signal transduction network of a generic fibroblast cell. The network consists of several main signaling pathways, including the receptor tyrosine kinase, the G-protein coupled receptor, and the Integrin signaling pathway. The network consists of 130 nodes, each representing a signaling molecule (mainly proteins). Nodes are governed by Boolean dynamics including canalizing functions as well as totalistic Boolean functions that depend only on the overall fraction of active nodes. We categorize the Boolean functions into several different classes. Using a mean-field approach we generate a mathematical formula for the probability of a node becoming active at any time step. The model... Biosystems journals http://www.medworm.com/rss/comments.php?id=5578035 Tue, 27 Dec 2011 05:00:00 +0100 5578035 http://www.medworm.com/index.php?rid=5549440&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197791%26dopt%3DAbstract Authors: Fogel GB, Schwartz AW PMID: 22197791 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=5549440 Tue, 20 Dec 2011 05:00:00 +0100 5549440 http://www.medworm.com/index.php?rid=5549439&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197792%26dopt%3DAbstract Authors: Chan JY Abstract Recent evidence supports the existence of a mutator phenotype in cancer cells, although the mechanistic basis remains unknown. In this paper, it is shown that this enhanced genetic instability is generated by an amplified measurement uncertainty on genetic information during DNA replication. At baseline, an inherent measurement uncertainty implies an imprecision of the recognition, replication and transfer genetic information, and forms the basis for an intrinsic genetic instability in all biological cells. Genetic information is contained in the sequence of DNA bases, each existing due to proton tunnelling, as a coherent superposition of quantum states composed of both the canonical and rare tautomeric forms until decoherence by interaction with DNA polym... Biosystems journals http://www.medworm.com/rss/comments.php?id=5549439 Sat, 17 Dec 2011 05:00:00 +0100 5549439 http://www.medworm.com/index.php?rid=5549441&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197514%26dopt%3DAbstract Authors: Baixeries J, Hernández-Fernández A, Ferrer-I-Cancho R Abstract Recently, a random breakage model has been proposed to explain the negative correlation between mean chromosome length and chromosome number that is found in many groups of species and is consistent with Menzerath-Altmann law, a statistical law that defines the dependency between the mean size of the whole and the number of parts in quantitative linguistics. Here, the central assumption of the model, namely that genome size is independent from chromosome number is reviewed. This assumption is shown to be unrealistic from the perspective of chromosome structure and the statistical analysis of real genomes. A general class of random models, including that random breakage model, is analyzed. For any model within... Biosystems journals http://www.medworm.com/rss/comments.php?id=5549441 Fri, 16 Dec 2011 05:00:00 +0100 5549441 http://www.medworm.com/index.php?rid=5533795&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155363%26dopt%3DAbstract Authors: Martorano SR, Yang HM, Venturino E, Massad E Abstract The use of antiretroviral therapy has proven to be remarkably effective in controlling the progression of human immunodeficiency virus (HIV) infection and prolonging patient's survival. Therapy however may fail and therefore these benefits can be compromised by the emergence of HIV strains that are resistant to the therapy. In view of these facts, the question of finding the reason for which drug-resistant strains emerge during therapy has become a worldwide problem of great interest. This paper presents a deterministic HIV-1 model to examine the mechanisms underlying the emergence of drug-resistance during therapy. The aim of this study is to determine whether, and how fast, antiretroviral therapy may determine the eme... Biosystems journals http://www.medworm.com/rss/comments.php?id=5533795 Wed, 07 Dec 2011 05:00:00 +0100 5533795 http://www.medworm.com/index.php?rid=5533794&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22172775%26dopt%3DAbstract Authors: Yang Y, Xiao Y, Wang N, Wu J Abstract Pharmacokinetics were melded with a viral dynamical model to design an optimal drug administration regimen such that the basic reproductive number for the virus was minimized. One-compartmental models with two kinds of drug delivery routes, intravenous and extravascular with multiple dosages, and two drug elimination rates, first order and Michaelis-Menten rates, were considered. We defined explicitly the basic reproductive number for the viral dynamical model melded with pharmacokinetics. When the average plasma drug concentration was constant, intravenous administration of the drug with small dosages applied frequently minimized the basic reproductive number. For extravascular administration, the basic reproductive number initially d... Biosystems journals http://www.medworm.com/rss/comments.php?id=5533794 Wed, 07 Dec 2011 05:00:00 +0100 5533794 http://www.medworm.com/index.php?rid=5533796&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154946%26dopt%3DAbstract Authors: Igamberdiev AU, Roussel MR Abstract Rubisco, the most abundant protein serving as the primary engine generating organic biomass on Earth, is characterized by a low catalytic constant (in higher plants approx. 3s(-1)) and low specificity for CO(2) leading to photorespiration. We analyze here why this enzyme evolved as the main carbon fixation engine. The high concentration of Rubisco exceeding the concentration of its substrate CO(2) by 2-3 orders of magnitude makes application of Michaelis-Menten kinetics invalid and requires alternative kinetic approaches to describe photosynthetic CO(2) assimilation. Efficient operation of Rubisco is supported by a strong flux of CO(2) to the chloroplast stroma provided by fast equilibration of bicarbonate and CO(2) and forwarding the la... Biosystems journals http://www.medworm.com/rss/comments.php?id=5533796 Sun, 04 Dec 2011 05:00:00 +0100 5533796 http://www.medworm.com/index.php?rid=5493119&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22142839%26dopt%3DAbstract Authors: Dellis AT, Kominis IK Abstract Magnetic-sensitive radical-ion-pair reactions are understood to underlie the biochemical magnetic compass used by avian species for navigation. Recent experiments have provided growing evidence for the radical-ion-pair magnetoreception mechanism, while recent theoretical advances have unravelled the quantum nature of radical-ion-pair reactions, which were shown to manifest a host of quantum-information-science concepts and effects, like quantum measurement, quantum jumps and the quantum Zeno effect. We here show that the quantum Zeno effect provides for the robustness of the avian compass mechanism, and immunizes its magnetic and angular sensitivity against the deleterious and molecule-specific exchange and dipolar interactions. PMID: 221... Biosystems journals http://www.medworm.com/rss/comments.php?id=5493119 Sat, 26 Nov 2011 05:00:00 +0100 5493119 http://www.medworm.com/index.php?rid=5493121&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22122974%26dopt%3DAbstract Authors: Wallace R Abstract Unlike the universal genetic code and ordered protein folding, direct application of Tlusty's method to the glycome produces a reducto ad absurdum: From the beginning a complicated system of chemical cognition is needed so that external information constrains and tunes what would otherwise be a monstrously large 'glycan code error network'. Further, the glycan manufacture machinery itself must be regulated by yet other levels of chemical cognition to ensure that what is produced matches what was chosen for production. Application of a rate distortion index theorem/operator method at this second stage appears possible, permitting analytic characterization of the complicated 'glycan spectra' associated with cellular interactions and their dynamics. The reg... Biosystems journals http://www.medworm.com/rss/comments.php?id=5493121 Wed, 23 Nov 2011 05:00:00 +0100 5493121 http://www.medworm.com/index.php?rid=5493120&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22133717%26dopt%3DAbstract Authors: Banerjee A Abstract Exploring common features and universal qualities shared by a particular class of networks in biological and other domains is one of the important aspects of evolutionary study. In an evolving system, evolutionary mechanism can cause functional changes that forces the system to adapt to new configurations of interaction pattern between the components of that system (e.g. gene duplication and mutation play a vital role for changing the connectivity structure in many biological networks. The evolutionary relation between two systems can be retraced by their structural differences). The eigenvalues of the normalized graph Laplacian not only capture the global properties of a network, but also local structures that are produced by graph evolutions (like mot... Biosystems journals http://www.medworm.com/rss/comments.php?id=5493120 Wed, 23 Nov 2011 05:00:00 +0100 5493120 http://www.medworm.com/index.php?rid=5439865&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100871%26dopt%3DAbstract We present a novel method to analyze the identifiability of model parameters based on the interpretation of the empirical observability Gramian. This allows a unifying view of both, the observability of the system's states (with dynamics) and the identifiability of the system's parameters (without dynamics). We give an iterative algorithm, in order to find an optimized set of states and parameters to be estimated. For this set, estimation results using an Unscented Kalman Filter (UKF) are presented. Two parameters are of special interest for diagnostic purposes: the glucose effectiveness S(G) characterizes the ability of plasma glucose clearance. The insulin sensitivity S(I) quantifies the impact from the plasma insulin to the interstitial insulin subsystem. Applying the identifiability an... Biosystems journals http://www.medworm.com/rss/comments.php?id=5439865 Sat, 12 Nov 2011 05:00:00 +0100 5439865 http://www.medworm.com/index.php?rid=5439863&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100873%26dopt%3DAbstract Authors: Shah K, Krishnamachari A Abstract Genomes of almost all organisms have been found to exhibit several periodicities, the most prominent one is the three base periodicity. It is more pronounced in the gene coding regions and has been exploited to identify the segments of a genome that code for a protein. The reason for this three base periodicity in the gene-coding region has been attributed to inhomogeneous nucleotide compositions in the three codon positions. However, this reason cannot explain the three base periodicity present at the level of the whole genome where the codon concept is not applicable. Even though the distribution of each nucleotide is uniform at the positions 0(mod 3), 1(mod 3) and 2(mod 3) when the whole genome data is considered, our analysis reveals t... Biosystems journals http://www.medworm.com/rss/comments.php?id=5439863 Sat, 12 Nov 2011 05:00:00 +0100 5439863 http://www.medworm.com/index.php?rid=5439864&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100872%26dopt%3DAbstract We present a single non-cellular finite automaton model first shown to exhibit self-organizing behavior with intermittency and criticality, through a self-referential process. We propose a method to make self-referential contradiction a dynamic process of interaction with the selves in first person and third person description. The process represents thinking as inner dialogue with the self in second person. The dynamic effect of the rewrite shows characters proper to internal measurement, disequilibration by equilibration and transfer of inconsistency to the neighborhood by local resolution of the inconsistency. As the result, the advent of contradiction is postponed by the rewrite. The duality of internal measurement subject prevents inner dialogue in second person from lapsing into mono... Biosystems journals http://www.medworm.com/rss/comments.php?id=5439864 Thu, 10 Nov 2011 05:00:00 +0100 5439864 http://www.medworm.com/index.php?rid=5439862&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22101250%26dopt%3DAbstract Authors: Kandhavelu M, Lihavainen E, Muthukrishnan AB, Yli-Harja O, Ribeiro AS Abstract In vitro studies show that the transcriptional dynamics in Escherichia coli is sensitive to Mg(2+) concentration in the cell. We study in vivo how Mg(2+) affects the production of RNA molecules under the control of the lar promoter, P(lar), a lac promoter variant. The target RNA codes for RFP followed by 96 MS2d-GFP binding sites, allowing in vivo detection of individual RNA molecules following transcription. As Mg(2+) concentration is increased, transcripts' production first increases, but then decreases. Results were confirmed by qPCR and gel assay. Analysis of cell to cell diversity in RNA production shows that the variance of RNA numbers changes with Mg(2+). Gel assay confirms changes in the... Biosystems journals http://www.medworm.com/rss/comments.php?id=5439862 Wed, 09 Nov 2011 05:00:00 +0100 5439862 http://www.medworm.com/index.php?rid=5419314&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22056808%26dopt%3DAbstract Authors: Sciarrino A, Sorba P Abstract Imposing a minimum principle in the framework of the so-called crystal basis model of the genetic code, we determine the structure of the minimum set of anticodons which allows the translational-transcription for animal mitochondrial code. The results are in very good agreement with the observed anticodons. PMID: 22056808 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=5419314 Tue, 25 Oct 2011 04:00:00 +0100 5419314 http://www.medworm.com/index.php?rid=5379484&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22024451%26dopt%3DAbstract Authors: Flynn CM, Hunt KA, Gralnick JA, Srienc F Abstract A stoichiometric model describing the central metabolism of Shewanella oneidensis MR-1 wild-type and derivative strains was developed and used in elementary mode analysis (EMA). Shewanella oneidensis MR-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. The metabolic model presented here was adapted and verified by comparing the growth phenotypes of 13 single- and 1 double-knockout strains, while considering respiration via aerobic, anaerobic fumarate, and anaerobic metal reduction (Mtr) pathways, and utilizing acetate, n-acetylglucosamine... Biosystems journals http://www.medworm.com/rss/comments.php?id=5379484 Mon, 17 Oct 2011 04:00:00 +0100 5379484 http://www.medworm.com/index.php?rid=5379486&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22019848%26dopt%3DAbstract Authors: Takahashi H, Sakurai T, Sakai H, Bakkum DJ, Suzurikawa J, Kanzaki R Abstract Individual neurons are heterogeneous and have profound impact on population activity in a complex cortical network. Precise experimental control of the firing of multiple neurons would be therefore beneficial to advance our understanding of cell-network interactions. Except for direct intracellular stimulation, however, it is difficult to gain precise control of targeted neurons without inducing antidromic activation of untargeted neurons. To overcome this problem, we attempt to create a sparse group of photosensitized neurons via transfection of Channelrhodopsin-2 (ChR2) in primary dissociated cultures and then deliver light-addressed stimulation exclusively to these target neurons. We first show... Biosystems journals http://www.medworm.com/rss/comments.php?id=5379486 Fri, 14 Oct 2011 04:00:00 +0100 5379486 http://www.medworm.com/index.php?rid=5379485&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22020107%26dopt%3DAbstract Authors: Shakarian P, Roos P, Johnson A Abstract Evolutionary graph theory (EGT), studies the ability of a mutant gene to overtake a finite structured population. In this review, we describe the original framework for EGT and the major work that has followed it. This review looks at the calculation of the "fixation probability" - the probability of a mutant taking over a population and focuses on game-theoretic applications. We look at varying topics such as alternate evolutionary dynamics, time to fixation, special topological cases, and game theoretic results. Throughout the review, we examine several interesting open problems that warrant further research. PMID: 22020107 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=5379485 Wed, 12 Oct 2011 04:00:00 +0100 5379485 http://www.medworm.com/index.php?rid=5344572&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22008408%26dopt%3DAbstract Authors: Zhong W, Kokubo S, Tanimoto J Abstract Cooperation in the prisoner's dilemma (PD) played on various networks has been explained by so-called network reciprocity. Most of the previous studies presumed that players can offer either cooperation (C) or defection (D). This discrete strategy seems unrealistic in the real world, since actual provisions might not be discrete, but rather continuous. This paper studies the differences between continuous and discrete strategies in two aspects under the condition that the payoff function of the former is a linear interpolation of the payoff matrix of the latter. The first part of this paper proves theoretically that for two-player games, continuous and discrete strategies have different equilibria and game dynamics in a well-mixed but... Biosystems journals http://www.medworm.com/rss/comments.php?id=5344572 Wed, 12 Oct 2011 04:00:00 +0100 5344572 http://www.medworm.com/index.php?rid=5344573&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22001523%26dopt%3DAbstract Authors: Saha AA, Craddock TJ, Tuszynski JA Abstract This paper considers the possibility of stochastic resonance (SR) in tubulin dimers. A formula for the signal-to-noise ratio (SNR) of tubulin as a function of temperature is derived. The effective potential experienced by a delocalized electron in such a dimer is postulated to be a symmetric bimodal well. Inter-well and intra-well motions are described by Kramers rate theory and the Langevin formalism respectively. The frequency-dependent expression for the SNR shows that the response of the electron-tubulin dimer system is enhanced by ambient dipolar oscillations in specific frequency regimes. This is a characteristic of SR. Biophysical implications of this property such as the relevance to 8.085MHz microtubule resonance and the... Biosystems journals http://www.medworm.com/rss/comments.php?id=5344573 Fri, 07 Oct 2011 04:00:00 +0100 5344573 http://www.medworm.com/index.php?rid=5296475&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21963775%26dopt%3DAbstract This article analyzes the general problem of how the dynamical coupling between internal control (brain), body and environment is used in the generation of specific behaviors. Based on the Evolutionary Robotics (ER) paradigm, four computational models are described to support discussions including descriptions on performance after a series of structural, sensorimotor or mutational perturbations, or are developed in the absence of them. Experimental results suggest that 'dynamic determinacy' - i.e. the continuous presence of a unique dynamical attractor that must be chased during functional behaviors - is a common dynamic phenomenon in the analyzed robust and adaptive agents. These agents show dynamical states that are definitely and unequivocally characterized via transient dynamics toward... Biosystems journals http://www.medworm.com/rss/comments.php?id=5296475 Sat, 24 Sep 2011 04:00:00 +0100 5296475 http://www.medworm.com/index.php?rid=5278819&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945426%26dopt%3DAbstract Authors: Nowshiravan Rahatabad F, Jafari AH, Fallah A, Razjouyan J Abstract The aim of this paper is to create a model for mapping the surface electromyogram (EMG) signals to the force that generated by human arm muscles. Because the parameters of each person's muscle are individual, the model of the muscle must have two characteristics: (1) The model must be adjustable for each subject. (2) The relationship between the input and output of model must be affected by the force-length and the force-velocity behaviors are proven through Hill's experiments. Hill's model is a kinematic mechanistic model with three elements, i.e. one contractile component and two nonlinear spring elements. In this research, fuzzy systems are applied to improve the muscle model. The advantages of using fuz... Biosystems journals http://www.medworm.com/rss/comments.php?id=5278819 Sat, 17 Sep 2011 04:00:00 +0100 5278819 http://www.medworm.com/index.php?rid=5278818&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945744%26dopt%3DAbstract Authors: Shah K, Krishnamachari A Abstract Computational prediction of the origin of replication is a challenging problem and of immense interest to biologists. Several methods have been proposed for identifying the replicon site for various classes of organisms. However, these methods have limited applicability since the replication mechanism is different in different organisms. We propose a correlation measure and show that it is correctly able to predict the origin of replication in most of the bacterial genomes. When applied to Methanocaldococcus jannaschii, Plasmodium falciparum apicoplast and Nicotiana tabacum plastid, this correlation based method is able to correctly predict the origin of replication whereas the generally used GC skew measure fails. Thus, this correlation b... Biosystems journals http://www.medworm.com/rss/comments.php?id=5278818 Sat, 17 Sep 2011 04:00:00 +0100 5278818 http://www.medworm.com/index.php?rid=5218761&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21906654%26dopt%3DAbstract Authors: Musso F, Feverati G Abstract We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing machines. The use of Turing machines allows for very simple mechanisms of code growth and code activation/inactivation through point mutations. To any value of the point mutation probability corresponds a maximum amount of active code that can be maintained by selection and the Turing machines that reach it are said to be at the error threshold. Simulations with our model show that the Turing machines population evolve toward the error threshold. Mathematical descriptions of the model point out that this behaviour is due more to the mutation-selection dynamics than to the intrinsic nature of the Turing machines. This indicates that this result i... Biosystems journals http://www.medworm.com/rss/comments.php?id=5218761 Wed, 31 Aug 2011 04:00:00 +0100 5218761 http://www.medworm.com/index.php?rid=5175091&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21872639%26dopt%3DAbstract In this study, we developed a co-culture method of stem cell-derived neuronal networks and CNS networks and observed spontaneous activity in the co-culture samples. By using a microfabricated poly(dimethylsiloxane) device having two culture compartments and 20 connecting microconduits, we are able to compartmentalize P19-derived neurons and mouse cortical neurons and connect them via the microconduits. Furthermore, we combined the co-culture device and a microelectrode array (MEA)-based recording system and recorded spontaneous activity in the co-cultured networks. We found that periodic synchronized bursting spreading over both neuronal networks occurred during the second week in vitro and that P19-derived neurons in the co-cultured networks had different developmental processes compared ... Biosystems journals http://www.medworm.com/rss/comments.php?id=5175091 Sun, 21 Aug 2011 23:00:00 +0100 5175091 http://www.medworm.com/index.php?rid=5175094&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21871947%26dopt%3DAbstract Authors: Nacher JC, Ryabov VB Abstract The widespread use of microarrays provided a first glimpse at some simple laws and organizing principles that govern the transcriptome. Previous analyses have shown that the transcriptional organization is very heterogeneous and characterized by a power-law decay for gene expression levels. Moreover, a simple law was unveiled suggesting that gene expression dynamic changes under stress are proportional to their initial expression values. However, to elucidate and assess the underlying governing principles of transcriptional organization, we do not only need to identify them, but also provide theoretical models that are able to faithfully capture and reproduce them. Here we present a method to investigate the gene expression dynamics inspired b... Biosystems journals http://www.medworm.com/rss/comments.php?id=5175094 Thu, 18 Aug 2011 23:00:00 +0100 5175094 http://www.medworm.com/index.php?rid=5097839&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21784125%26dopt%3DAbstract Authors: Fernández JD, Vico FJ Biological molecular motors are nanoscale devices capable of transforming chemical energy into mechanical work, which are being researched in many scientific disciplines. From a computational point of view, the characteristics and dynamics of these motors are studied at multiple time scales, ranging from very detailed and complex molecular dynamics simulations spanning a few microseconds, to extremely simple and coarse-grained theoretical models of their working cycles. However, this research is performed only in the (relatively few) instances known from molecular biology. In this work, results from elastic network analysis and behaviour-finding methods are applied to explore a subset of the configuration space of template molecular structures that are a... Biosystems journals http://www.medworm.com/rss/comments.php?id=5097839 Sun, 17 Jul 2011 23:00:00 +0100 5097839 http://www.medworm.com/index.php?rid=5097840&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21777653%26dopt%3DAbstract Authors: Gong Y, Hao Y, Lin X, Wang L, Ma X Toxins such as tetraethylammonium (TEA) and tetrodotoxin (TTX) may reduce the number of working potassium and sodium ion channels by poisoning and making them blocked, respectively. In this paper, we study how channel blocking (CB) affects the time delay-induced multiple coherence resonance (MCR), i.e., a phenomenon that the spiking of neuronal networks intermittently reaches the most ordered state, in stochastic Hodgkin-Huxley neuron networks. It is found that potassium and sodium CB have distinct effects. For potassium CB, the MCR occurs more frequently as the CB develops, but for sodium CB the MCR is badly impaired and only the first coherence resonance (CR) holds and, consequently, the MCR evolves into a single CR as sodium CB develops. W... Biosystems journals http://www.medworm.com/rss/comments.php?id=5097840 Wed, 13 Jul 2011 23:00:00 +0100 5097840 http://www.medworm.com/index.php?rid=5051797&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763747%26dopt%3DAbstract Authors: Garay J, Móri TF We introduce an evolutionary game in which envy and charity can be considered as a consequence of Darwinian competition, i.e. individuals aim at increasing their own proportion rather than their absolute contribution to the next generation, and other-regarding-preference is a "method" for that. If the damage is additive and its cost is low, an envious strategy defeats a neutral strategy (rational strategy maximizing its own income). If damage is multiplicative, then coexistence of neutral and envious strategists is possible. Envy is a conditional spiteful strategy, thus in envious groups there is less damage than in spiteful groups, so envy decreases the total cost of spiteful competition. Although envy can be selected out in a mixed population of envious, ne... Biosystems journals http://www.medworm.com/rss/comments.php?id=5051797 Thu, 07 Jul 2011 23:00:00 +0100 5051797 http://www.medworm.com/index.php?rid=5051798&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21745534%26dopt%3DAbstract Authors: Aita T, Husimi Y, Nishigaki K To measure the similarity or dissimilarity between two given biological sequences, several papers proposed metrics based on the "word-composition vector". The essence of these metrics is as follows. First, we count the appearance frequencies of all the K-tuple words throughout each of two given sequences. Then, the two given sequences are transformed into their respective word-composition vectors. Next, the distance metrics, for example the angle between the two vectors, are calculated. A significant issue is to determine the optimal word size K. With a mathematical model of mutational events (including substitutions, insertions, deletions and duplications) that occur in sequences, we analyzed how the angle between the composition vectors depends ... Biosystems journals http://www.medworm.com/rss/comments.php?id=5051798 Thu, 30 Jun 2011 23:00:00 +0100 5051798 http://www.medworm.com/index.php?rid=5006590&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21729737%26dopt%3DAbstract Authors: Kulasiri D, He Y, Samarasinghe S After a very brief introduction to a mechanistic and statistical theory of molecular fluctuations in chemical reactions developed by Joel Keizer, we explore the robustness of a circadian rhythm model by using the theory and the exact stochastic simulation (ESS). The comparative study shows that the theory reflects the effects of the dynamics of the model on the robustness more than ESS does. Even though the theory is a macroscopic one, the robustness of the model compares well with that computed from the ESS when the system size is larger than 50. The robustness increases nonlinearly with the system size and it reaches an asymptotic value at higher system sizes. As we can expect from the dynamics of the system, the robustness is minimum near th... Biosystems journals http://www.medworm.com/rss/comments.php?id=5006590 Fri, 24 Jun 2011 23:00:00 +0100 5006590 http://www.medworm.com/index.php?rid=5006508&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21729738%26dopt%3DAbstract Authors: Lee JH, Lee SH, Chung WH, Lee ES, Park TH, Deaton R, Zhang BT Recent results of corpus-based linguistics demonstrate that context-appropriate sentences can be generated by a stochastic constraint satisfaction process. Exploiting the similarity of constraint satisfaction and DNA self-assembly, we explore a DNA assembly model of sentence generation. The words and phrases in a language corpus are encoded as DNA molecules to build a language model of the corpus. Given a seed word, the new sentences are constructed by a parallel DNA assembly process based on the probability distribution of the word and phrase molecules. Here, we present our DNA code word design and report on successful demonstration of their feasibility in wet DNA experiments of a small scale. PMID: 21729738 [P... Biosystems journals http://www.medworm.com/rss/comments.php?id=5006508 Fri, 24 Jun 2011 23:00:00 +0100 5006508 http://www.medworm.com/index.php?rid=4959257&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21683757%26dopt%3DAbstract Authors: Pan Z, Yamaguchi R, Doi S The electrical excitation (action potential generation) of sinoatrial node (cardiac pacemaker) cells is directly related to various ion channels (pore-forming proteins) in cell membranes. In order to analyze the relation between action potential generation and ion channels, we use the Yanagihara-Noma-Irisawa (YNI) model of sinoatrial node cells, which is described by the Hodgkin-Huxley-type equations with seven variables. In this paper, we analyze the global bifurcation structure of the YNI model by varying various conductances of ion channels, and examine the effects of these conductance changes on pacemaker rhythm (frequency of action potential generation). The coupling effect on pacemaker rhythm is also examined approximately by applying external c... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959257 Sun, 12 Jun 2011 23:00:00 +0100 4959257 http://www.medworm.com/index.php?rid=4959258&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21683119%26dopt%3DAbstract Authors: Khrennikov A We propose a model of quantum-like (QL) processing of mental information. This model is based on quantum information theory. However, in contrast to models of "quantum physical brain" reducing mental activity (at least at the highest level) to quantum physical phenomena in the brain, our model matches well with the basic neuronal paradigm of the cognitive science. QL information processing is based (surprisingly) on classical electromagnetic signals induced by joint activity of neurons. This novel approach to quantum information is based on representation of quantum mechanics as a version of classical signal theory which was recently elaborated by the author. The brain uses the QL representation (QLR) for working with abstract concepts; concrete images are describ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959258 Sat, 11 Jun 2011 23:00:00 +0100 4959258 http://www.medworm.com/index.php?rid=4959264&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21669250%26dopt%3DAbstract Authors: Seligmann H Genomic amino acid usages coevolve with cloverleaf formation capacities of corresponding primate mitochondrial tRNAs, also for antisense tRNAs, suggesting translational function for sense and antisense tRNAs. Some antisense tRNAs are antitermination tRNAs (anticodons match stops (UAR: UAA, UAG; AGR: AGA, AGG)). Genomes possessing antitermination tRNAs avoid corresponding stops in frames 0 and +1, preventing translational antitermination. In frame +2, AGR stop frequencies and corresponding antisense antitermination tRNAs coevolve positively. This suggests expression of frameshifted overlapping genes, potentially shortening genomes, increasing metabolic efficiency. Blast analyses of hypothetical proteins translated between one and seven +1, respectively, +2 frameshif... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959264 Sun, 05 Jun 2011 23:00:00 +0100 4959264 http://www.medworm.com/index.php?rid=4959263&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21672605%26dopt%3DAbstract Authors: Comte P, Vassiliev S, Houghten S, Bruce D The prediction of protein side-chain conformation is central for understanding protein functions. Side-chain packing is a sub-problem of protein folding and its computational complexity has been shown to be NP-hard. We investigated the capabilities of a hybrid (genetic algorithm/simulated annealing) technique for side-chain packing and for the generation of an ensemble of low energy side-chain conformations. Our method first relies on obtaining a near-optimal low energy protein conformation by optimizing its amino-acid side-chains. Upon convergence, the genetic algorithm is allowed to undergo forward and "backward" evolution by alternating selection pressures between minimal and higher energy setpoints. We show that this technique is v... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959263 Sun, 05 Jun 2011 23:00:00 +0100 4959263 http://www.medworm.com/index.php?rid=4959261&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21672606%26dopt%3DAbstract Authors: Su M, Hui C Although pathogens and predators have been widely used as bio-control agents against problematic prey species, little has been done to examine the prevalence and aggregation of pathogens in spatially structured eco-epidemiological systems. Here, we present a spatial model of a predator-prey/host-parasite system based on pair approximation and spatially stochastic simulations, with the predation pressure indicated by predator abundance and predation rates. Susceptible prey can not only be infected by contacting adjacent infected individuals but also by the global transmission of pathogens. The disease prevalence was found to follow a hump-shaped function in response to predation pressure. Moreover, predation pressure was not always negatively correlated with pathoge... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959261 Sun, 05 Jun 2011 23:00:00 +0100 4959261 http://www.medworm.com/index.php?rid=4959260&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21679746%26dopt%3DAbstract Authors: Cheon S, Liang F Recently, the stochastic approximation Monte Carlo algorithm has been proposed by Liang et al. (2007) as a general-purpose stochastic optimization and simulation algorithm. An annealing version of this algorithm was developed for real small protein folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding. The predicted protein structures are rather close to the true structures. PMID: 21679746 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4959260 Sun, 05 Jun 2011 23:00:00 +0100 4959260 http://www.medworm.com/index.php?rid=4959259&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21679747%26dopt%3DAbstract We present the results of extensive in silico simulation tests, which confirm the feasibility of our design. PMID: 21679747 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4959259 Sun, 05 Jun 2011 23:00:00 +0100 4959259 http://www.medworm.com/index.php?rid=4959265&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21664944%26dopt%3DAbstract Authors: Hoppe A, Richter C, Holzhütter HG PMID: 21664944 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4959265 Wed, 01 Jun 2011 23:00:00 +0100 4959265 http://www.medworm.com/index.php?rid=4959267&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21664228%26dopt%3DAbstract Authors: Noori HR Recent experimental studies strongly suggest the influence of glial purinergic transmission in the modulation of synaptic dynamics. By releasing adenosine triphosphate (ATP), which accumulates as adenosine, astrocytes tonically suppressed synaptic transmission. The delayed multi-step feedback of the glial ATP with the neuron suggests the existence of a discrete hysteresis phenomena. By integration of this hysteretic behavior into a delayed leaky integrate-and-fire model for the tripartite synapses, a significant sensitivity of the pre- and postsynaptic firing frequency patterns to the adenosine feedback-delays is observed that might be of importance for adenosine-related neurological deficits, such as sleep disorders. PMID: 21664228 [PubMed - as supplied by publis... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959267 Tue, 31 May 2011 23:00:00 +0100 4959267 http://www.medworm.com/index.php?rid=4959266&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21664229%26dopt%3DAbstract Monte Carlo simulation from proton slip to "coupled" proton flow in ATP synthase based on the bi-site mechanism. Biosystems. 2011 Jun 1; Authors: Qian J, Liang J ATP synthase couples proton flow to ATP synthesis, but is leaky to protons at very low nucleotide concentration. Based on the bi-site mechanism, we simulated the proton conduction from proton slip to "coupled" proton flow in ATP synthase using the Monte Carlo method. Good agreement is obtained between the simulated and available experimental results. Our model provides deeper insight into the nucleotide dependence of ATP catalysis, and the kinetic cooperativity in three catalysis subunits. The results of simulation support the bi-site mechanism in ATP synthesis. PMID: 21664229 [PubMed - as supplied by publisher] (S... Biosystems journals http://www.medworm.com/rss/comments.php?id=4959266 Tue, 31 May 2011 23:00:00 +0100 4959266 http://www.medworm.com/index.php?rid=4911261&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21645586%26dopt%3DAbstract Authors: Faust K, Croes D, van Helden J The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields groups of functionally related genes. In order to determine their biological function, associated gene groups are often projected onto known pathways or tested for enrichment of known functions. However, these approaches are not flexible enough to deal with variations or novel pathways. During the last decade, we developed and refined an approach that predicts metabolic pathways from a global metabolic network encompassing all known reactions and their substrates/products, by extracting a subgraph connecting at best a set of seed nodes (compounds, reactions, enzymes or enzyme-coding genes). In this review, we summarize this work, while discussing the... Biosystems journals http://www.medworm.com/rss/comments.php?id=4911261 Thu, 26 May 2011 23:00:00 +0100 4911261 http://www.medworm.com/index.php?rid=4911263&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21620930%26dopt%3DAbstract Authors: Watanabe S, Tero A, Takamatsu A, Nakagaki T Traffic optimization of railroad networks was considered using an algorithm that was biologically inspired by an amoeba-like organism, plasmodium of the true slime mold, Physarum polycephalum. The organism developed a transportation network consisting of a tubular structure to transport protoplasm. It was reported that plasmodium can find the shortest path interconnecting multiple food sites during an adaptation process (Nakagaki et al., 2001. Biophys. Chem. 92, 47-52). By mimicking the adaptation process a path-finding algorithm was developed by Tero et al. (2007). In this paper, the algorithm is newly modified for applications of traffic distribution optimization in transportation networks of infrastructure such as railroads under ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4911263 Wed, 18 May 2011 23:00:00 +0100 4911263 http://www.medworm.com/index.php?rid=4911262&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21620931%26dopt%3DAbstract Authors: Schuster S, de Figueiredo LF, Schroeter A, Kaleta C Elementary-mode analysis is a powerful method for detecting all potential pathways in a metabolic network and computing the associated molar yields. Metabolic pathways can be interpreted as different strategies of organisms. Thus, methods from Evolutionary Game Theory can be employed. In Flux Balance Analysis (FBA), it is usually assumed that molar yields of relevant products (such as biomass or ATP) have been maximized during evolution. This has been questioned on game-theoretical grounds. In particular, in situations that can be characterized as a Prisoner's Dilemma, maximization of flux is not in line with maximization of yield. Under other conditions (that is, for other parameter values of maximal velocities), a Harmony g... Biosystems journals http://www.medworm.com/rss/comments.php?id=4911262 Wed, 18 May 2011 23:00:00 +0100 4911262 http://www.medworm.com/index.php?rid=4911264&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21619911%26dopt%3DAbstract Authors: Kaleta C, de Figueiredo LF, Heiland I, Klamt S, Schuster S PMID: 21619911 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4911264 Tue, 17 May 2011 23:00:00 +0100 4911264 http://www.medworm.com/index.php?rid=4861089&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605622%26dopt%3DAbstract Authors: Jürchott K, Guo KT, Catchpole G, Feher K, Willmitzer L, Schichor C, Selbig J Gas chromatography-mass spectrometry (GC-MS) profiles were generated from U87 glioma cells and human mesenchymal stem cells (hMSC). 37 metabolites representing glycolysis intermediates, TCA cycle metabolites, amino acids and lipids were selected for a detailed analysis. The concentrations of these metabolites were compared and Pearson correlation coefficients were used to calculate the relationship between pairs of metabolites. Metabolite profiles and correlation patterns differ significantly between the two cell lines. These profiles can be considered as a signature of the underlying biochemical system and provide snap-shots of the metabolism in mesenchymal stem cells and tumor cells. PMID: 2160... Biosystems journals http://www.medworm.com/rss/comments.php?id=4861089 Fri, 13 May 2011 23:00:00 +0100 4861089 http://www.medworm.com/index.php?rid=4861090&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605621%26dopt%3DAbstract Authors: Ichikawa K Localized activation of proteins in a cell is crucial for the segregation of cellular functions leading, for example, to the development of polarized cells and chemotaxis. If there is a physical diffusion barrier, localized activation of proteins will emerge. In case of no physical barrier, however, it is not clear to what extent the protein activation is localized within a three dimensional intracellular space. In the previous report we showed a simulation result of localized activation of Ca(2+)/calmodulin-dependent kinase II (CaMKII) within a dendritic spine of a neuron, and this localization was enhanced by the diffusion of calmodulin. However, a dendritic spine will act as a physical diffusion barrier. Here, we report that the localization of activated proteins... Biosystems journals http://www.medworm.com/rss/comments.php?id=4861090 Thu, 12 May 2011 23:00:00 +0100 4861090 http://www.medworm.com/index.php?rid=4861091&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21600265%26dopt%3DAbstract Authors: Nakajima K, Haruna T In this paper, we propose a new class of cellular automata based on the modification of its state space. It is introduced to model a computation which is exposed to an environment. We formalized the computation as extension and projection processes of its state space and resulting misidentifications of the state. This is motivated to embed the role of an environment into the system itself, which naturally induces self-organized internal perturbations rather than the usual external perturbations. Implementing this structure into the elementary cellular automata, we characterized its effect by means of input entropy and power spectral analysis. As a result, the cellular automata with this structure showed robust class IV behavior and a 1/f power spectrum in ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4861091 Tue, 10 May 2011 23:00:00 +0100 4861091 http://www.medworm.com/index.php?rid=4861092&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21575673%26dopt%3DAbstract We present four case studies of visualizing data of diverse kind in biochemical networks on metabolic level by using Omix and the OVL scripting language. These worked examples demonstrate the power of OVL in conjunction with pleasing visualization, an important requirement for successful interdisciplinary communication in the interface between more experimental and more theoretical researchers. PMID: 21575673 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4861092 Fri, 06 May 2011 23:00:00 +0100 4861092 http://www.medworm.com/index.php?rid=4804748&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21550380%26dopt%3DAbstract Authors: Bozorgmehr JE One of the prevailing arguments in molecular evolution is that the duplicates of genes can acquire novel functionality. This is because only one of the paralogs need maintain the ancestral function, leaving room for natural experimentation due to a respite in purifying selection. Although many duplicates can subsequently become disabled by nullifying mutations, a few may also go on to diverge along a novel evolutionary trajectory. Here, evidence is provided that demonstrates how this scenario may not always be true. Rather, in the case of the highly conserved KPNA importin family, an initial relaxation in selection induced a frameshift that was later suppressed and heavily compensated for as part of a reparative and optimizing process. Despite a resulting diverge... Biosystems journals http://www.medworm.com/rss/comments.php?id=4804748 Wed, 27 Apr 2011 23:00:00 +0100 4804748 http://www.medworm.com/index.php?rid=4804750&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21536097%26dopt%3DAbstract Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes. Biosystems. 2011 Apr 22; Authors: Pey J, Theodoropoulos C, Rezola A, Rubio A, Cascante M, Planes FJ The elementary flux modes (EFMs) approach is an efficient computational tool to predict novel metabolic pathways. Elucidating the physiological relevance of EFMs in a particular cellular state is still an open challenge. Different methods have been presented to carry out this task. However, these methods typically use little experimental data, exploiting methodologies where an a priori optimization function is used to deal with the indetermination underlying metabolic networks. Available "omics" data represent an opportunity to refine current meth... Biosystems journals http://www.medworm.com/rss/comments.php?id=4804750 Thu, 21 Apr 2011 23:00:00 +0100 4804750 http://www.medworm.com/index.php?rid=4804749&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21540075%26dopt%3DAbstract Authors: Mwasa A, Tchuenche JM Cholera, an acute gastro-intestinal infection and a waterborne disease continues to emerge in developing countries. We formulate a mathematical model that captures some essential dynamics of cholera transmission to study the impact of public health educational campaigns, vaccination and treatment as control strategies in curtailing the disease. The education-induced, vaccination-induced and treatment-induced reproductive numbers R(E), R(V), R(T) respectively and the combined reproductive number R(C) are compared with the basic reproduction number R(0) to assess the possible community benefits of these control measures. A Lyapunov functional approach is also used to analyse the stability of the equilibrium points. We perform sensitivity analysis on the key... Biosystems journals http://www.medworm.com/rss/comments.php?id=4804749 Tue, 19 Apr 2011 23:00:00 +0100 4804749 http://www.medworm.com/index.php?rid=4804751&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21530610%26dopt%3DAbstract Authors: Adamatzky A, Alonso-Sanz R Plasmodium of a cellular slime mould Physarum polycephalum is a unique living substrate proved to be efficient in solving many computational problems with natural spatial parallelism. The plasmodium solves a problem represented by a configuration of source of nutrients by building an efficient foraging and intra-cellular transportation network. The transportation networks developed by the plasmodium are similar to transport networks built by social insects and simulated trails in multi-agent societies. In the paper we are attempting to answer the question "How close plasmodium of P. polycephalum approximates man-made motorway networks in Spain and Portugal, and what are the differences between existing motorway structure and plasmodium network of pro... Biosystems journals http://www.medworm.com/rss/comments.php?id=4804751 Sat, 16 Apr 2011 23:00:00 +0100 4804751 http://www.medworm.com/index.php?rid=4804752&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21524683%26dopt%3DAbstract Authors: Sualp M, Can T PMID: 21524683 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4804752 Fri, 15 Apr 2011 23:00:00 +0100 4804752 http://www.medworm.com/index.php?rid=4804753&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21511001%26dopt%3DAbstract Authors: Zhang H, Liu X DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA compu... Biosystems journals http://www.medworm.com/rss/comments.php?id=4804753 Mon, 11 Apr 2011 23:00:00 +0100 4804753 http://www.medworm.com/index.php?rid=4697867&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21477635%26dopt%3DAbstract Authors: Vourvouhaki E, Carvalho CS We study the correlation of the occurrence of coronary heart disease (CHD) with the presence of the single-nucleotide polymorphism (SNP) at the -308 position of the tumor necrosis factor alpha (TNF-α) gene. We also consider the inuence of the occurrence of type 2 diabetes (t2DM). Using Bayesian inference, we _rst pursue a bottom-up approach to compute the working hypothesis and the probabilities derivable from the data. We then pursue a top-down approach by modelling the signal pathway that causally connects the SNP with the emergence of CHD. We compute the functional form of the probability of CHD conditional on the presence of the SNP in terms of both the statistical and biochemical properties of the system. From the probability of occurrence of a... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697867 Mon, 04 Apr 2011 23:00:00 +0100 4697867 http://www.medworm.com/index.php?rid=4697868&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21466836%26dopt%3DAbstract This article provides discussions on this sort of coordination based on a mobile object-tracking task with situated, embodied and minimal agents, and tests for robust yet adaptive behaviour. The proposed scenario provides examples of behavioural mechanisms that counterbalance the functional organization of internal control activity and agents' situatedness to enable the evolution of a two-agent interaction task. Discussions in this article suggest that future studies of distributed cognition should take into account that there are at least two possible modes of interpreting distributed mechanisms and that these have a qualitatively different effect on behavioural robustness. PMID: 21466836 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4697868 Fri, 01 Apr 2011 23:00:00 +0100 4697868 http://www.medworm.com/index.php?rid=4697872&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21440033%26dopt%3DAbstract Authors: Takayanagi T Cell-mediated cytotoxicity assays are widely implemented to evaluate cell-mediated cytotoxic activity, and some assays are analyzed using the analogy of enzyme kinetics. In the analogy, the effector cell is regarded as the enzyme, the target cell as the substrate, the effector cell-target cell conjugate as the enzyme-substrate complex and the dead target cell as the product. However, the assumptions analogous to those of enzyme kinetics are not always true in cell-mediated cytotoxicity assays, and the parameter analogous to the Michaelis-Menten constant is not constant but is dependent on the number of effector cells. Therefore I present novel mathematical models for cell-mediated cytotoxicity assays without applying enzyme kinetics. I instead use combinations and... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697872 Wed, 30 Mar 2011 23:00:00 +0100 4697872 http://www.medworm.com/index.php?rid=4697871&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21440034%26dopt%3DAbstract This article offers a novel sequence-based approach to discriminate outer membrane proteins (OMPs). The first step is to use a new representation approach, factor analysis scales of generalized amino acid information (FASGAI) representing hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility and electronic properties, etc., to characterize sequences of OMPs and non-OMPs. The subsequent data is then transformed into a uniform matrix by the auto cross covariance (ACC). The second step is to develop discrimination predictors of OMPs from non-OMPs using a support vector machine (SVM). The SVM predictors thus successfully produce a high Matthews correlation coefficient (MCC) of 0.916 on 208 OMPs from non-OMPs including 206 α-helical mem... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697871 Tue, 29 Mar 2011 23:00:00 +0100 4697871 http://www.medworm.com/index.php?rid=4697869&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21457751%26dopt%3DAbstract Authors: Wang W, Liu H, Li Z, Guo Z, Yang Y Investigating the likely success of epidemic invasion is important in the epidemic management and control. In the present study, the invasion of epidemic is initially introduced to a predator-prey system, both species of which are considered to be subject to the Allee effect. Mathematically, the invasion dynamics is described by three nonlinear diffusion-reaction equations and the spatial implicit and explicit models are designed. By means of extensive numerical simulations, the results of spatial implicit model show that the Allee effect has an opposite impact on the invasion criteria and local dynamics when that on the different species. As the intensity of the Allee effect increases, the domain of epidemic invasion reduces and the system d... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697869 Tue, 29 Mar 2011 23:00:00 +0100 4697869 http://www.medworm.com/index.php?rid=4697870&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21453748%26dopt%3DAbstract Authors: Alfieri R, Bartocci E, Merelli E, Milanesi L The cell cycle is a complex biological system frequently investigated from a mathematical perspective. In fact, over the past years a huge number of deterministic mathematical models describing the dynamics and the regulation of this process have been proposed. A crucial point concerning the cell cycle modeling is the combination of continuous and discrete dynamics in order to obtain results which are coherent with the biological context. To face with this problem we propose a novel approach to the mathematical modeling of biological processes based on the use of hybrid systems. This new methodology essentially consists in a model reduction (using the modified Prony's method) which allows to define the crucial features of the dynami... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697870 Mon, 28 Mar 2011 23:00:00 +0100 4697870 http://www.medworm.com/index.php?rid=4697873&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21439348%26dopt%3DAbstract Authors: Paprocki B, Szczepanski J There has been a growing interest in the estimation of information carried by a single neuron and multiple single units or population of neurons to specific stimuli. In this paper we analyze, inspired by article of Levy and Baxter (2002), the efficiency of a neuronal communication by considering dendrosomatic summation as a Shannon-type channel (1948) and by considering such uncertain synaptic transmission as part of the dendrosomatic computation. Specifically, we study Mutual Information between input and output signals for different types of neuronal network architectures by applying efficient entropy estimators. We analyze the influence of the following quantities affecting transmission abilities of neurons: synaptic failure, activation threshold, ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4697873 Wed, 23 Mar 2011 00:00:00 +0100 4697873 http://www.medworm.com/index.php?rid=4642129&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21396427%26dopt%3DAbstract Authors: Ramlan EI, Zauner KP Despite an exponential increase in computing power over the past decades, present information technology falls far short of expectations in areas such as cognitive systems and micro robotics. Organisms demonstrate that it is possible to implement information processing in a radically different way from what we have available in present technology, and that there are clear advantages from the perspective of power consumption, integration density, and real-time processing of ambiguous data. Accordingly, the question whether the current silicon substrate and associated computing paradigm is the most suitable approach to all types of computation has come to the fore. Macromolecular materials, so successfully employed by nature, possess uniquely promising prope... Biosystems journals http://www.medworm.com/rss/comments.php?id=4642129 Tue, 15 Mar 2011 00:00:00 +0100 4642129 http://www.medworm.com/index.php?rid=4642126&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21419191%26dopt%3DAbstract Authors: Samoilova OP, Ptushenko VV, Kuvykin IV, Kiselev SA, Ptushenko OS, Tikhonov AN In this work, using a PAM-fluorimetry technique, we have compared effects of plant adaptation to the light or dark conditions on the kinetics of chlorophyll a fluorescence yield in Tradecantia leaves of several species (T. albiflora, T. fluminensis, T. navicularis, and T. sillamontana), which represent plants of different ecotypes. Two fluorescence parameters were used to assess photosynthetic performance in vivo: non-photochemical quenching (NPQ) of chlorophyll fluorescence (q(NPQ)) determined by energy losses in the light-harvesting antenna of photosystem 2 (PS2), and PS2 operating efficiency (Φ(PSII)). Comparative study of light-induced changes in q(NPQ) and Φ(PSII) has demonstrated that shade-t... Biosystems journals http://www.medworm.com/rss/comments.php?id=4642126 Tue, 15 Mar 2011 00:00:00 +0100 4642126 http://www.medworm.com/index.php?rid=4580651&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21376778%26dopt%3DAbstract Authors: Ichinose G, Kobayashi M By assuming the random intensity of selection, the emergence of cooperation on a network is studied. We constructed an evolutionary model in which an individual plays the prisoner's dilemma game, and updates both its strategy and neighbor connections in response to its relative success in the game. The constant (strong or weak) and random intensities of selection are compared. The random intensities of selection are introduced to realize complex environmental effects on the fitness of each individual. Breaking the links on the network is realized according to fixed global parameters. We found that cooperative clusters emerged when cooperators unilaterally broke the link with defectors. The emergent networks under these conditions had a high clustering c... Biosystems journals http://www.medworm.com/rss/comments.php?id=4580651 Wed, 02 Mar 2011 00:00:00 +0100 4580651 http://www.medworm.com/index.php?rid=4580650&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21376779%26dopt%3DAbstract Authors: Zdravković S, Satarić MV Interaction between nucleotides at a same site belonging to different strands is studied. This interaction is modelled by a Morse potential which depends on two parameters. We study a relationship between the parameters characterizing AT and CG pairs. We show that certain circumstances, i.e. certain values of these parameters, bring about a negligible influence of inhomogeneity on the solitonic dynamics. PMID: 21376779 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4580650 Wed, 02 Mar 2011 00:00:00 +0100 4580650 http://www.medworm.com/index.php?rid=4580652&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21356270%26dopt%3DAbstract Authors: Ribeiro AS, Lloyd-Price J, Chowdhury S, Yli-Harja O Gene regulatory networks (GRNs) are parallel information processing systems, binding past events to future actions. Since cell types stably remain in restricted subsets of the possible states of the GRN, they are likely the dynamical attractors of the GRN. These attractors differ in which genes are active and in the amount of information propagating within the network. Using mutual information (I) as a measure of information propagation between genes in a GRN, modeled as finite-sized Random Boolean Networks (RBN), we study how the dynamical regime of the GRN affects I within attractors (I(A)). The spectra ofI(A) of individual RBNs are found to be scattered and diverse, and distributions ofI(A) of ensembles are non-trivial and... Biosystems journals http://www.medworm.com/rss/comments.php?id=4580652 Sat, 26 Feb 2011 00:00:00 +0100 4580652 http://www.medworm.com/index.php?rid=4525847&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21315797%26dopt%3DAbstract Authors: Klamt S, von Kamp A CellNetAnalyzer (CNA) is a MATLAB toolbox providing computational methods for studying structure and function of metabolic and cellular signaling networks. In order to allow non-experts to use these methods easily, CNA provides GUI-based interactive network maps as a means of parameter input and result visualization. However, with the availability of high-throughput data, there is a need to make CNA's functionality also accessible in batch mode for automatic data processing. Furthermore, as some algorithms of CNA are of general relevance for network analysis it would be desirable if they could be called as sub-routines by other applications. For this purpose, we developed an API (application programming interface) for CNA allowing users (i) to access the co... Biosystems journals http://www.medworm.com/rss/comments.php?id=4525847 Fri, 18 Feb 2011 00:00:00 +0100 4525847 http://www.medworm.com/index.php?rid=4525846&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21315798%26dopt%3DAbstract Authors: Kar TK, Batabyal A This paper focuses on the study of a nonlinear mathematical SIR epidemic model with a vaccination program. We have discussed the existence and the stability of both the disease free and endemic equilibrium. Vaccine induced reproduction number is determined and the impact of vaccination in reducing the vaccine induced reproduction number is discussed. Then to achieve control of the disease, a control problem is formulated and it is shown that an optimal control exists for our model. The optimality system is derived and solved numerically using the Runge-Kutta fourth order procedure. PMID: 21315798 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4525846 Fri, 18 Feb 2011 00:00:00 +0100 4525846 http://www.medworm.com/index.php?rid=4525848&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21315135%26dopt%3DAbstract Authors: Fernandez-Leon JA, Acosta GG, Mayosky MA Behavioural robustness at antibody and immune network level is discussed. The robustness of the immune response that drives an autonomous mobile robot is examined with two computational experiments in the autonomous mobile robots trajectory generation context in unknown environments. The immune response is met based on the immune network metaphor for different low-level behaviours coordination. These behaviours are activated when a robot sense the appropriate conditions in the environment in relation to the network current state. Results are obtained over a case study in computer simulation as well as in laboratory experiments with a Khepera II microrobot. In this work, we develop a set of tests where such an immune response is external... Biosystems journals http://www.medworm.com/rss/comments.php?id=4525848 Wed, 16 Feb 2011 00:00:00 +0100 4525848 http://www.medworm.com/index.php?rid=4471378&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21277348%26dopt%3DAbstract Authors: Leyton P, Zárate RA, Fuentes S, Paipa C, Gómez-Jeria JS, Leyton Y The effect of the aluminum oxide on the thermal synthesis of the glycine-glutamic acid (Gly-Glu-(Gly-Glu)(n) polymer is described. The thermal synthesis in the molten state was carried out in the absence and presence of the oxide. In both cases, the vibrational spectra showed characteristic group frequencies corresponding predominantly to a Gly-Glu-(Gly-Glu)(n) sequence in the polymeric structure. The theoretical spectral data support the experimental proposed Gly-Glu-(Gly-Glu)(n) sequence for the polymer. The SEM-EDX characterization of the solid phase involved in the thermal synthesis showed that the aluminum oxide participates as a site for nucleation and growth of the polymer, explaining the increase of 25... Biosystems journals http://www.medworm.com/rss/comments.php?id=4471378 Fri, 28 Jan 2011 00:00:00 +0100 4471378 http://www.medworm.com/index.php?rid=4404941&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21256918%26dopt%3DAbstract This article investigates the computational properties of gene regulatory networks defined in terms of the speed and the accuracy of the output of a gene network. It will be shown that there is no single optimal set of parameters, but instead, there is a trade-off between speed and accuracy. Using the trade-off it will also be shown how systems with various parameters can be ranked with respect to their computational efficiency. Numerical analysis suggests that the trade-off can be improved when the output gene is repressing itself, even though the accuracy or the speed of the auto-regulated system may be worse than the unregulated system. PMID: 21256918 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4404941 Thu, 20 Jan 2011 00:00:00 +0100 4404941 http://www.medworm.com/index.php?rid=4404940&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21256919%26dopt%3DAbstract Authors: Arhondakis S, Kossida S Using publicly available microarray data from the frontal cortex of 30 individuals, spanning the ages of 26 to 106 years old, we investigate the expression patterns of compositionally distinct genes during human brain aging. Our analyses revealed that at advance ages, GC-poor genes appear to be induced while GC-rich genes are repressed. Interestingly, investigations upon two different types of genes, named pivotal (permanently expressed genes) and non-pivotal (on-off regulated genes), revealed an induction of the GC-poor pivotal genes and a repression of the GC-richer non-pivotal genes at advanced ages. Summarizing, this study shows that genes with different compositional properties have opposite age-related expression patterns, suggesting an implicatio... Biosystems journals http://www.medworm.com/rss/comments.php?id=4404940 Thu, 20 Jan 2011 00:00:00 +0100 4404940 http://www.medworm.com/index.php?rid=4404942&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21238534%26dopt%3DAbstract Authors: Tian Y, Kasperski A, Chen L This work presents the first mathematical model of a bioprocess with product inhibition and impulse effect. To begin with, an exemplary mathematical bioprocess model with product inhibition and impulse effect is formulated. Then, according to the model, the analysis of bioprocess stability is presented. The article expresses the product oscillation period, which provides the precise feeding time frame for the regulator bioprocess to achieve an equivalent stable output as that of a bioprocess with impulse effect in the same production environment. Moreover, in this work, the optimization of the production process with respect to the tunable parameters is investigated, and analytical expressions of their optimal values are provided. Numerical simulati... Biosystems journals http://www.medworm.com/rss/comments.php?id=4404942 Fri, 14 Jan 2011 00:00:00 +0100 4404942 http://www.medworm.com/index.php?rid=4404944&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21237247%26dopt%3DAbstract Authors: Guo L, Liang T, Lu Z High-throughput sequencing is a powerful tool for discovering and profiling microRNAs (miRNAs) to gain further insights into their biogenesis and function. Due to shorter size, short RNAs from deep sequencing dataset are prone to map to multiple loci with an equal number of mismatches, especially among multicopy miRNA precursors and homologous miRNA genes. Systematic analysis of SOLiD sequencing dataset showed that 37.94% short RNAs could simultaneously map to more than one miRNA precursor, and more short RNAs were found to have multiple genomic loci. Improper selection from candidate loci might lose some mapping information, influence miRNA expression profile or even mislead to identify novel miRNAs. A comprehensive study indicated several potential featu... Biosystems journals http://www.medworm.com/rss/comments.php?id=4404944 Thu, 13 Jan 2011 00:00:00 +0100 4404944 http://www.medworm.com/index.php?rid=4404947&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21236313%26dopt%3DAbstract Authors: Bandeira de Melo EB, Araújo AF In social insects, the superposition of simple individual behavioral rules leads to the emergence of complex collective patterns and helps solve difficult problems inherent to surviving in hostile habitats. Modelling ant colony foraging reveals strategies arising from the insects' self-organization and helps develop of new computational strategies in order to solve complex problems. This paper presents advances in modelling ants' behavior when foraging in a confined and dynamic environment, based on experiments with the Argentine ant Linepithema humile in a relatively complex artificial network. We propose a model which overcomes the problem of stagnation observed in earlier models by taking into account additional biological aspects, by using n... Biosystems journals http://www.medworm.com/rss/comments.php?id=4404947 Wed, 12 Jan 2011 00:00:00 +0100 4404947 http://www.medworm.com/index.php?rid=4404950&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21232576%26dopt%3DAbstract Authors: Wang W, Li W, Li Z, Zhang H Spatiotemporal dynamics of a predator-prey system is considered under the assumption that the predator is sensitive to colored noise. Mathematically, the model consists of two coupled diffusion-reactions. By means of extensive numerical simulations, the complex invasion pattern formations of the system are identified. The results show that a geographical invasion emerges without regional persistence when the intensity of colored noise is small. Remarkably, as the noise intensity increases, the species spreads via a patchy invasion only when the system is affected by red noise. Meanwhile, the relationship between local stability and global invasion is also considered. The predator, which becomes extinct in the system without diffusion, could invade l... Biosystems journals http://www.medworm.com/rss/comments.php?id=4404950 Tue, 11 Jan 2011 00:00:00 +0100 4404950 http://www.medworm.com/index.php?rid=4338541&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21219964%26dopt%3DAbstract Authors: Nikoloski Z, Grimbs S, Klie S, Selbig J Integration of high-throughput data with functional annotation by graph-theoretic methods has been postulated as promising way to unravel the function of unan- notated genes. Here, we first review the existing graph-theoretic approaches for automated gene function annotation and classify them into two categories with re- spect to their relation to two instances of transductive learning on networks-with dynamic costs and with constant costs-depending on whether or not ontological relationship between functional terms is employed. The determined categories al- low to characterize the computational complexity of the existing approaches and establish the relation to classical graph-theoretic problems, such as bisection and multiway cut. In a... Biosystems journals http://www.medworm.com/rss/comments.php?id=4338541 Fri, 07 Jan 2011 00:00:00 +0100 4338541 http://www.medworm.com/index.php?rid=4338540&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21219965%26dopt%3DAbstract Authors: Okosun KO, Makinde OD We derived and analyzed rigorously a mathematical model that describes the dynamics of malaria infection with the recruitment of infected immigrants, treatment of infectives and spray of insecticides against mosquitoes in the population. Both qualitative and quantitative analysis of the deterministic model are performed with respect to stability of the disease free and endemic equilibria. It is found that in the absence of infected immigrants disease-free equilibrium is achievable and is locally asymptotically stable. Using Pontryagins Maximum Principle, the optimal strategies for disease control is established. Finally, numerical simulations are performed to illustrate the analytical results. PMID: 21219965 [PubMed - as supplied by publisher] (Source... Biosystems journals http://www.medworm.com/rss/comments.php?id=4338540 Fri, 07 Jan 2011 00:00:00 +0100 4338540 http://www.medworm.com/index.php?rid=4338539&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21219966%26dopt%3DAbstract Authors: Fogel GB, Fogel DB The behaviors of individuals and species are often explained in terms of evolutionary stable strategies (ESSs). The analysis of ESSs determines which, if any, combinations of behaviors cannot be invaded by alternative strategies. Two assumptions required to generate an ESS (i.e., an infinite population and payoffs described only on the average) do not hold under natural conditions. Previous experiments indicated that under more realistic conditions of finite populations and stochastic payoffs, populations may evolve in trajectories that are unrelated to an ESS, even in very simple games. The simulations offered here extend earlier research by employing truncation selection with random parental selection in a hawk-dove game. Payoffs are determined in pairwise... Biosystems journals http://www.medworm.com/rss/comments.php?id=4338539 Fri, 07 Jan 2011 00:00:00 +0100 4338539 http://www.medworm.com/index.php?rid=4338542&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21216278%26dopt%3DAbstract In this study, a comparative analysis of the synonymous codon usage in the hypervariable region of theVP2 (vVP2) gene of the vvIBDV strains was done on viruses serially passaged in chicken embryos. Sequencing demonstrated that codons change during the serial passage in the vVP2 gene of the viruses. Nine codon mutations resulted in amino acids changes. The amino acid changes were I256V, I296L in isolate XA1989, A222P, I242V, Q253H, I256V in isolate XA1998, and Q253H, I256V, I296L in isolate XA2004. Three of the nine amino acid changes occurred at residue 256. The codons of the amino acids A232, N233, I234, T269, T283 and H338 changed to the synonymous codons in XA1989 after the 16th passage, in XA1998 after the 24th passage and in XA2004 22nd passage viruses. These mutations change the key ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4338542 Thu, 06 Jan 2011 00:00:00 +0100 4338542 http://www.medworm.com/index.php?rid=4338543&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21215790%26dopt%3DAbstract In conclusion, we propose that IPT1, GDA1, CSG and AUR1 gene deletions may be novel candidates of drug targets for cancer therapy according to the results of flux balance and variability analyses coupled with robustness analysis. PMID: 21215790 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4338543 Wed, 05 Jan 2011 00:00:00 +0100 4338543 http://www.medworm.com/index.php?rid=4338544&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21195740%26dopt%3DAbstract Discussion. PMID: 21195740 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4338544 Fri, 31 Dec 2010 00:00:00 +0100 4338544 http://www.medworm.com/index.php?rid=4338545&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21195126%26dopt%3DAbstract Authors: Goldstein BN, Aksirov AM, Zakrjevskaya DT Our simple kinetic model, based on the classic "binding change mechanism", describes the stepping kinetics for the rotary enzyme motors. The model shows that the cooperative interactions between active sites in the motor enzyme F1-ATPase induce the stepping product release. This phenomenon results from non-harmonic oscillations in the enzyme forms. The found rate constants, corresponding to the stepping phenomenon, are close to the rate constants known for the F1-ATPase. The duration of dwells during the product release is shown to depend on the ATP concentration in accordance with the known experimental data. PMID: 21195126 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4338545 Thu, 30 Dec 2010 00:00:00 +0100 4338545 http://www.medworm.com/index.php?rid=4277019&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21168470%26dopt%3DAbstract Authors: Dawy Z, Yaacoub E, Nassar M, Abdallah R, Zeineddine HA The primary goal of this article is to infer genetic interactions based on gene expression data. A new method for multiorganism Bayesian gene network estimation is presented based on multitask learning. When the input datasets are sparse, as is the case in microarray gene expression data, it becomes difficult to separate random correlations from true correlations that would lead to actual edges when modeling the gene interactions as a Bayesian network. Multitask learning takes advantage of the similarity between related tasks, in order to construct a more accurate model of the underlying relationships represented by the Bayesian networks. The proposed method is tested on synthetic data to illustrate its validity. Then it i... Biosystems journals http://www.medworm.com/rss/comments.php?id=4277019 Thu, 16 Dec 2010 00:00:00 +0100 4277019 http://www.medworm.com/index.php?rid=4277055&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21167904%26dopt%3DAbstract Authors: Ogawa KI, Miyake Y Many conventional models have used the positional information hypothesis to explain each elementary process of morphogenesis during the development of multicellular organisms. Their models assume that the steady concentration patterns of morphogens formed in an extracellular environment have an important property of positional information, so-called "robustness". However, recent experiments reported that a steady morphogen pattern, the concentration gradient of the Bicoid protein, during early Drosophila embryonic development is not robust for embryo-to-embryo variavility. These reports encourage a reconsideration of a long-standing problem in systematic cell differentiation: what is the entity of positional information for cells? And, what is the origin of ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4277055 Wed, 15 Dec 2010 00:00:00 +0100 4277055 http://www.medworm.com/index.php?rid=4277082&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21167250%26dopt%3DAbstract Authors: Saito S, Narikiyo O The long-time dynamics of somatic adaptability in immune system is simulated by a simple physical model defined in the shape space. The immune system described by the model exhibits a scale free behavior as is observed in living systems. The balance between the positive and negative feedbacks of the model leads to a robust immune system where the positive one corresponds to the formation of memory cells and the negative one to immunosuppression. Also the immunosenescence of the system is discussed based on the time-dependence of the epigenetic landscape of the adaptive immune cells in the shape space. PMID: 21167250 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4277082 Tue, 14 Dec 2010 00:00:00 +0100 4277082 http://www.medworm.com/index.php?rid=4277116&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21146581%26dopt%3DAbstract Authors: Buiu C, Arsene O, Cipu C, Patrascu M A P system represents a distributed and parallel bio-inspired computing model in which basic data structures are multi-sets or strings. Numerical P systems have been recently introduced and they use numerical variables and local programs (or evolution rules), usually in a deterministic way. They may find interesting applications in areas such as computational biology, process control or robotics. The first simulator of numerical P systems (SNUPS) has been designed, implemented and made available to the scientific community by the authors of this paper. SNUPS allows a wide range of applications, from modeling and simulation of ordinary differential equations, to the use of membrane systems as computational blocks of cognitive architectures, ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4277116 Thu, 09 Dec 2010 00:00:00 +0100 4277116 http://www.medworm.com/index.php?rid=4277153&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21145369%26dopt%3DAbstract Authors: Pérès S, Vallée F, Beurton-Aimar M, Mazat JP Elementary flux mode analysis is a powerful tool for the theoretical study of metabolic networks. However, when the networks are complex, the determination of elementary flux modes leads to combinatorial explosion of their number which prevents from drawing simple conclusions from their analysis. To deal with this problem we have developed a method based on the Agglomeration of Common Motifs (ACoM) for classifying elementary flux modes. We applied this algorithm to describe the decomposition into elementary flux modes of the central carbon metabolism in Bacillus subtilis and of the yeast mitochondrial energy metabolism. ACoM helps to give biological meaning to the different elementary flux modes and to the relatedness between rea... Biosystems journals http://www.medworm.com/rss/comments.php?id=4277153 Wed, 08 Dec 2010 00:00:00 +0100 4277153 http://www.medworm.com/index.php?rid=4277180&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21144882%26dopt%3DAbstract Authors: Vilaça P, Rocha I, Rocha M BACKGROUND AND SCOPE: Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events. IMPLEMENTATION AND PERFORMANCES: This work proposes a novel software tool that implements methods for the phenotype simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aim... Biosystems journals http://www.medworm.com/rss/comments.php?id=4277180 Tue, 07 Dec 2010 00:00:00 +0100 4277180 http://www.medworm.com/index.php?rid=4218887&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21095218%26dopt%3DAbstract Authors: Lee AJ, Lin MC, Hsu CM Many methods have been proposed for mining protein complexes from a protein-protein interaction network; however, most of them focus on unweighted networks and cannot find overlapping protein complexes. Since one protein may serve different roles within different functional groups, mining overlapping protein complexes in a weighted protein-protein interaction network has attracted more and more attention recently. In this paper, we propose an effective method, called MDOS (Mining Dense Overlapping Subgraphs), for mining dense overlaping protein complexes (subgraphs) in a weighted protein-protein interaction network. The proposed method can integrate the information about known complexes into a weighted protein-protein interaction network to improve the m... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218887 Sat, 20 Nov 2010 00:00:00 +0100 4218887 http://www.medworm.com/index.php?rid=4218886&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21095219%26dopt%3DAbstract Authors: Iwamoto K, Hamada H, Eguchi Y, Okamoto M After DNA damage, cells activate p53, a tumor suppressor gene, and select a cell fate (e.g., DNA repair, cell cycle arrest, or apoptosis). Recently, a p53 oscillatory behavior was observed following DNA damage. However, the relationship between this p53 oscillation and cell-fate selection is unclear. Here, we present a novel model of the DNA damage signaling pathway that includes p53 and whole cell cycle regulation and explore the relationship between p53 oscillation and cell fate selection. The simulation run without DNA damage qualitatively realized experimentally observed data from several cell cycle regulators, indicating that our model was biologically appropriate. Moreover, the comprehensive sensitivity analysis for the proposed m... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218886 Sat, 20 Nov 2010 00:00:00 +0100 4218886 http://www.medworm.com/index.php?rid=4218892&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093534%26dopt%3DAbstract Authors: Igamberdiev AU PMID: 21093534 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4218892 Thu, 18 Nov 2010 00:00:00 +0100 4218892 http://www.medworm.com/index.php?rid=4218891&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093535%26dopt%3DAbstract Authors: Farazdaghi H Photosynthesis is the origin of oxygenic life on the planet, and its models are the core of all models of plant biology, agriculture, environmental quality and global climate change. A theory is presented here, based on single process biochemical reactions of Rubisco, recognizing that: In the light, Rubisco activase helps separate Rubisco from the stored ribulose-1,5-bisphosphate (RuBP), activates Rubisco with carbamylation and addition of Mg(2+), and then produces two products, in two steps: (Step 1) Reaction of Rubisco with RuBP produces a Rubisco-enediol complex, which is the carboxylase-oxygenase enzyme (Enco) and (Step 2) Enco captures CO(2) and/or O(2) and produces intermediate products leading to production and release of 3-phosphoglycerate (PGA) and Rubisc... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218891 Thu, 18 Nov 2010 00:00:00 +0100 4218891 http://www.medworm.com/index.php?rid=4218889&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093537%26dopt%3DAbstract Authors: Lemon G, Howard D, Rose FR, King JR This paper presents a simulation modelling framework to study the growth of blood vessels and cells through a porous tissue engineering scaffold. The model simulates the migration of capillaries and the formation of a vascular network through a single pore of a tissue engineering scaffold when it is embedded in living tissue. The model also describes how the flow of blood through the network changes as growth proceeds. Results are given for how the different strategies of seeding the pore with cells affects the extent of vascularisation. Also simulations are made to compare results where the values of different model parameters are varied such as the pore dimensions, the density of endothelial cells seeded into the pore, and the release rate... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218889 Thu, 18 Nov 2010 00:00:00 +0100 4218889 http://www.medworm.com/index.php?rid=4218888&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093538%26dopt%3DAbstract Authors: Bier M, Cao FJ Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the amount of free energy that ATP hydrolysis makes available. This indicates that backsteps are not simply the forward stepping cycle run backwards. We propose here a simple effective model that consistently includes the backstep transition. Using this model, we show how more backstepping increases the entropy of the final state, and probably also the activation state, thus reducing their free energy. This free energy reduction of the activation state (related to backstepping) speeds up the catalytic cycle of the kinesin, making bo... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218888 Thu, 18 Nov 2010 00:00:00 +0100 4218888 http://www.medworm.com/index.php?rid=4218890&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093536%26dopt%3DAbstract Authors: Yang HM, Macoris MD, Galvani KC, Andrighetti MT The dengue virus is a vector-borne disease transmitted by mosquito Aedes aegypti and the incidence is strongly influenced by temperature and humidity which vary seasonally. To assess the effects of temperature on dengue transmission, mathematical models are developed based on the population dynamics theory. However, depending on the hypotheses of the modelling, different outcomes regarding to the risk of epidemics are obtained. We address this question comparing two simple models supplied with model's parameters estimated from temperature-controlled experiments, especially the entomological parameters regarded to the mosquito's life cycle in different temperatures. Once obtained the mortality and transition rates of different sta... Biosystems journals http://www.medworm.com/rss/comments.php?id=4218890 Wed, 17 Nov 2010 00:00:00 +0100 4218890 http://www.medworm.com/index.php?rid=4185825&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21078361%26dopt%3DAbstract Authors: Kihara K, Mori K, Suzuki S, Hosoda K, Yamada A, Matsuyama SI, Kashiwagi A, Yomo T Predator-prey interactions have been found at all levels within ecosystems. Despite their ecological ubiquity and importance, the process of transition to a stable coexistent state has been poorly verified experimentally. To investigate the stabilization process of predator-prey interactions, we previously constructed a reproducible experimental predator-prey system between Dictyostelium discoideum and Escherichia coli, and showed that the phenotypically changed E. coli contributed to stabilization of the system. In the present study, we focused on the transition to stable coexistence of both species after the phenotypic change in E. coli. Analysis of E. coli cells isolated from co-culture plates... Biosystems journals http://www.medworm.com/rss/comments.php?id=4185825 Fri, 12 Nov 2010 00:00:00 +0100 4185825 http://www.medworm.com/index.php?rid=4185824&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21078362%26dopt%3DAbstract Authors: Namiki S, Kanzaki R We investigated a population activity of central olfactory neurons after termination of odor input. Olfactory response of projection neurons in the moth primary olfactory center was characterized using in vivo intracellular recording and staining techniques. The population activity changed rapidly to the different state after the stimulus offset. The response after stimulus offset represents information regarding odor identity. We analyzed the spatial distribution of offset-activated glomeruli in a virtual neuronal population that was reconstructed using accumulated individual recordings obtained from different specimens. The offset-activated glomeruli tended to be widely distributed, whereas the onset-activated glomeruli were relatively clustered. These re... Biosystems journals http://www.medworm.com/rss/comments.php?id=4185824 Fri, 12 Nov 2010 00:00:00 +0100 4185824 http://www.medworm.com/index.php?rid=4185823&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21078363%26dopt%3DAbstract COMPUTATIONAL ANALYSIS OF THE OSCILLATORY DYNAMICS IN THE PROCESSES OF CO(2) ASSIMILATION AND PHOTORESPIRATION. Biosystems. 2010 Nov 12; Authors: Dubinsky AY, Ivlev AA The computational analysis of the model system consisting of the processes of CO(2) assimilation and photorespiration shows the appearance of sustained oscillations in the system which might reflect their presence in photosynthesizing cells. Concentrations of CO(2) and O(2) oscillate in opposite phases causing Rubisco switching continuously between the carboxylase (CO(2) assimilation) and the oxygenase (photorespiration) reactions. The results of modeling are consistent with carbon isotopic and other observed data. They show that the oscillation period varies from about 1s to 3s depending on the values of paramet... Biosystems journals http://www.medworm.com/rss/comments.php?id=4185823 Fri, 12 Nov 2010 00:00:00 +0100 4185823 http://www.medworm.com/index.php?rid=4185826&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21075168%26dopt%3DAbstract Authors: Grimbs S, Arnold A, Koseska A, Kurths J, Selbig J, Nikoloski Z The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationari... Biosystems journals http://www.medworm.com/rss/comments.php?id=4185826 Thu, 11 Nov 2010 00:00:00 +0100 4185826 http://www.medworm.com/index.php?rid=4185827&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21073914%26dopt%3DAbstract We report on the first phase implementation of the tool new version and demonstrate the functionalities of model visualization, presentation of model components, rate constants, initial conditions and of model annotation. The demonstration also includes export of a model to the Systems Biology Mark-Up Language format and remote numerical simulation of the model. PMID: 21073914 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4185827 Tue, 09 Nov 2010 00:00:00 +0100 4185827 http://www.medworm.com/index.php?rid=4166865&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21070830%26dopt%3DAbstract Authors: Vredenberg W In this paper the model and simulation of primary photochemical and photo-electrochemical reactions in dark-adapted intact plant leaves is presented. A descriptive algorithm has been derived from analyses of variable chlorophyll a fluorescence and P700 oxidation kinetics upon excitation with multi-turnover pulses (MTFs) of variable intensity and duration. These analyses have led to definition and formulation of rate equations that describe the sequence of primary linear electron transfer (LET) steps in photosystem II (PSII) and of cyclic electron transport (CET) in PSI. The model considers heterogeneity in PSII reaction centers (RCs) associated with the S-states of the OEC and incorporates in a dark-adapted state the presence of a 15 to 35% fraction of Q(B) -nonre... Biosystems journals http://www.medworm.com/rss/comments.php?id=4166865 Mon, 08 Nov 2010 00:00:00 +0100 4166865 http://www.medworm.com/index.php?rid=4166864&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21070831%26dopt%3DAbstract Authors: Tsuda S, Jones J The regeneration process of contractile oscillation in the plasmodium of Physarum polycephalum is investigated experimentally and modelled computationally. When placed in a well, the Physarum cell restructures the body (fusion of small granule-like cells) and shows various complex oscillation patterns. After it completed the restructuring and regained synchronized oscillation within the body, the cell shows bilateral oscillation or rotating wave pattern. This regeneration process did not depend on the well size and all the cases tested here showed similar time course. Phase synchronization analysis based on Hilbert Transform also suggested that the cell can develop a fully synchronized oscillation within a fixed time no matter what the cell size is. A particle... Biosystems journals http://www.medworm.com/rss/comments.php?id=4166864 Mon, 08 Nov 2010 00:00:00 +0100 4166864 http://www.medworm.com/index.php?rid=4166863&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21070832%26dopt%3DAbstract We present Rhodobase, a web-based meta-analytical tool for analysis of transcriptional regulation in a model anoxygenic photosynthetic bacterium, Rhodobacter sphaeroides. The gene association meta-analysis is based on the pooled data from 100 of R. sphaeroides whole-genome DNA microarrays. Gene-centric regulatory networks were visualized using the StarNet approach (PLoS ONE. 2008, 3:e1717) with several modifications. We developed a means to identify and visualize operons and superoperons. We designed a framework for the cross-genome search for transcription factor binding sites that takes into account high GC-content and oligonucleotide usage profile characteristic of the R. sphaeroides genome. To facilitate reconstruction of directional relationships between co-regulated genes, we screen... Biosystems journals http://www.medworm.com/rss/comments.php?id=4166863 Mon, 08 Nov 2010 00:00:00 +0100 4166863 http://www.medworm.com/index.php?rid=4166867&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21055440%26dopt%3DAbstract Authors: Herrmann-Pillath C, Salthe SN Many problems in evolutionary theory are cast in dyadic terms, such as the polar oppositions of organism and environment. We argue that a triadic conceptual structure offers an alternative perspective under which the information generating role of evolution as a physical process can be analyzed, and propose a new diagrammatic approach. Peirce's natural philosophy was deeply influenced by his reception of both Darwin's theory and thermodynamics. Thus, we elaborate on a new synthesis which puts together his theory of signs and modern Maximum Entropy approaches to evolution in a process discourse. Following recent contributions to the naturalization of Peircean semiosis, pointing towards 'physiosemiosis' or 'pansemiosis', we show that triadic structu... Biosystems journals http://www.medworm.com/rss/comments.php?id=4166867 Tue, 02 Nov 2010 00:00:00 +0100 4166867 http://www.medworm.com/index.php?rid=4166866&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21055441%26dopt%3DAbstract Authors: Keerberg O, Ivanova H, Keerberg H, Pärnik T, Talts P, Gardeström P Rates of carbon fluxes and pool sizes of photosynthetic metabolites in different cellular compartments of barley protoplasts were calculated from the time curves of their labeling in the medium of (14)CO(2). Using membrane filtration procedure, kinetics of (14)C incorporation into the products of steady-state photosynthesis was determined separately in chloroplasts, mitochondria and cytosol of barley protoplasts illuminated for different periods in the air containing (14)CO(2). To extract the quantitative information, analytical labeling functions P(t) describing the dependence of (14)C content in the primary, intermediate and end products of a linear reaction chain upon the duration of tracer feeding have be... Biosystems journals http://www.medworm.com/rss/comments.php?id=4166866 Tue, 02 Nov 2010 00:00:00 +0100 4166866 http://www.medworm.com/index.php?rid=4139693&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21035518%26dopt%3DAbstract Authors: Wakiyama M, Tanimoto J This paper numerically investigates 2×2 games involving the Prisoner's Dilemma, Chicken, Hero, Leader, Stag Hunt, and Trivial Games in which agents have a strategy expressed by five-bit, two-memory length. Our motivation is to explore how grouping for game interaction and strategy adaptation influence ST reciprocity and R reciprocity (Tanimoto and Sagara, 2007a [Tanimoto, J., Sagara, H., 2007a. A study on emergence of coordinated alternating reciprocity in a 2×2 game with 2-memory length strategy. Biosystems 90(3), 728-737]. Enhanced R reciprocity is observed with the stronger grouping for game interaction when a relatively stronger grouping for strategy adaptation is assumed. On the other hand, enhanced ST reciprocity emerged with the stronger groupin... Biosystems journals http://www.medworm.com/rss/comments.php?id=4139693 Thu, 28 Oct 2010 00:00:00 +0100 4139693 http://www.medworm.com/index.php?rid=4123708&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21029763%26dopt%3DAbstract Authors: Ebenhöh O, Houwaart T, Lokstein H, Schlede S, Tirok K Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependen... Biosystems journals http://www.medworm.com/rss/comments.php?id=4123708 Mon, 25 Oct 2010 00:00:00 +0100 4123708 http://www.medworm.com/index.php?rid=4107969&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20974211%26dopt%3DAbstract Authors: Yamasaki K, Nanjo KZ, Chiba S To quantify symmetry and entropy inherent in the discrete patterns such as spatial self-organization in cell sorting and mussel bed ecosystems, we introduce the discrete Walsh analysis. This analysis enables us to estimate the degree of the complicated symmetry, and to extract the symmetry from the pattern that seems to be the asymmetric. The results obtained in this paper are summarized as follows. (I) The geometrical patterns of the cell sorting become systematic with the predominance of the particular symmetry. This implies that not only the entropy but also the particular symmetry can decrease in the biological process. (II) The magnitude of the symmetry is related to the absolute value of the adhesion, and the type of the symmetry is related ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4107969 Thu, 21 Oct 2010 23:00:00 +0100 4107969 http://www.medworm.com/index.php?rid=4107970&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20970473%26dopt%3DAbstract Authors: Kunita I, Sakurazawa S, Honda H We observed a three-dimensional up-and-down movement of an actin filament sliding on heavy mero-myosin (HMM) molecules in an in vitro motility assay. The up-and-down movement occurred along the direction perpendicular to the planar glass plane on which the filament demonstrated a sliding movement. The height length of the up-and-down movement was measured by monitoring the extent of diminishing fluorescent emission from the marker attached to the filament in the evanescent field of attenuation. The height lengths whose distribution exhibits a local maximum were found around the two values, 150nm and 90nm, separately. This undulating three-dimensional movement of an actin filament suggests that the interactions between myosin (HMM) molecules and ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4107970 Tue, 19 Oct 2010 23:00:00 +0100 4107970 http://www.medworm.com/index.php?rid=4107971&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20969916%26dopt%3DAbstract Authors: Guo Y, Tan J A simple kinetic model structure for chlorophyll fluorescence (ChlF) from photosystem II (PSII) offers practical usefulness in quantitative analysis and extraction of information from measured ChlF. In this work, the major PSII phototransduction kinetics was represented with only five state variables. Parameters were estimated through a least-squares algorithm. The developed model structure could produce the well-known OJIP pattern and fit measured ChlF. Influences of PQ pool size, active Q(B) sites, and Q(A) reduction rate on ChlF emission were simulated and discussed in light of the existing literature. PMID: 20969916 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4107971 Mon, 18 Oct 2010 23:00:00 +0100 4107971 http://www.medworm.com/index.php?rid=4088473&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20955762%26dopt%3DAbstract Authors: Yamauchi A, Tanimoto J, Hagishima A Despite hundreds of studies on the Prisoner's Dilemma (PD) game, understanding about network reciprocity remains a unsolved puzzle. Thus, we performed a series of Full Factorial Design of Experiments (FFDOE) to evaluate what dominates emerging cooperation in the PD game on various networks. The results qualitatively reveal the influence of each factor and show that some combinations of factors have complicated interactions. Remarkably, the choice of strategy update rule or update dynamics is much more important than the type of network imposed or, at least, the factorial effect of the average degree of the network reported by Nowak (Science 314, 5805, 1560-1563, 2006) and Ohtsuki et al. (Nature 441, 502-505, 2006). Furthermore, the decision ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4088473 Thu, 14 Oct 2010 23:00:00 +0100 4088473 http://www.medworm.com/index.php?rid=4088475&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20951761%26dopt%3DAbstract Authors: Bruhn D, Mikkelsen TN, Herbst M, Kutsch WL, Ball MC, Pilegaard K To understand what governs the patterns of net ecosystem exchange of CO(2), an understanding of factors influencing the component fluxes, ecosystem respiration and gross primary production, is needed. In the present paper, we introduce an alternative method for estimating daytime ecosystem respiration based on whole ecosystem fluxes from a linear regression of photosynthetic photon flux density data vs. daytime net ecosystem exchange data at forest ecosystem level. This method is based on the principles of the Kok-method applied at leaf level for estimating daytime respiration. We demonstrate the method with field data and provide a discussion of the limitations of the method. PMID: 20951761 [PubMed - as supp... Biosystems journals http://www.medworm.com/rss/comments.php?id=4088475 Wed, 13 Oct 2010 23:00:00 +0100 4088475 http://www.medworm.com/index.php?rid=4088474&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20951762%26dopt%3DAbstract Authors: Belyaeva NE, Schmitt FJ, Paschenko VZ, Riznichenko GY, Rubin AB, Renger G Our recently presented PS II model (Belyaeva et al. 2008) was improved in order to permit a consistent simulation of Single Flash Induced Transient Fluorescence Yield (SFITFY) traces that were earlier measured by Steffen and coworkers (Steffen et al. 2005) on whole leaves of Arabidopsis (A.) thaliana at four different energies of the actinic flash. As the essential modification, the shape of the actinic flash was explicitly taken into account assuming that an exponentially decaying rate simulates the time dependent excitation of PS II by the 10ns actinic flash. The maximum amplitude of this excitation exceeds that of the measuring light by 9 orders of magnitude. A very good fit the of SFITFY data was ac... Biosystems journals http://www.medworm.com/rss/comments.php?id=4088474 Wed, 13 Oct 2010 23:00:00 +0100 4088474 http://www.medworm.com/index.php?rid=4088477&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20950669%26dopt%3DAbstract Authors: André MJ In closed systems, the O(2) compensation point (Γ(O)) was previously defined as the upper limit of O(2) level, at a given CO(2) level, above which plants cannot have positive carbon balance and survive. Studies with (18)O(2) measure the actual O(2) uptake by photorespiration due to the dual function of Rubisco, the enzyme that fixes CO(2) and takes O(2) as an alternative substrate. One-step modelling of CO(2) and O(2) uptakes allows calculating a plant specificity factor (Sp) as the sum of the biochemical specificity of Rubisco and a biophysical specificity, function of the resistance to CO(2) transfer from the atmosphere to Rubisco. The crossing points (Cx, Ox) are defined as CO(2) and O(2) concentrations for which O(2) and CO(2) uptakes are equal. It is observed t... Biosystems journals http://www.medworm.com/rss/comments.php?id=4088477 Mon, 11 Oct 2010 23:00:00 +0100 4088477 http://www.medworm.com/index.php?rid=4088476&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20950670%26dopt%3DAbstract Authors: André MJ The studies of Rubisco characteristics observed during plant evolution show that the variation of the Rubisco specificity factor only improved by two times from cyanobacteria to modern C3 plants. However we note important variations of the ratio between the maximum rates of oxygenation and carboxylation (V(O)/V(C)). Modelling in vivo(18)O(2) data in plant gas exchange shows that the oxygenation reaction of Rubisco plays a regulating role when the photochemical energy exceeds the carboxylation capacity. A protective index 'oxygenation capacity' is postulated, related to the ratio V(O)/V(C) of Rubisco, and hence to the sink energy effect of photorespiration. Analysing the trends of Rubisco parameters along the evolutionary scale, we show: (1) the increase of both V(C) ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4088476 Mon, 11 Oct 2010 23:00:00 +0100 4088476 http://www.medworm.com/index.php?rid=4062992&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20934483%26dopt%3DAbstract Authors: Kovalenko IB, Abaturova AM, Riznichenko GY, Rubin AB We designed 3D multiparticle computer models to simulate diffusion and interactions of spinach plastocyanin and ferredoxin with plant photosystem 1 in a solution. Using these models we studied kinetic characteristics of plastocyanin-photosystem 1 and ferredoxin-photosystem 1 complex formation at a variety of ionic strength values. The computer multiparticle models demonstrate non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Our calculations show that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the doc... Biosystems journals http://www.medworm.com/rss/comments.php?id=4062992 Wed, 06 Oct 2010 23:00:00 +0100 4062992 http://www.medworm.com/index.php?rid=4062991&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20934484%26dopt%3DAbstract Authors: Nicolis SC, Dussutour A A mathematical model of food recruitment and resource exploitation in group-living organisms accounting for direct traffic of individuals between the available sources is developed. It is shown that traffic between sources gives rise to the enhancement of the range of stability of the homogeneous mode of exploitation and of the range of coexistence of homogeneous and semiinhomogeneous ones, as well as the appear- ance of symmetry breaking transitions leading to fully inhomogeneous exploitation modes. PMID: 20934484 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=4062991 Wed, 06 Oct 2010 23:00:00 +0100 4062991 http://www.medworm.com/index.php?rid=4062990&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20934485%26dopt%3DAbstract Authors: Eberle C, Ament C Understanding the simultaneous interaction of the glucose and insulin homeostasis in realtime is very important for clinical treatment as well as for research issues. Until now only plasma glucose concentrations can be measured real-time. To support a secure, effective and rapid treatment e.g. of diabetes a real-time estimation of plasma insulin would be of great value. A novel approach using an Unscented Kalman Filter that provides an estimate of the current plasma insulin concentration is presented, which is operates on the measurement of the plasma glucose and Bergman's Minimal Model of the glucose insulin homeostasis. We can prove that process observability is obtained in this case. Hence, a successful estimator design is possible. Since the process is no... Biosystems journals http://www.medworm.com/rss/comments.php?id=4062990 Wed, 06 Oct 2010 23:00:00 +0100 4062990 http://www.medworm.com/index.php?rid=4062993&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20933572%26dopt%3DAbstract Authors: Igamberdiev AU, Kleczkowski LA Stable operation of photosynthesis is based on the establishment of local equilibria of metabolites in the Calvin cycle. This concerns especially equilibration of stromal contents of adenylates and pyridine nucleotides and buffering of CO(2) concentration to prevent its depletion at the sites of Rubisco. Thermodynamic buffering that controls the homeostatic flux in the Calvin cycle is achieved by equilibrium enzymes such as glyceraldehyde phosphate dehydrogenase, transaldolase and transketolase. Their role is to prevent depletion of ribulose-1,5-bisphosphate, even at high [CO(2)], and to maintain conditions where the only control is exerted by the CO(2) supply. Buffering of adenylates is achieved mainly by chloroplastic adenylate kinase, whereas ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4062993 Tue, 05 Oct 2010 23:00:00 +0100 4062993 http://www.medworm.com/index.php?rid=4062994&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20932875%26dopt%3DAbstract Authors: Fernandez-Leon JA In this work, based on behavioural and dynamical evidence, a study of simulated agents with the capacity to change feedback from their bodies to accomplish a one-legged walking task is proposed to understand the emergence of coupled dynamics for robust behaviour. Agents evolve with evolutionary-defined biases that modify incoming body signals (sensory offsets). Analyses on whether these agents show further dependence to their environmental coupled dynamics than others with no feedback control is described in this article. The ability to sustain behaviours is tested during lifetime experiments with mutational and sensory perturbations after evolution. Using dynamical systems analysis, this work identifies conditions for the emergence of dynamical mechanisms th... Biosystems journals http://www.medworm.com/rss/comments.php?id=4062994 Sun, 03 Oct 2010 23:00:00 +0100 4062994 http://www.medworm.com/index.php?rid=4043740&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20920549%26dopt%3DAbstract Authors: Jin Y, Meng Y The relationship between robustness and evolvability (easiness to evolve), and the evolutionary emergence of robust genetic circuits in biology have attracted much attention in systems biology. This paper investigates in silico the influence of the cis-regulation logic and the coupling of feedback loops on the evolvability and robustness of gene regulatory motifs that can generate sustained oscillation. Our simulation results indicate that both evolvability and robustness of the considered regulatory motifs depend on the cis-regulation logic and the way in which positive and negative feedback loops are coupled. Most interestingly, our findings suggest that robust regulatory motifs can emerge from evolution without an explicit selection pressure on robustness and ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4043740 Thu, 30 Sep 2010 23:00:00 +0100 4043740 http://www.medworm.com/index.php?rid=4043741&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20888889%26dopt%3DAbstract Authors: Marashi SA, Bockmayr A Genome-scale metabolic reconstructions are comprehensive, yet incomplete, models of real-world metabolic networks. While ux coupling analysis (FCA) has proved an appropriate method for analyzing metabolic relationships and for detecting functionally related reactions in such models, little is known about the impact of missing reactions on the accuracy of FCA. Based on an alternative characterization of ux coupling relations using elementary ux modes, this paper studies the changes that ux coupling relations may undergo due to missing reactions. In particular, we show that two uncoupled reactions in a metabolic network may be detected as directionally, partially or fully coupled in an incomplete version of the same network. Even a single missing reaction ... Biosystems journals http://www.medworm.com/rss/comments.php?id=4043741 Wed, 29 Sep 2010 23:00:00 +0100 4043741 http://www.medworm.com/index.php?rid=4004081&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851737%26dopt%3DAbstract We present a model-based method for estimating the effective concentration of the active drug applied by a pressure pulse to an individual cell in a patch-clamp setup, which could be of practical use in the analysis of ligand-induced whole-cell currents recorded in patch-clamp experiments. Our modelling results outline several important factors which may be involved in the high variability of the electric response of the cells, and indicate that with a pressure pulse duration of 1s and diameter of the perfusion tip of 600μm, elevated amounts of drug can accumulate locally between the pipette tip and the cell. Hence, the effective agonist concentration at the cell membrane level can be consistently higher than the initial concentration inside the perfusion tubes. We performed finite-diff... Biosystems journals http://www.medworm.com/rss/comments.php?id=4004081 Tue, 21 Sep 2010 23:00:00 +0100 4004081 http://www.medworm.com/index.php?rid=4003605&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20869424%26dopt%3DAbstract Authors: Mushayabasa S, Tchuenche JM, Bhunu CP, Ngarakana-Gwasira E A mathematical model was designed to explore the co-interaction of gonorrhea and HIV in the presence of antiretroviral therapy and gonorrhea treatment. Qualitative and comprehensive mathematical techniques have been used to analyse the model. The gonorrhea-only and HIV-only sub-models are first considered. Analytic expressions for the threshold parameter in each sub-model and the co-interaction model are derived. Global dynamics of this co-interaction shows that whenever the threshold parameter for the respective sub-models and co-interaction model is less than unity, the epidemics dies out, while the reverse results in persistence of the epidemics in the community. The impact of gonorrhea and its treatment on HIV dyna... Biosystems journals http://www.medworm.com/rss/comments.php?id=4003605 Tue, 21 Sep 2010 23:00:00 +0100 4003605 http://www.medworm.com/index.php?rid=4004028&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851738%26dopt%3DAbstract Authors: Gong Y, Xie Y, Lin X, Hao Y We have numerically studied the effect of a particular kind of non-Gaussian colored noise (NGN), characterized by the deviation q from Gaussian noise (q=1), on intracellular cytosolic calcium (Ca(2+)) oscillations. It is found that, as q is increased, the Ca(2+) oscillation regularity increases and reaches a best performance at an optimal q, and then decreases with further increasing q, which represents the occurrence of coherence resonance, i.e., the most regular Ca(2+) oscillations. Similar phenomena occur for different values of noise intensity and correlation time of the NGN. This phenomenon of deviation-optimized Ca(2+) oscillations show that, external non-Gaussian noises of different types can enhance and even optimize the intracellular Ca(2+)... Biosystems journals http://www.medworm.com/rss/comments.php?id=4004028 Mon, 20 Sep 2010 23:00:00 +0100 4004028 http://www.medworm.com/index.php?rid=4003970&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851739%26dopt%3DAbstract Authors: Hohm T, Zitzler E In the context of Systems Biology, computer simulations of gene regulatory networks provide a powerful tool to validate hypotheses and to explore possible system behaviors. Nevertheless, modeling a system poses some challenges of its own: especially the step of model calibration is often difficult due to insufficient data. For example when considering developmental systems, mostly qualitative data describing the developmental trajectory is available while common calibration techniques rely on high-resolution quantitative data. Focusing on the calibration of differential equation models for developmental systems, this study investigates different approaches to utilize the available data to overcome these difficulties. More specifically, the fact that developme... Biosystems journals http://www.medworm.com/rss/comments.php?id=4003970 Mon, 20 Sep 2010 23:00:00 +0100 4003970 http://www.medworm.com/index.php?rid=4004123&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851736%26dopt%3DAbstract Authors: Garay J I propose a hypothesis on the origin of chiral homogeneity of bio-molecules based on chiral catalysis. The first chiral active centre may have formed on the surface of complexes comprising metal ions, amino acids, other coenzymes and oligomers (short RNAs). The complexes must have been dominated by short RNAs capable of self-reproduction with ligation. Most of the first complexes may have catalysed the production of nucleotides. A basic assumption is that such complexes can be assembled from their components almost freely, in a huge variety of combinations. This assumption implies that "a few" components can constitute "a huge" number of active centre types. Moreover, an experiment is proposed to test the performance of such complexes in vitro. If the complexes were bu... Biosystems journals http://www.medworm.com/rss/comments.php?id=4004123 Sun, 19 Sep 2010 23:00:00 +0100 4004123 http://www.medworm.com/index.php?rid=4003906&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20858527%26dopt%3DAbstract Authors: Barbarossa MV, Kuttler C, Fekete A, Rothballer M The bacterial strain Pseudomonas putida IsoF, isolated from a tomato rhizosphere, possesses a quorum sensing regulation system, which allows the bacteria to recognise aspects of their environment or to communicate with each other by the so-called autoinducer molecules. In an experimental study, the time series of the autoinducer production did not show the expected behaviour, as it was observed for other bacterial species by indirect measurements. The modelling approach introduced here allows an explanation of the behaviour, supporting the hypothesis of the existence of a further (not yet detected) enzyme, which degrades the autoinducer into an inactive form. Especially the properties of the considered delay di_erential system a... Biosystems journals http://www.medworm.com/rss/comments.php?id=4003906 Fri, 17 Sep 2010 23:00:00 +0100 4003906 http://www.medworm.com/index.php?rid=4003835&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20858528%26dopt%3DAbstract Authors: Wallace R Tlusty's topological rate distortion analysis of the genetic code is applied to protein symmetries and protein folding rates. Unlike the genetic case, numerous thermodynamically accessible 'protein folding codes' can be identified from empirical classiffications. Folding rates follow from a topologicallydriven rate distortion argument, a model that can, in principle, be extended to intrinsically disordered proteins. The elaborate cellular regulatory machinery of the endoplasmic reticulum and heat shock proteins is needed to prevent transition between the various thermodynamically 'natural' sets of hydrophobic-core protein conformations, and its corrosion by aging would account for the subsequent onset of many protein folding disorders. These results imply markedly di... Biosystems journals http://www.medworm.com/rss/comments.php?id=4003835 Fri, 17 Sep 2010 23:00:00 +0100 4003835 http://www.medworm.com/index.php?rid=3973431&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20837095%26dopt%3DAbstract Authors: Pichierri F We perform a quantum mechanical study of the peptides that are part of the LH2 complex from Rhodopseudomonas acidophila, a non-sulfur purple bacteria that has the ability of producing chemical energy from photosynthesis. The electronic structure calculations indicate that the transmembrane helices of these peptides are characterized by dipole moments with a magnitude of about 150 D. When the full nonamer assembly made of eighteen peptides is considered, then a macrodipole of magnitude 806 D is built up from the vector sum of each monomer dipole. The macrodipole is oriented normal to the membrane plane and with the positive tip toward the cytoplasm thereby indicating that the electronic charge of the protein scaffold is polarized toward the periplasm. The results ob... Biosystems journals http://www.medworm.com/rss/comments.php?id=3973431 Thu, 09 Sep 2010 23:00:00 +0100 3973431 http://www.medworm.com/index.php?rid=3973430&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20837096%26dopt%3DAbstract Authors: Lobo D, Vico FJ The evolution of most novelties in animal form and function have long puzzled biologists. Studying the developmental process or the anatomical properties of an organism provide scarce information into the means by which its morphology evolved. Novelty is believed to be a product of the evolution of the gene regulation, rather than the emergence of new structural genes. In order to gain further insight into the evolution of novelty and diversity, we propose a simple computational model of gene regulation that controls the development of locomotive multicellular organisms through a fixed set of simple structural genes. Organisms, modeled as two-dimensional spring networks, are simulated in a virtual environment to evaluate their steering behavior, which feeds an ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3973430 Thu, 09 Sep 2010 23:00:00 +0100 3973430 http://www.medworm.com/index.php?rid=3973429&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20837097%26dopt%3DAbstract Authors: Pfeiffer T, Almenberg J Predictions markets are marketplaces for trading contracts with payoffs that depend on the outcome of future events. Popular examples are markets on the outcome of presidential elections, where contracts pay $1 if a specific candidate wins the election and $0 if someone else wins. Contract prices on prediction markets can be interpreted as forecasts regarding the outcome of future events. Further attractive properties include the potential to aggregate private information, to generate and disseminate a consensus among the market participants, and to offer incentives for the acquisition of information. It has been argued that these properties might be valuable in the context of scientific research. In this review, we give an overview of key properties of... Biosystems journals http://www.medworm.com/rss/comments.php?id=3973429 Thu, 09 Sep 2010 23:00:00 +0100 3973429 http://www.medworm.com/index.php?rid=3973428&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20837098%26dopt%3DAbstract Authors: Tschiersch H, Borisjuk L, Rutten T, Rolletschek H Seeds are generally viewed in the context of plant reproduction and the supply of food and feed, but only seldom as a site of photosynthesis. However, the seeds of many plant species are green, at least during their early development, which raises the issue of the significance of this greening for seed development. Here we describe the two contrasting modes of photosynthesis in the developing seed. The dicotyledonous pea seed has a green embryo, while the monocotyledonous barley caryopsis has a chlorenchymatic layer surrounding its non-green endosperm (storage organ). We have employed pulse-amplitude-modulated fluorescence and oxygen-sensitive microsensors to localize and describe gradient distributions of photosynthetic activi... Biosystems journals http://www.medworm.com/rss/comments.php?id=3973428 Thu, 09 Sep 2010 23:00:00 +0100 3973428 http://www.medworm.com/index.php?rid=3955164&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20826194%26dopt%3DAbstract Authors: Duggins AJ A model of consciousness is proposed, in which the experience attributable to a single sensory neuron is related to its instantaneous firing rate. In that this can only be quantified within statistical limits from the incidence of spikes across multiple presentations of a stimulus, consciousness remains inaccessible to direct measurement on a single trial. In this way, the model disambiguates subjective experience from objective neural properties. The model adopts a quantum mechanical formalism, in which the state of the neuron is represented as a vector in a complex vector space. PMID: 20826194 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3955164 Thu, 02 Sep 2010 23:00:00 +0100 3955164 http://www.medworm.com/index.php?rid=3955163&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20826195%26dopt%3DAbstract OVERVIEW: EARLY HISTORY OF CROP GROWTH AND PHOTOSYNTHESIS MODELING. Biosystems. 2010 Sep 3; Authors: El-Sharkawy MA As in industrial and engineering systems, there is a need to quantitatively study and analyze the many constituents of complex natural biological systems as well as agro-ecosystems via research-based mechanistic modeling. This objective is normally addressed by developing mathematically-built descriptions of multilevel biological processes to provide biologists a means to integrate quantitatively experimental research findings that might lead to a better understanding of the whole systems and their interactions with surrounding environments. Aided with the power of computational capacities associated with computer technology then available, pioneering cropping sys... Biosystems journals http://www.medworm.com/rss/comments.php?id=3955163 Thu, 02 Sep 2010 23:00:00 +0100 3955163 http://www.medworm.com/index.php?rid=3912160&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20739004%26dopt%3DAbstract Authors: Roussel MR, Igamberdiev AU We classify mathematical models that can be used to describe photosynthetic oscillations using ideas from nonlinear dynamics, and discuss potential mechanisms for photosynthetic oscillations in the context of this classification. We then turn our attention to recent experiments with leaves transferred to a low CO(2) atmosphere which revealed stochastic oscillations with a period of a few seconds. Rubisco is the enzyme that takes both CO(2) and O(2) as substrates correspondingly for photosynthetic assimilation and for photorespiration. Photosynthesis depletes CO(2) and produces O(2) while respiration and photorespiration work in the opposite direction, so the product of one process becomes the reactant of the other coupled process. We examine the poss... Biosystems journals http://www.medworm.com/rss/comments.php?id=3912160 Sat, 21 Aug 2010 23:00:00 +0100 3912160 http://www.medworm.com/index.php?rid=3912161&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20736046%26dopt%3DAbstract Authors: Vershubskii AV, Kuvykin IV, Priklonskii VI, Tikhonov AN In this work, we summarize results of computer simulation of electron and proton transport processes coupled to ATP synthesis in chloroplasts performed within the frames of a mathematical model developed as a system of differential equations for concentrations of electron carriers and hydrogen ion inside and outside the granal and stromal thylakoids. The model accounts topological peculiarities and lateral heterogeneity of the chloroplast lamellar system. This allowed us to analyze the influence of restricted diffusion of protons inside small compartments of a chloroplast (e.g., in the narrow inter-thylakoid gap) on electron transport processes. The model adequately describes two modes of pH-dependent feedback control of ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3912161 Fri, 20 Aug 2010 23:00:00 +0100 3912161 http://www.medworm.com/index.php?rid=3890794&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20723577%26dopt%3DAbstract Authors: Egri-Nagy A, Galliot B, Naef F, Nehaniv CL PMID: 20723577 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3890794 Sun, 15 Aug 2010 23:00:00 +0100 3890794 http://www.medworm.com/index.php?rid=3890795&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20708063%26dopt%3DAbstract This study shows that onset of type 1 diabetes is due to a collective, dynamical instability, rather than being caused by a single etiological factor. It is also a numbers game between regulatory T-cells and auto-reactive T-cells. The problem in the onset of this disease is that there are not enough of the regulatory cells that suppress the immune response against the body's insulin-producing pancreatic islet cells. PMID: 20708063 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3890795 Mon, 09 Aug 2010 23:00:00 +0100 3890795 http://www.medworm.com/index.php?rid=3872190&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20705115%26dopt%3DAbstract Authors: Tongra T, Mehta P, Mathur S, Agrawal D, Bharti S, Los DA, Allakhverdiev SI, Jajoo A Effects of change in pH have been investigated on spinach leaf discs by measuring fluorescence induction kinetics using Plant Efficiency Analyzer (PEA). On the basis of computational analysis of the results, we have reported that acidic pH causes a significant inhibition of the donor and the acceptor side of PS II. Energy flux models have been presented using the software Biolyzer HP 3. Effects of pH were investigated on the antenna size heterogeneity of PS II and a relative change in the proportions of alpha, beta, and gamma centers was observed. PMID: 20705115 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3872190 Sun, 08 Aug 2010 23:00:00 +0100 3872190 http://www.medworm.com/index.php?rid=3872189&cid=s_34542_70_f&fid=34542&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20705116%26dopt%3DAbstract Authors: Sadeghi S, Thompson M It is evident that complex animate materials, which operate far from equilibrium, exhibit sensory responses to the environment through emergent patterns. Formation of such patterns is often the underlying mechanism of an active response to environmental changes and can be interpreted as a result of the distributed parallel information processing taking place within the material. Such emergent patterns are not limited to biological entities; indeed there is a wide range of complex nonlinear dissipative systems which exhibit interesting emergent patterns within a range of parameters. As one example, the present paper describes the detection of emergent phenomena associated with surface electrochemical processes that allow the system to respond to input info... Biosystems journals http://www.medworm.com/rss/comments.php?id=3872189 Sun, 08 Aug 2010 23:00:00 +0100 3872189