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. Thu, 18 Mar 2010 16:29:47 +0100 http://www.medworm.com/index.php?rid=3372435&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%3D20226228%26dopt%3DAbstract In this study, we compare four alternative modeling approaches based on Michaelis-Menten kinetics for the bimolecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass-action, convenience kinetics, lin-log and power-law). Using the mechanistic model for E. coli central carbon metabolism as a benchmark, we investigate the alternative modeling approaches through comparative simulations analyses. The good dynamic behavior and the powerful predictive capabilities obtained using the hybrid model composed of Michaelis-Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large scale networks where the exact rate laws are unknown. PMID: 20226228 [PubMed - as supplied by publisher] ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3372435 Tue, 09 Mar 2010 00:00:00 +0100 3372435 http://www.medworm.com/index.php?rid=3354897&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%3D20211223%26dopt%3DAbstract Authors: Gregory R, Saunders VA, Saunders JR An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been employed to simulate interactions of virtual temperate bacteriophages (phages) and their bacterial hosts. Outcomes of infection mimic those of a phage such as lambda, which can enter either the lytic or lysogenic cycle, depending on the nutritional status of the host. Infection of different hosts possessing differing restriction and modification systems is also simulated. Phages restricted upon infection of one restricting host can be adapted (by host-controlled modification of the phage genome) and subsequently propagate with full effciency on this host. However, such ability is lost if the progeny phages are passaged through a new host with a dif... Biosystems journals http://www.medworm.com/rss/comments.php?id=3354897 Fri, 05 Mar 2010 00:00:00 +0100 3354897 http://www.medworm.com/index.php?rid=3354896&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%3D20211683%26dopt%3DAbstract Authors: Zhang X, Song X, Wang H MicroRNAs (miRNAs) are a class of small non-coding RNAs discovered in recent years, which are found to play important regulatory roles in various organisms. As the number of experimentally validated miRNAs is rapidly increasing, systematic analysis on the characteristics of these known miRNAs is necessary and indispensable, especially for computational prediction of new miRNAs. We extensively analyzed precursor sequences for all experimentally validated mature miRNAs in metazoan species, focusing on the characteristics at the level of primary sequences and secondary structures. An observation over the secondary structures of 2729 miRNA precursors (pre-miRNAs) reveals that these hairpin structures can be approximately classified into two types: one with ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3354896 Thu, 04 Mar 2010 00:00:00 +0100 3354896 http://www.medworm.com/index.php?rid=3347306&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%3D20206662%26dopt%3DAbstract Authors: Nacher JC, Araki N Recent studies have suggested that non coding RNA molecules (ncRNA) could play an important role in the regulatory architecture of eukaryotic cells. This new RNA-based regulation might indicate the existence of a hidden layer in the central dogma. In spite of its importance, the large-scale structure as well as the local interaction pattern of the ncRNA regulatory network has not been investigated. In this work, we collected regulatory interactions between ncRNA molecules and their regulated protein targets. We then constructed the ncRNA-protein interaction network corresponding to six model organisms, including H. sapiens. The large-scale network analysis of ncRNA-protein interactions revealed a high degree of similarity for the degree distribution to that ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3347306 Wed, 03 Mar 2010 00:00:00 +0100 3347306 http://www.medworm.com/index.php?rid=3347305&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%3D20206663%26dopt%3DAbstract Authors: Ioannou A, Fokianos K, Promponas VJ We compare several spectral domain based clustering methods for partitioning protein sequence data. The main instrument for this exercise is the spectral density ratio model, which specifies that the logarithmic ratio of two or more unknown spectral density functions has a parametric linear combination of cosines. Maximum likelihood inference is worked out in detail and it is shown that its output yields several distance measures among independent stationary time series. These similarity indices are suitable for clustering time series data based on their second order properties. Other spectral domain based distances are investigated as well; and we compare all methods and distances to the problem of producing segmentations of bacterial outer... Biosystems journals http://www.medworm.com/rss/comments.php?id=3347305 Wed, 03 Mar 2010 00:00:00 +0100 3347305 http://www.medworm.com/index.php?rid=3320559&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%3D20184939%26dopt%3DAbstract Authors: Niizato T, Gunji YP We usually think that there is a clear cut between known facts and unknown facts. In category theory, this can correspond to equivalence of categories for partial map and pointed set. If this relation is satisfied, we implicitly ignore the difference of "before encoding" and "after encoding". In this paper, we admit this discrepancy in the context of organizational endo-perspective, and make weak condition of equivalence of categories for partial map and pointed set to connect learning systems. PMID: 20184939 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3320559 Mon, 22 Feb 2010 00:00:00 +0100 3320559 http://www.medworm.com/index.php?rid=3312103&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%3D20178826%26dopt%3DAbstract Authors: Cifra M, Pokorný J, Havelka D, Kučera O Microtubules are electrically polar structures fulfilling prerequisites for generation of oscillatory electric field in the kHz-GHz region. Energy supply for excitation of elasto-electrical vibrations in microtubules may be provided from GTP-hydrolysis; motor protein-microtubule interactions; and energy efflux from mitochondria. We calculated electric field generated by axial longitudinal vibration modes of microtubules for random, and coherent excitation. In case of coherent excitation of vibrations, the electric field intensity is highest at the end of microtubule. The dielectrophoretic force exerted by electric field on the surrounding molecules will influence the kinetics of microtubule polymerization via change in the pro... Biosystems journals http://www.medworm.com/rss/comments.php?id=3312103 Sat, 20 Feb 2010 00:00:00 +0100 3312103 http://www.medworm.com/index.php?rid=3303178&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%3D20176076%26dopt%3DAbstract Authors: Mitterauer B Based on the formalism of logical balance, imbalances of information processing in tripartite synapses are described as a possible explanation for the pathophysiology of endogenous psychoses like depression, mania and schizophrenia. A tripartite synapse consists of the presynapse, the synaptic cleft, the postsynapse (neuronal components) and the glia (glial components). According to the logic of balance in a living system, the number of values and the number of variables must be equal. In a tripartite synapse the neuronal components are interpreted as values, the glial components as variables. In line with this novel synaptic model, three elementary synaptic imbalances can be deduced. First, tripartite synapses are underbalanced if the variables outnumber the valu... Biosystems journals http://www.medworm.com/rss/comments.php?id=3303178 Fri, 19 Feb 2010 00:00:00 +0100 3303178 http://www.medworm.com/index.php?rid=3303179&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%3D20170709%26dopt%3DAbstract In this study, we constructed a model of the organism and attempted to simulate its locomotion and morphogenetic behavior. By modifying our previous model, we were able to get closer to the actual behavior. We also compared the behavior of the model with that of the real organism, demonstrating remarkable similarity between the two. PMID: 20170709 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3303179 Tue, 16 Feb 2010 00:00:00 +0100 3303179 http://www.medworm.com/index.php?rid=3269955&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%3D20149838%26dopt%3DAbstract Authors: De Mey F, Schillebeeckx F, Vanderelst D, Boen A, Peremans H Echolocating bats perceive the world through sound signals reecting from the objects around them. In these signals, information is contained about reector location and reector identity. Bats are able to extract and separate the cues for location from those that carry identication information. We propose a model based on Wiener deconvolution that also performs this separation for a virtual system mimicking the echolocation system of the lesser spearnosed bat, Phyllostomus discolor. In particular, the model simultaneously reconstructs the reflected echo signal and localizes the reflector from which the echo originates. The proposed technique is based on a model that performs a similar task based on information from the ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3269955 Mon, 08 Feb 2010 00:00:00 +0100 3269955 http://www.medworm.com/index.php?rid=3269954&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%3D20149839%26dopt%3DAbstract Authors: Ozasa K, Aono M, Maeda M, Hara M To explore possible forms of unconventional computers that have high capacities for adaptation and exploration, we propose a new approach to developing a biocomputer based on the photophobic reactions of microbes (Euglena gracilis), and perform the Monte-Carlo simulation of Euglena-based neural network computing, involving virtual optical feedback to the Euglena cells. The photophobic reactions of Euglena are obtained experimentally, and incorporated in the simulation, together with a feedback algorithm with a modified Hopfield-Tank model for solving a 4-city traveling salesman problem. The simulation shows high performances in terms of (1) reaching one of the best solutions of the problem, and (2) searching for a number of solutions via dynami... Biosystems journals http://www.medworm.com/rss/comments.php?id=3269954 Mon, 08 Feb 2010 00:00:00 +0100 3269954 http://www.medworm.com/index.php?rid=3263167&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%3D20144684%26dopt%3DAbstract Authors: Bennun A Incubation with noradrenaline (norepinephrine) of isolated membranes of rat's brain corpus striatum and cortex, showed that ionic-magnesium (Mg(2+)) is required for the neurotransmitter activatory response of Adenylate Cyclase [ATP pyrophosphate-lyase (cyclizing), (EC 4.6.1.1)], AC. An Mg(2+)-dependent response to the activatory effects of adrenaline, and subsequent inhibition by calcium, suggest capability for a turnover, associated with cyclic changes in membrane potential and participation in a short term-memory pathway. In the cell, the neurotransmitter by activating AC generates intracellular cyclic AMP. Calcium entrance in the cell inhibits the enzyme. The increment of cyclic AMP activates kinaseA and their protein phosphorylating activity, allowing a long term ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3263167 Fri, 05 Feb 2010 00:00:00 +0100 3263167 http://www.medworm.com/index.php?rid=3248967&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%3D20132862%26dopt%3DAbstract Authors: Bókkon I, Dai J, Antal I A novel molecular hypothesis about visual perception and imagery has recently been proposed (Bókkon, 2009. BioSystems). This hypothesis states that external electromagnetic visible photons are converted into electrical signals in the retina and are then conveyed to V1. These retinotopic electrical signals (spike-related electrical signals along classical axonal-dendritic pathways) can be converted into synchronized bioluminescent photonic signals (inside the neurons) by neurocellular radical reactions (redox process) in retinotopically-organized V1 mitochondrial cytochrome oxidase-rich visual areas. The bioluminescent photonic signals (inside the neurons) generated by neurocellular redox/radical reactions in synchronized V1 neurons make it po... Biosystems journals http://www.medworm.com/rss/comments.php?id=3248967 Mon, 01 Feb 2010 00:00:00 +0100 3248967 http://www.medworm.com/index.php?rid=3213083&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%3D20097257%26dopt%3DAbstract Authors: Würtz P, Annila A Ecological succession is described by the 2(nd) law of thermodynamics. According to the universal law of the maximal energy dispersal, an ecosystem evolves toward a stationary state in its surroundings by consuming free energy via diverse mechanisms. Species are the mechanisms that conduct energy down along gradients between repositories of energy which consist of populations at various thermodynamic levels. The salient characteristics of succession, growing biomass production, increasing species richness and shifting distributions of species are found as consequences of the universal quest to diminish energy density differences in least time. The analysis reveals that during succession the ecosystem's energy transduction network, i.e., the food web orga... Biosystems journals http://www.medworm.com/rss/comments.php?id=3213083 Thu, 21 Jan 2010 00:00:00 +0100 3213083 http://www.medworm.com/index.php?rid=3213084&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%3D20096748%26dopt%3DAbstract MONITORING IN A PREDATOR-PREY SYSTEMS VIA A CLASS OF HIGH ORDER OBSERVER DESIGN. Biosystems. 2010 Jan 20; Authors: Mata-Machuca JL, Martínez-Guerra R, Aguilar-López R The goal of this work is the monitoring of the corresponding species in a class of predator-prey systems, this issue is important from the ecology point of view to analyze the population dynamics. The above is done via a nonlinear observer design which contains on its structure a high order polynomial form of the estimation error. A theoretical frame is provided in order to show the convergence characteristics of the proposed observer, where it can be concluded that the performance of the observer is improved as the order of the polynomial is high. The proposed methodology is applied to a class of Lotka-... Biosystems journals http://www.medworm.com/rss/comments.php?id=3213084 Wed, 20 Jan 2010 00:00:00 +0100 3213084 http://www.medworm.com/index.php?rid=3186420&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%3D20079398%26dopt%3DAbstract Authors: Molski MA The growth of biological systems described by the Gompertz and West-Brown-Enquist functions is considered in the framework of the space-like supersymmetric quantum mechanics. It has been shown that the supersymmetric effect of a fermion-boson conversion has a biological analogue in the phenomenon of a growth-regression transformation under the influence of a cycle-non-specific drug of a constant concentration. The results obtained reveal that the biological growth can be viewed as the macroscopic quantum phenomenon endowed with the space-like supersymmetric properties not established so far in the domain of biology and medicine. PMID: 20079398 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3186420 Tue, 12 Jan 2010 00:00:00 +0100 3186420 http://www.medworm.com/index.php?rid=3186419&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%3D20079399%26dopt%3DAbstract Authors: Azuaje F, Devaux Y, Wagner DR The network-based representation and analysis of biological systems contributes to a greater understanding of their structures and functions at different levels of complexity. These techniques can also be used to identify potential novel therapeutic targets based on the characterisation of vulnerable or highly-influential network components. There is a need to investigate methods for estimating the impact of molecular perturbations. The prediction of high-impact or critical targets can aid in the identification of novel strategies for controlling the level of activation of specific, therapeutically-relevant genes or proteins. Here, we report a new computational strategy for the analysis of the vulnerability of cellular signalling networks based on... Biosystems journals http://www.medworm.com/rss/comments.php?id=3186419 Tue, 12 Jan 2010 00:00:00 +0100 3186419 http://www.medworm.com/index.php?rid=3142152&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%3D20045444%26dopt%3DAbstract Authors: Debnath R, Kurita T Microarrays have thousands to tens-of-thousands of gene features, but only a few hundred patient samples are available. The fundamental problem in microarray data analysis is identifying genes whose disruption causes congenital or acquired disease in humans. In this paper, we propose a new evolutionary method that can efficiently select a subset of potentially informative genes for support vector machine (SVM) classifiers. The proposed method uses SVM with a given subset of gene features to evaluate the fitness function, and new subsets of features are selected based on the estimates of generalization error of SVMs and frequency of occurrence of the features in the evolutionary approach. Thus, in theory, selected genes reflect some extent of generalization ... Biosystems journals http://www.medworm.com/rss/comments.php?id=3142152 Wed, 30 Dec 2009 00:00:00 +0100 3142152 http://www.medworm.com/index.php?rid=3075831&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%3D19995591%26dopt%3DAbstract Authors: Sun GQ, Lili , Jin Z A spatial version of the predator-prey model with Holling III functional response, which includes some important factors such as external periodic forces, noise, and difiusion processes is investigated. For the model only with difiusion, it exhibits spiral waves in the two-dimensional space. However, combined with noise, it has the feature of chaotic patterns. Moreover, the oscillations become more obvious when the noise intensity is increased. Furthermore, the spatially extended system with external periodic forces and noise exhibits a resonant pattern and frequency-locking phenomena. These results may help us to understand the effects arising from the undeniable susceptibility to random fluctuations in the real ecosystems. PMID: 19995591 [PubMed - as... Biosystems journals http://www.medworm.com/rss/comments.php?id=3075831 Sat, 05 Dec 2009 00:00:00 +0100 3075831 http://www.medworm.com/index.php?rid=3075830&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%3D19995592%26dopt%3DAbstract Authors: Lima HW, Lee SH, Yang KA, Lee JY, Yoo SI, Park TH, Zhang BT Recent progress in molecular computation suggests the possibility of pattern classification in vitro. Weighted sum is a primitive operation required by many pattern classification problems. Here we present a DNA-based molecular computation method for implementing the weighted-sum operation and its use for molecular pattern classification in a test tube. The weights of the classifier are encoded as the mixing ratios of the differentially labeled probe DNA molecules, which are competitively hybridized with the input-encoding target molecules to compute the decision boundary of classification. The computation result is detected by fluorescence signals. We experimentally verify the underlying weight encoding scheme and de... Biosystems journals http://www.medworm.com/rss/comments.php?id=3075830 Sat, 05 Dec 2009 00:00:00 +0100 3075830 http://www.medworm.com/index.php?rid=3067510&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%3D19962421%26dopt%3DAbstract Authors: Acuña V, Marchetti-Spaccamela A, Sagot MF, Stougie L In the context of the study into elementary modes of metabolic networks, we prove two complexity results. Enumerating elementary modes containing a specific reaction is hard in an enumeration complexity sense. The decision problem if there exists an elementary mode containing two specific reactions is NP-complete. The complexity of enumerating all elementary modes remains open. PMID: 19962421 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3067510 Wed, 02 Dec 2009 00:00:00 +0100 3067510 http://www.medworm.com/index.php?rid=3067509&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%3D19962422%26dopt%3DAbstract Authors: Raimundo SM, Massad E, Yang HM The successful elimination of vectorial and transfusional transmission of Chagas' disease from some countries is a result of the reduction of domestic density of the primary vector T. infestans, of almost 100% of coverage in blood serological selection and to the fact that the basic reproductive number of Chagas' disease is very close to one (1.25). Therefore, congenital transmission is currently the only way of acquiring Chagas' Disease in such regions. In this paper we propose a model of congenital transmission of Chagas' disease. Its aim is to provide an estimation of the time period it will take to eliminate this form of transmission in regiouns where vetorial transmission was reduced to close to zero, like in Brazil. PMID: 19962422 [PubM... Biosystems journals http://www.medworm.com/rss/comments.php?id=3067509 Wed, 02 Dec 2009 00:00:00 +0100 3067509 http://www.medworm.com/index.php?rid=3067511&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%3D19961895%26dopt%3DAbstract Authors: Ma W, Yu C, Zhang W, Zhou P, Hu J A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the "RNA world", a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be "immediately" a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme wou... Biosystems journals http://www.medworm.com/rss/comments.php?id=3067511 Tue, 01 Dec 2009 00:00:00 +0100 3067511 http://www.medworm.com/index.php?rid=3000787&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%3D19917456%26dopt%3DAbstract Authors: Jin Y, Hallinan J PMID: 19917456 [PubMed - in process] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=3000787 Wed, 18 Nov 2009 11:48:07 +0100 3000787 http://www.medworm.com/index.php?rid=3000788&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%3D19909783%26dopt%3DAbstract Authors: Kim HB, Evans I, Smallwood R, Holcombe M, Qwarnstrom EE Activation of the transcription factor NF-kappaB is central to control of immune and inflammatory responses. Cytokine induced activation through the classical or canonical pathway relies on degradation of the inhibitor, IkappaBalpha and regulation by the IKKbeta kinase. In addition, the NF-kappaB is activated through the NF-kappaB-inducing kinase, NIK. Analysis of the IKK/NIK inter-relationship and its impact on NF-kappaB control, were analysed by mathematical modelling, using matrix formalism and stoichiometrically balanced reactions. The analysis considered a range of bio-reactions and core metabolites and their role in relation to kinase activation and in control of specific steps of the NF-kappaB pathway. The model pr... Biosystems journals http://www.medworm.com/rss/comments.php?id=3000788 Mon, 09 Nov 2009 00:00:00 +0100 3000788 http://www.medworm.com/index.php?rid=2960126&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%3D19883726%26dopt%3DAbstract This study, inspired by the discovery that preferential attachment rules computed by complex technological networks obey Bose-Einstein statistics, is the first rigorous attempt to examine whether analogues of Bose-Einstein condensation precipitate learned decision making in live biological systems as bioenergetics optimization predicts. By exploiting the ciliate Spirostomum ambiguum's capacity to learn and store behavioral strategies advertising mating availability into heuristics of topologically invariant computational networks, three distinct phases of strategy use were found to map onto statistical distributions described by Bose-Einstein, Fermi-Dirac, and classical Maxwell-Boltzmann behavior. Ciliates that sensitized or habituated signaling patterns to emit brief periods of either dec... Biosystems journals http://www.medworm.com/rss/comments.php?id=2960126 Fri, 30 Oct 2009 00:00:00 +0100 2960126 http://www.medworm.com/index.php?rid=2960125&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%3D19883727%26dopt%3DAbstract Authors: Neumann GF A trade-off between the parameters of Lotka-Volterra systems is used to give verifica-tions of known relations between intrinsic growth rate and limiting capacity and the stability type of the resulting dynamical system. The well known rock-paper-scissors game serves as a template for toxin mediated interactions, which is best represented by the bacteriocin producing E.coli bacteria. There, we have three strains of the same species. The producer produces a toxin lethal to the sensitive, while the resistant is able to protect itself from that toxin. Due to the fact that there are costs for production and for resistance, a dynamics similar to the rock-paper-scissors game results. By using an adaptive dynamics approach for competitive Lotka-Volterra systems and assumin... Biosystems journals http://www.medworm.com/rss/comments.php?id=2960125 Fri, 30 Oct 2009 00:00:00 +0100 2960125 http://www.medworm.com/index.php?rid=2954198&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%3D19879323%26dopt%3DAbstract Authors: Laird RA, Sherratt TN Actuarial senescence is characterized by an increase in mortality rate with increasing chronological age. The reliability theory of senescence proposes that organisms' vital functions can be modelled as a suite of damageable, irreplaceable elements (typically genes or their products) that protect their bearer from condition-dependent death so long as at least one of the elements remains intact. Current incarnations of the reliability theory of senescence are continuous-time models with no explicit evolutionary component. Here, we use elementary probability theory and evolutionary dynamics analysis to derive a discrete-time version of the reliability theory of senescence. We include three variations on this theme: the 'Series' model in which damage to any ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2954198 Wed, 28 Oct 2009 00:00:00 +0100 2954198 http://www.medworm.com/index.php?rid=2948529&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%3D19874865%26dopt%3DAbstract Authors: Wagner N, Pross A, Tannenbaumy E A kinetic analysis and simulation of the replication reactions of two competing replicators - one non-metabolic (thermodynamic), the other metabolic, is presented. Our analysis indicates that in a rich resource environment the non-metabolic replicator is likely to be kinetically selected for over the metabolic replicator. However, in the more typical resource-poor environment it will be the metabolic replicator that is the kinetically more stable entity, and the one that will be kinetically selected for. Accordingly, a causal relationship between the emergence of a simple replicator and the emergence of a metabolic system is indicated. The results lend further support for the "replication first" school of thought in the origin of life problem b... Biosystems journals http://www.medworm.com/rss/comments.php?id=2948529 Mon, 26 Oct 2009 00:00:00 +0100 2948529 http://www.medworm.com/index.php?rid=2935536&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%3D19853016%26dopt%3DAbstract In this study we use random Boolean networks (RBNs) as an abstract model of gene regulatory systems. By applying Di_erential Evolution (DE), an evolution-based optimization technique, we produce networks with increased stability. DE requires relatively few user-specified parameters, has fast convergence and does not rely on initial conditions to find the global minima within multi-dimensional search spaces. The stability of networks is evaluated by taking parameters such as their network sensitivity, attractor cycle length and number of attractor basins into account. In this study we present an evolutionary approach to produce networks with specific properties (high stability) starting from chaotic regimes. From this chaotic regime and randomly generated classical RBNs with static input de... Biosystems journals http://www.medworm.com/rss/comments.php?id=2935536 Tue, 20 Oct 2009 00:00:00 +0100 2935536 http://www.medworm.com/index.php?rid=2912653&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%3D19837129%26dopt%3DAbstract Authors: Perc M, Szolnoki A Prevalence of cooperation within groups of selfish individuals is puzzling in that it contradicts with the basic premise of natural selection. Favoring players with higher fitness, the latter is key for understanding the challenges faced by cooperators when competing with defectors. Evolutionary game theory provides a competent theoretical framework for addressing the subtleties of cooperation in such situations, which are known as social dilemmas. Recent advances point towards the fact that the evolution of strategies alone may be insufficient to fully exploit the benefits offered by cooperative behavior. Indeed, while spatial structure and heterogeneity, for example, have been recognized as potent promoters of cooperation, coevolutionary rules can extend t... Biosystems journals http://www.medworm.com/rss/comments.php?id=2912653 Wed, 14 Oct 2009 23:00:00 +0100 2912653 http://www.medworm.com/index.php?rid=2912652&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%3D19837130%26dopt%3DAbstract Authors: Schütze J, Wolf J Glycolytic oscillations occur in many cell types and have been intensively studied in yeast. Recent experimental and theoretical research has been focussed on the oscillatory dynamics and the synchronisation mechanism in stirred yeast cell suspensions. Here we are interested in the spatio-temporal organisation of glycolysis in cell layers. To this end we study a grid of a few thousand compartments each containing a cell. The intracellular dynamics is described by a core model of glycolysis. The compartments can exchange metabolites via diffusion. The conditions for oscillatory dynamics in a single compartment are investigated by bifurcation analysis. The spatio-temporal behaviour of the cell layer is studied by simulations. The model predicts the propaga... Biosystems journals http://www.medworm.com/rss/comments.php?id=2912652 Wed, 14 Oct 2009 23:00:00 +0100 2912652 http://www.medworm.com/index.php?rid=2887490&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%3D19819296%26dopt%3DAbstract Authors: Clemenswrzodek , Schr̈oder A, Dr̈ager A, Dierkw.e , Berendzen K, Kronfeld M, Harter K, Zell A Summary In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the programincludes all necessary data and algorithms to performevery step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job processing and command line options, makingModuleMas... Biosystems journals http://www.medworm.com/rss/comments.php?id=2887490 Wed, 07 Oct 2009 23:00:00 +0100 2887490 http://www.medworm.com/index.php?rid=2839367&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%3D19781596%26dopt%3DAbstract Discussions on the nature of cellular intelligence, however, have not systematically pursued yet the question of whether there is a fundamental way of sensing the environment, which may characterize prokaryotic cells, or not. The molecular systems found in bacterial signaling are extremely diverse, ranging from very simple transcription regulators (single proteins comprising just two domains) to the multi-component, multi-pathway signaling cascades that regulate crucial stages of the cell cycle, such as sporulation, biofilm formation, dormancy, pathogenesis or flagellar biosynthesis. The combined complexity of the environment and of the cellular way of life is reflected as a whole in the aggregate of signaling elements: an interesting power-law relationship emerges in that regard. In a bas... Biosystems journals http://www.medworm.com/rss/comments.php?id=2839367 Mon, 21 Sep 2009 23:00:00 +0100 2839367 http://www.medworm.com/index.php?rid=2804916&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%3D19755136%26dopt%3DAbstract Authors: Seligmann H Stem-loop hairpins formed by mitochondrial light strand replication origins (OL) and by heavy strand DNA coding for tRNAs that form OL-like structures initiate mitochondrial replication. The loops are recognized by one of the two active sites of the vertebrate mitochondrial gamma polymerase, which are homologuous to the active sites of class II amino-acyl tRNA synthetases. Therefore, the polymerase site recognizing the OL loop could recognize tRNA anticodon loops and sequence similarity between anticodon and OL loops should predict initiation of DNA replication at tRNAs. Strengths of genome-wide deamination gradients starting at tRNA genes estimate extents by which replication starts at that tRNA. Deaminations (A->G and C->T) occur proportionally to time spen... Biosystems journals http://www.medworm.com/rss/comments.php?id=2804916 Fri, 11 Sep 2009 23:00:00 +0100 2804916 http://www.medworm.com/index.php?rid=2797589&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%3D19751799%26dopt%3DAbstract Authors: Itakura J, Kurosaki M, Itakura Y, Maekawa S, Asahina Y, Izumi N, Enomoto N We created agent-based models that visually simulate conditions of chronic viral infections using two software. The results from two models were consistent, when they have same parameters during the actual simulation. The simulation results comprise a transient phase and an equilibrium phase, and unlike the mathematical model, virus count transit smoothly to the equilibrium phase without overshooting which correlates with actual biology in vivo of certain viruses. We investigated the effects caused by varying all the parameters included in concept; increasing virus lifespan, uninfected cell lifespan, uninfected cell regeneration rate, virus production count from infected cells, and infection rate had po... Biosystems journals http://www.medworm.com/rss/comments.php?id=2797589 Thu, 10 Sep 2009 23:00:00 +0100 2797589 http://www.medworm.com/index.php?rid=2782596&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%3D19735694%26dopt%3DAbstract Authors: Gonze D Switches (bistability) and oscillations (limit cycle) are omnipresent in genetic networks. Synthetic genetic networks producing bistability and oscillations have been designed and constructed experimentally. However, in real biological systems, regulatory circuits are usually interconnected and the dynamics of those complex networks is often richer than the dynamics of simple modules. Here we coupled the genetic Toggle switch and the Repressilator, two prototypic systems exhibiting bistability and oscillations, respectively. We studied two types of coupling. In the first type, the bistable switch is under the control of the oscillator. Numerical simulation of this system allows us to determine the conditions under which a periodic switch between the two stable steady s... Biosystems journals http://www.medworm.com/rss/comments.php?id=2782596 Thu, 03 Sep 2009 23:00:00 +0100 2782596 http://www.medworm.com/index.php?rid=2775294&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%3D19733619%26dopt%3DAbstract Authors: Tomassini M, Pestelacci E, Luthi L Using a new dynamical network model of society in which pairwise interactions are weighted according to mutual satisfaction, we show that cooperation is the norm in the Hawks-Doves game when individuals are allowed to break ties with undesirable neighbors and to make new acquaintances in their extended neighborhood. Moreover, cooperation is robust with respect to rather strong strategy perturbations. We also discuss the empirical structure of the emerging networks, and the reasons that allow cooperators to thrive in the population. Given the metaphorical importance of this game for social interaction, this is an encouraging positive result as standard theory for large mixing populations prescribes that a certain fraction of defectors must alw... Biosystems journals http://www.medworm.com/rss/comments.php?id=2775294 Wed, 02 Sep 2009 23:00:00 +0100 2775294 http://www.medworm.com/index.php?rid=2745839&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%3D19712721%26dopt%3DAbstract Authors: Waxman D, Stoletzki N In this paper we investigate some of the mathematical properties of mei-otic recombination. Working within the framework of a genetic model with n loci, where a alleles are possible at each locus, we find that the proportion of all possible diploid parental genotypes that can produce a particular haploid gamete is exp [-n log [alpha(2)/2alpha-1])]. We show that this proportion connects recombination with a fractal geometry of dimension log(2alpha-1)/ log(alpha). The fractal dimension of a geometric object manifests itself when it is measured at increasingly smaller length scales. Decreasing the length scale of a geometric object is found to be directly analogous, in a genetics problem, to specifying a multilocus haplotype at a larger number of loci, and i... Biosystems journals http://www.medworm.com/rss/comments.php?id=2745839 Sun, 23 Aug 2009 23:00:00 +0100 2745839 http://www.medworm.com/index.php?rid=2735184&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%3D19699257%26dopt%3DAbstract Authors: Jestin JL The first symmetry by base substitutions of degeneracy in the genetic code was described by Rumer (1966) and the other symmetries were identified later by Lehmann (2000), Jestin and Soulé (2006, 2007). Here, a rationale accounting for these symmetries is reported. The number of non-synonymous substitutions over the replicated coding sequence is written as a function of the substitution matrix, whose elements are the number of substitutions from any codon to any other codon. The p-adic distance used as a similarity measure and applied to this matrix is shown to be biologically relevant. The rationale indicates that symmetries by base substitutions of degeneracy in the genetic code are symmetries of the measures of the number of non-synonymous substitutions for se... Biosystems journals http://www.medworm.com/rss/comments.php?id=2735184 Tue, 18 Aug 2009 23:00:00 +0100 2735184 http://www.medworm.com/index.php?rid=2725356&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%3D19695304%26dopt%3DAbstract Authors: Stefanidis K, Loutradis D, Anastasiadou V, Beretsos P, Bletsa R, Dinopoulou V, Lekka K, Elenis E, Kiapekou E, Koussoulakos S, Fotinos A, Antsaklis A Oxytocin is a nine amino acid peptide involved in a wide spectrum of physiological functions; predominantly those concerning reproduction and differentiation are of interest. Oxytocin receptors are expressed at early developmental stages of mammals, suggesting that oxytocin might be involved in the determination of the germ stem cell line, at the very early stages of mammalian development. In this respect, the proximate aim of the present study was to confirm and further analyze the existence of oxytocin receptors at a very early level of cell commitment, that is, the determination of germ cells derived from embryoid bodies. To ac... Biosystems journals http://www.medworm.com/rss/comments.php?id=2725356 Sun, 16 Aug 2009 23:00:00 +0100 2725356 http://www.medworm.com/index.php?rid=2725355&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%3D19695305%26dopt%3DAbstract Authors: Barrios AF, Achenie LE Analysis of different architectures of quorum sensing networks has been the center of attention in recent times. The approach employs mathematical models to uncover the factors behind the dynamics. Quorum sensing networks mostly display autoregulation such as Pseudomonas aeruginosa and Vibrio cholerae. However, Es cherichia coli autoinducer 2 (AI-2) synthesis does not display autoinduction (i.e. autoregulation). This and other features have raised questions about the actual function of AI-2 inside the cell. In this paper we propose a model for lsr operon regulation which explains or at least is consistent with AI-2 uptake in E. coli. The model was employed to determine the main factors that control the concentration of the signal and the uptake activatio... Biosystems journals http://www.medworm.com/rss/comments.php?id=2725355 Sun, 16 Aug 2009 23:00:00 +0100 2725355 http://www.medworm.com/index.php?rid=2713251&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%3D19686801%26dopt%3DAbstract Authors: Clark KB Learning to reciprocate socially valued actions, such as cheating and cooperation, marks evolutionary advances in animal intelligence thought unequalled by even colonial microbes known to secure respective individual or group fitness tradeoffs through genetic and epigenetic processes. However, solitary ciliates, unique among microbes for their emulation of simple Hebbian-like learning contingent upon feedback between behavioral output and vibration-activated mechanosensitive Ca(2+) channels, might be the best candidates to learn to reciprocate necessary preconjugant touches perceived during complex 'courtship rituals'. Testing this hypothesis here with mock social trials involving an ambiguous vibration source, the large heterotrich ciliate Spirostomum ambiguum showed... Biosystems journals http://www.medworm.com/rss/comments.php?id=2713251 Thu, 13 Aug 2009 23:00:00 +0100 2713251 http://www.medworm.com/index.php?rid=2713250&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%3D19686802%26dopt%3DAbstract Authors: Rodrigoweinert W, Lopes HS The simulation of the dynamics of a cellular systems based on cellular automata (CA) can be computationally expensive. This is particularly true when such simulation is part of a procedure of rule induction to find suitable transition rules for the CA. Several efforts have been described in the literature to make this problem more treatable. This work presents a study about the efficiency of dynamic behavior forecasting parameters (DBFPs) used for the induction of transition rules of CA for a specific problem: the classification by the majority rule. A total of 8 DBFPs were analyzed for the 31 best-performing rules found in the literature. Some of these DBFPs were highly correlated each other, meaning they yield the same information. Also, most rules... Biosystems journals http://www.medworm.com/rss/comments.php?id=2713250 Thu, 13 Aug 2009 23:00:00 +0100 2713250 http://www.medworm.com/index.php?rid=2713252&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%3D19682535%26dopt%3DAbstract In this study, we develop a spatially struc-tured population model, which is described by coupled-map lattices and incorporates both dispersal and colored environmental noise. A method for generating time series with desired spatial correlation and color is introduced. Then, we use these generated time series to analyze the in fl uence of noise color on synchrony in population dynamics. The noise color refers to the temporal correlation in the time series data of the noise, and is expressed as the degree of ( fi rst-order) autocorrelation for autoregressive noise. Patterns of spatial synchrony are considered for stable, periodic and chaotic population dynamics. Numerical simulations verify that environmental noise color has a major in fl uence on the level ofsynchrony, which depends strong... Biosystems journals http://www.medworm.com/rss/comments.php?id=2713252 Mon, 10 Aug 2009 23:00:00 +0100 2713252 http://www.medworm.com/index.php?rid=2703204&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%3D19679161%26dopt%3DAbstract Authors: Zhan S, Miller JF, Tyrrell AM Biology presents incomparable, but desirable, characteristics compared to engineered systems. Inspired by biological development, we have devised a multi-layered design architecture that attempts to capture the favourable characteristics of biological mechanisms for application to design problems. We have identified and implemented essential features of Genetic Regulatory Networks (GRNs) and cell signalling which lead to self-organization and cell differentiation. We have applied this to electronic circuit design. PMID: 19679161 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2703204 Sun, 09 Aug 2009 23:00:00 +0100 2703204 http://www.medworm.com/index.php?rid=2691989&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%3D19664681%26dopt%3DAbstract We present a four-step method for the systematic construction and analysis of discrete models of GRNs by means of a declarative approach. Instead of in-stantiating the models as in classical modeling approaches, the biological knowledge on the network structure and its dynamics is formulated in the form of constraints. The compatibility of the network structure with the constraints is queried and in case of inconsistencies, some constraints are relaxed. Common properties of the consistent models are then analyzed by means of dedicated languages. Two such languages are introduced in the paper. Removing ques-tionable constraints or adding interesting ones allows to further analyze the models. This approach allows to identify the best experiments to be carried out, in order to discriminate se... Biosystems journals http://www.medworm.com/rss/comments.php?id=2691989 Mon, 03 Aug 2009 23:00:00 +0100 2691989 http://www.medworm.com/index.php?rid=2660990&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%3D19643160%26dopt%3DAbstract We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé (2007), and the rearrangements of the table by Delarue (2007) and Rodin and Rodin (2008), respectively. PMID: 19643160 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2660990 Sun, 26 Jul 2009 23:00:00 +0100 2660990 http://www.medworm.com/index.php?rid=2627461&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%3D19615426%26dopt%3DAbstract Authors: Shi J, Dong ML The selectivity of noise and coupling for coherence biresonance(CBR) and array-enhanced coherence biresonance(AECBR) in coupled neural systems has been investigated. It is shown that, depending on the coupling strength and noise intensity, various coherence behaviors and phenomena are exhibited, including CBR, coherence resonance without tuning, AECBR and undamped signal transmission. There exist optimal coupling and noise regions for occurrence of CBR and AECBR in the transmission of noise-induced oscillations(NIO). PMID: 19615426 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2627461 Mon, 13 Jul 2009 23:00:00 +0100 2627461 http://www.medworm.com/index.php?rid=2615550&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%3D19607875%26dopt%3DAbstract We report an experiment in which three-vertex colorability for a 6-vertex graph with 9 edges is solved by constructing a DNA molecule representing the colored graph itself. Our findings show that computation based on "shape processing" is a viable alternative to symbol processing when computing by molecular self- assembly. PMID: 19607875 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2615550 Sun, 12 Jul 2009 23:00:00 +0100 2615550 http://www.medworm.com/index.php?rid=2615549&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%3D19607876%26dopt%3DAbstract We present an efficient algorithm for individual-based, stochastic simulation of biological populations in continuous time. A simple method for its implementation is given and it is compared to Gillespie's commonly-used Direct Method. These two methods are proven to be exactly equivalent and, using a basic evolutionary model, it is demonstrated that the new algorithm can run thousands of times faster. Furthermore, while computational cost per event increases linearly with population size under the Direct Method, this cost is independent of population size under the new algorithm. We argue that this gain in efficiency opens up the possibility to explore a new class of models in population biology. PMID: 19607876 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2615549 Sun, 12 Jul 2009 23:00:00 +0100 2615549 http://www.medworm.com/index.php?rid=2602957&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%3D19596047%26dopt%3DAbstract Authors: Mojica NS, Navarro J, Marijuán PC, Lahoz-Beltra R The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e., the "bauplan" discussion. Thirty years ago, however, Lynn and Tucker studied the biological mechanisms responsible for defining organelles position inside cells. The fact that differentiated structures performing a specific function within the eukaryotic cell (i.e. mitochondrion, vacuole, or chloroplast) were occupying specific positions in the protoplasm was the observational and experimental support of t... Biosystems journals http://www.medworm.com/rss/comments.php?id=2602957 Thu, 09 Jul 2009 23:00:00 +0100 2602957 http://www.medworm.com/index.php?rid=2602958&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%3D19595737%26dopt%3DAbstract Authors: Marín D, Martín M, Sabater B We have deduced equations to quantify the entropy associated to the compartmentalization of components in eukaryotic cells as a function of cell and compartment volumes, and of the concentration of solutes. On the basis of known and plausible values of volume and solute concentrations and the deduced equations, we estimate that the contribution of compartmentalization to the decrease of entropy is approximately -14.4x10(-14) JK(-1)cell(-1) (-0.7 JK(-1)L(-1)) in the case of Saccharomyces cerevisiae, a typical eukaryotic cell, and approximately -49.6x10(-14) JK(-1)cell(-1) (-1.0 JK(-1)L(-1)) in the more complex Chlamydomonas reinhardtii. When compared with other potential contributing factors, such as the informational entropy of DNA and th... Biosystems journals http://www.medworm.com/rss/comments.php?id=2602958 Wed, 08 Jul 2009 23:00:00 +0100 2602958 http://www.medworm.com/index.php?rid=2602959&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%3D19591895%26dopt%3DAbstract Authors: Baek H Recently, the population dynamic systems with impulsive controls have been researched by many authors. However, most of them are reluctant to study the seasonal effects on prey. Thus, in this paper, an impulsively controlled two-prey one-predator system with the Beddington-De Angelis type functional response and seasonal effects is investigated. By using the Floquet theory, the sufficient conditions for the existence of a globally asymptotically stable two-prey-free periodic solution are established. Further, it is proven that this system is permanent under some conditions via a comparison method involving multiple Lyapunov functions and meanwhile the conditions for extinction of one of the two prey and permanence of the remaining two species are given. PMID: 195918... Biosystems journals http://www.medworm.com/rss/comments.php?id=2602959 Mon, 06 Jul 2009 23:00:00 +0100 2602959 http://www.medworm.com/index.php?rid=2585486&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%3D19583993%26dopt%3DAbstract This study obtains homologies of query proteins with known accession numbers using BLAST to retrieve GO terms for sequence-based subnuclear localization prediction. A prediction method PGAC, which involves mining informative GO terms associated with amino-acid composition features, is proposed to design a support vector machine-based classifier. PGAC yields 55 informative GO terms with training and test accuracies of 85.7% and 76.3%, respectively, using a data set SNL_35 (561 proteins in 9 localizations) with 35% sequence identity. Upon comparison with Nuc-PLoc, which combines amphiphilic pseudo amino acid composition of a protein with its position-specific scoring matrix, PGAC using the data set SNL_80 yields a leave-one-out cross-validation accuracy of 81.1%, which is better than that of... Biosystems journals http://www.medworm.com/rss/comments.php?id=2585486 Fri, 03 Jul 2009 23:00:00 +0100 2585486 http://www.medworm.com/index.php?rid=2580572&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%3D19580845%26dopt%3DAbstract Authors: Xie P Telomerase is a specialized cellular ribonucleoprotein complex that can synthesize long stretches of a DNA primer by using an intrinsic RNA template sequence. This requires that the telomerase must be able to carry out both nucleotide and repeat additions. Here, based on available structures and experimental data, a model is presented to describe these two addition activities. In the model, the forward movement of the polymerase active site along the template during the processive nucleotide addition is rectified through the incorporation of a matched base, via the Brownian ratchet mechanism. The unpairing of the DNA:RNA hybrid and then repositioning of product 3'-end after each round of repeat synthesis, which are prerequisites for the processive repeat addition, are ca... Biosystems journals http://www.medworm.com/rss/comments.php?id=2580572 Thu, 02 Jul 2009 23:00:00 +0100 2580572 http://www.medworm.com/index.php?rid=2580574&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%3D19577612%26dopt%3DAbstract Authors: Nguyen MN, Ma J, Fogel GB, Rajapakse JC Genes are often classified into biologically-related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying genes by using di-codon usage as features. The method is illustrated on 1,841 HLA sequences which are classified into two major classes, HLA-I and HLA-II, and further classified into the subclasses of major classes. By using both codon and di-codon features, we show near perfect accuracies in the classification of HLA molecules into major classes a... Biosystems journals http://www.medworm.com/rss/comments.php?id=2580574 Wed, 01 Jul 2009 23:00:00 +0100 2580574 http://www.medworm.com/index.php?rid=2580573&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%3D19577613%26dopt%3DAbstract Authors: Nicolau M, Schoenauer M A novel approach to generating scale-free network topologies is introduced, based on an existing artificial Gene Regulatory Network model. From this model, different interaction networks can be extracted, based on an activation threshold. By using an evolutionary computation approach, the model is allowed to evolve, in order to reach specific network statistical measures. The results obtained show that, when the model uses a duplication and divergence initialisation, such as seen in nature, the resulting regulation networks not only are closer in topology to scale-free networks, but also require only a few evolutionary cycles to achieve a satisfactory error value. PMID: 19577613 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2580573 Wed, 01 Jul 2009 23:00:00 +0100 2580573 http://www.medworm.com/index.php?rid=2472876&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%3D19376192%26dopt%3DAbstract Authors: Horcholle-Bossavit G, Quenet B In the adult frog respiratory system, periods of rhythmic movements of the buccal floor are interspersed by lung ventilation episodes. The ventilatory activity results from the interaction of two hypothesized oscillators in the brainstem. Here, we model these oscillators with two coupled neural networks, whose co-activation results in the emergence of new dynamics. One of the networks is built with "loop chains" of excitatory and inhibitory neurones producing periodic activities. We define two groups of excitatory neurones whose oscillatory antiphasic sums of activities represent output signals as possible motor commands towards antagonist buccal muscles. The other oscillator is a small network with a self-modulated excitatory input to an excitat... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472876 Sat, 13 Jun 2009 07:39:20 +0100 2472876 http://www.medworm.com/index.php?rid=2472867&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%3D19393714%26dopt%3DAbstract Authors: Chen JR, Chang YI Biclustering, which performs simultaneous clustering of rows (e.g., genes) and columns (e.g., conditions), has proved of great value for finding interesting patterns from microarray data. To find biclusters, a model called pCluster was proposed. A pCluster consists of a set of genes and a set of conditions, where the expression levels of these genes have a similar variation under these conditions. Based on this model, most of the previous methods need to compute MDSs (maximum dimension sets) for every two genes in the microarray data. Since the number of genes is far larger than the number of conditions, this step is inefficient. Another method called MicroCluster was proposed. This method does not compute MDSs for every two genes, and transforms the problem ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472867 Sat, 13 Jun 2009 07:38:55 +0100 2472867 http://www.medworm.com/index.php?rid=2472858&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%3D19397950%26dopt%3DAbstract Authors: Torrealdea FJ, Sarasola C, d'Anjou A, Moujahid A, de Mendizábal NV The generation of spikes by neurons is energetically a costly process. This paper studies the consumption of energy and the information entropy in the signalling activity of a model neuron both when it is supposed isolated and when it is coupled to another neuron by an electrical synapse. The neuron has been modelled by a four-dimensional Hindmarsh-Rose type kinetic model for which an energy function has been deduced. For the isolated neuron values of energy consumption and information entropy at different signalling regimes have been computed. For two neurons coupled by a gap junction we have analyzed the roles of the membrane and synapse in the contribution of the energy that is required for their organi... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472858 Sat, 13 Jun 2009 07:38:32 +0100 2472858 http://www.medworm.com/index.php?rid=2472520&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%3D19477062%26dopt%3DAbstract Authors: Craddock TJ, Beauchemin C, Tuszynski JA Both direct and indirect experimental evidence has shown signaling, communication and conductivity in microtubules (MTs). Theoretical models have predicted that MTs can be potentially used for both classical and quantum information processing although controversies arose in regard to physiological temperature effects on these capabilities. In this paper, MTs have been studied using well-established principles of classical statistical physics as applied to information processing, information storage and signal propagation. To investigate the existence of information processing in MTs we used cellular automata (CA) models with neighbor rules based on the electrostatic properties of the molecular structure of tubulin, and both synchronous a... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472520 Sat, 13 Jun 2009 04:10:26 +0100 2472520 http://www.medworm.com/index.php?rid=2472411&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%3D19505631%26dopt%3DAbstract Authors: Aracena J, Goles E, Moreira A, Salinas L Deterministic Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states are to be updated. We study the robustness of the dynamical behavior of a Boolean network with respect to different update schedules (synchronous, block-sequential, sequential), which can provide modelers with a better understanding of the consequences of changes in this aspect of the model. For a given Boolean network, we define equivalence classes of update schedules with the same dynamical behavior, introducing a labeled graph which helps to understand the dependence of the dynamics with respect to the update, and to identify interac... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472411 Sat, 13 Jun 2009 03:20:50 +0100 2472411 http://www.medworm.com/index.php?rid=2472370&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%3D19505632%26dopt%3DAbstract Authors: Savino GV, Formigli CM It is difficult to design electronic nonlinear devices capable of reproducing complex oscillations because of the lack of general constructive rules, and because of stability problems related to the dynamical robustness of the circuits. This is particularly true for current analog electronic circuits that implement mathematical models of bursting and spiking neurons. Here we describe a novel, four-dimensional and dynamically robust nonlinear analog electronic circuit that is intrinsic excitable, and that displays frequency adaptation bursting and spiking oscillations. Despite differences from the classical Hodgkin-Huxley (HH) neuron model, its bifurcation sequences and dynamical properties are preserved, validating the circuit as a neuron model. The circ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472370 Sat, 13 Jun 2009 02:23:31 +0100 2472370 http://www.medworm.com/index.php?rid=2472362&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%3D19505633%26dopt%3DAbstract Authors: Ng KS, Yang HJ, Kim SH EEG signals are important to capture brain disorders. They are useful for analyzing the cognitive activity of the brain and diagnosing types of seizure and potential mental health problems. The Event Related Potential can be measured through the EEG signal. However, it is always difficult to interpret due to its low amplitude and sensitivity to changes of the mental activity. In this paper, we propose a novel approach to incrementally detect the pattern of this kind of EEG signal. This approach successfully summarizes the whole stream of the EEG signal by finding the correlations across the electrodes and discriminates the signals corresponding to various tasks into different patterns. It is also able to detect the transition period between different EEG... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472362 Sat, 13 Jun 2009 01:47:06 +0100 2472362 http://www.medworm.com/index.php?rid=2472478&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%3D19505529%26dopt%3DAbstract Authors: Benko TP, Perc M We use nonlinear time series analysis methods to analyze the dynamics of the sound-producing apparatus of the American crocodile (Crocodylus acutus). We capture its dynamics by analyzing a recording of the singing activity during mating time. First, we reconstruct the phase space from the sound recording and thereby reveal that the attractor needs no less than five degrees of freedom to fully evolve in the embedding space, which suggests that a rather complex nonlinear dynamics underlies its existence. Prior to investigating the dynamics more precisely, we test whether the reconstructed attractor satisfies the notions of determinism and stationarity, as a lack of either of these properties would preclude a meaningful further analysis. After positively establis... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472478 Fri, 05 Jun 2009 04:00:00 +0100 2472478 http://www.medworm.com/index.php?rid=2472454&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%3D19505530%26dopt%3DAbstract Authors: Yang ZR Identifying prokaryotes in silico is commonly based on DNA sequences. In experiments where DNA sequences may not be immediately available, we need to have a different approach to detect prokaryotes based on RNA or protein sequences. N-formylmetheonine (fMet) is known as a typical characteristic of prokaryotes. A web tool has been implemented here for predicting prokaryotes through detecting the N-formylmethionine residues in protein sequences. The predictor is constructed using support vector machine. An online predictor has been implemented using Python. The implemented predictor is able to achieve the total prediction accuracy 80% with the specificity 80% and the sensitivity 81%. PMID: 19505530 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2472454 Fri, 05 Jun 2009 04:00:00 +0100 2472454 http://www.medworm.com/index.php?rid=2472435&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%3D19505531%26dopt%3DAbstract Authors: Zoraida BS, Arock M, Ronald BS, Ponalagusamy R The biological Deoxyribonucleic acid (DNA) strand has been increasingly seen as a promising computing unit. A new algorithm is formulated in this paper to design any DNA-Boolean-operator with molecular beacons (MB) as its input. Boolean operators realized using the proposed design methodology is presented. The developed operators adopt a uniform representation for logical 0 and 1 for any Boolean operator. The Boolean operators designed in this work employ only a hybridization operation at each stage. Further, this paper for the first time brings out the realization of a binary adder and subtractor using Molecular Beacons. Simulation results of the DNA based binary adder and subtractor are given to validate the design. PMID: 19... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472435 Fri, 05 Jun 2009 04:00:00 +0100 2472435 http://www.medworm.com/index.php?rid=2472499&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%3D19486923%26dopt%3DAbstract In this study, we fabricated a novel variable wavelength surface plasmon resonance (SPR) sensor, which detects resonance conditions such as a maximum attenuation wavelength, measuring change of microscopic refractive index. Such a change was measured to detect a salmonella antigen-antibody reaction and a penicillinase-penicillin reaction. Our experiments were performed after immobilizing a salmonella antibody on the sensor chip. We measured the shift in resonant wavelength during the antigen-antibody reaction for 30min by injecting 5x10(7) cells/ml concentration of salmonella antigen solution into the sample chamber. Also, after immobilizing penicillinase on the sensor chip, we measured the shift in resonant wavelength during the reaction. Penicillin solution at 10mM was injected into the ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472499 Fri, 29 May 2009 04:00:00 +0100 2472499 http://www.medworm.com/index.php?rid=2472592&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%3D19464339%26dopt%3DAbstract Authors: Zhdanov VP A minimal model proposed by the author [Zhdanov, V.P., 2004. Stochastic kinetics of reproduction of virions inside a cell. Biosystems 77, 143-150] to describe intracellular viral kinetics includes genome replication, mRNA and protein synthesis and degradation, capsid assembly, and virion release from a cell. Here, this model is complemented by the terms describing the balance of the amino acid determining the rate of the synthesis of viral capsid protein. If the effect of virions on this balance is negligible, the model predicts either a steady state or unlimited growth of the virion population. In the latter case, the cell eventually reaches the situation when the amino-acid concentration is reduced due to the synthesis of viral protein. For this stage, the viral-g... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472592 Thu, 21 May 2009 04:00:00 +0100 2472592 http://www.medworm.com/index.php?rid=2472561&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%3D19464340%26dopt%3DAbstract Authors: Zaman G, Kang YH, Jung IH In this paper the optimal control strategies of an SIR (susceptible-infected-recovered) epidemic model with time delay are introduced. In order to do this, we consider an optimally controlled SIR epidemic model with time delay where a control means treatment for infectious hosts. We use optimal control approach to minimize the probability that the infected individuals spread and to maximize the total number of susceptible and recovered individuals. We first derive the basic reproduction number and investigate the dynamical behavior of the controlled SIR epidemic model. We also show the existence of an optimal control for the control system and present numerical simulations on real data regarding the course of Ebola virus in Congo. Our results indicate... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472561 Thu, 21 May 2009 04:00:00 +0100 2472561 http://www.medworm.com/index.php?rid=2472540&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%3D19464341%26dopt%3DAbstract Authors: Masuda T Kinesins are molecular motors that unidirectionally move along microtubules using the chemical energy of ATP. Although the core structure of kinesins is similar to that of myosins, the lever-arm hypothesis, which is widely accepted as a plausible mechanism to explain the behaviors of myosins, cannot be directly applied to kinesins. Masuda has proposed a mechanochemical process called the 'Driven-by-Detachment (DbD)' mechanism to explain the characteristic behaviors of myosins, including the backward movement of myosin VI and the loose coupling phenomenon of myosin II. The DbD mechanism assumes that the energy of ATP is mainly used to detach a myosin head from an actin filament by temporarily reducing the affinity of the myosin against the actin. After the affinity is ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472540 Thu, 21 May 2009 04:00:00 +0100 2472540 http://www.medworm.com/index.php?rid=2472609&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%3D19460417%26dopt%3DAbstract Authors: Jiao J, Yang X, Chen L In the natural world, there are many species whose individual members have a life history that they take them with two distinct stages: immaturity and maturity. In particular, we have in mind mammalian populations and some amphibious animals. We improve the assumption of a single population as a whole. It is assumed that the immature individuals and mature individuals are divided by a fixed period. This paper concentrates on the study of a stage-structured single population model with mature individuals in a polluted environment and pulse input of environmental toxin at fixed moments. Furthermore, the mature individuals are harvested continuously. We show that the population goes extinct if the harvesting rate is beyond a critical threshold. Conditions f... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472609 Tue, 19 May 2009 04:00:00 +0100 2472609 http://www.medworm.com/index.php?rid=2472653&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%3D19446001%26dopt%3DAbstract Authors: Guo H, Meng Y, Jin Y A major research challenge of multi-robot systems is to predict the emerging behaviors from the local interactions of the individual agents. Biological systems can generate robust and complex behaviors through relatively simple local interactions in a world characterized by rapid changes, high uncertainty, infinite richness, and limited availability of information. Gene Regulatory Networks (GRNs) play a central role in understanding natural evolution and development of biological organisms from cells. In this paper, inspired by biological organisms, we propose a distributed GRN-based algorithm for a multi-robot construction task. Through this algorithm, multiple robots can self-organize autonomously into different predefined shapes, and self-reorganize ada... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472653 Wed, 13 May 2009 04:00:00 +0100 2472653 http://www.medworm.com/index.php?rid=2472632&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%3D19446002%26dopt%3DAbstract Authors: Ahmad J, Bourdon J, Eveillard D, Fromentin J, Roux O, Sinoquet C The modelling of gene regulatory networks (GRNs) has classically been addressed through very different approaches. Among others, extensions of Thomas's asynchronous Boolean approach have been proposed, to better fit the dynamics of biological systems: genes may reach different discrete expression levels, depending on the states of other genes, called the regulators: thus, activations and inhibitions are triggered conditionally on the proper expression levels of these regulators. In contrast, some fine-grained propositions have focused on the molecular level as modelling the evolution of biological compound concentrations through differential equation systems. Both approaches are limited. The first one leads to an... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472632 Wed, 13 May 2009 04:00:00 +0100 2472632 http://www.medworm.com/index.php?rid=2472673&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%3D19442703%26dopt%3DAbstract Authors: Stone C, Bull L The Density Classification Task is a well known test problem for two-state discrete dynamical systems. For many years researchers have used a variety of evolutionary computation approaches to evolve solutions to this problem. In this paper, we investigate the evolvability of solutions when the underlying Cellular Automaton is augmented with a type of memory based on the Least Mean Square algorithm. To obtain high performance solutions using a simple non-hybrid genetic algorithm, we design a novel representation based on the ternary representation used for Learning Classifier Systems. The new representation is found able to produce superior performance to the bit string traditionally used for representing Cellular automata. Moreover, memory is shown to improve e... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472673 Tue, 12 May 2009 04:00:00 +0100 2472673 http://www.medworm.com/index.php?rid=2472794&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%3D19427355%26dopt%3DAbstract Authors: Cooper WG Evidence requiring transcriptase quantum processing is identified and elementary quantum methods are used to qualitatively describe origins and consequences of time-dependent coherent proton states populating informational DNA base pair sites in T4 phage, designated by G-C-->G'-C', G-C-->*G-*C and AT-->*A-*T. Coherent states at these 'point' DNA lesions are introduced as consequences of hydrogen bond arrangement, keto-amino-->enol-imine, where product protons are shared between two sets of indistinguishable electron lone-pairs, and thus, participate in coupled quantum oscillations at frequencies of approximately 10(13)s(-1). This quantum mixing of proton energy states introduces stability enhancements of approximately 0.25-7kcal/mole. Transcriptase geneti... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472794 Thu, 07 May 2009 04:00:00 +0100 2472794 http://www.medworm.com/index.php?rid=2472817&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%3D19426781%26dopt%3DAbstract Authors: Thaheld FH Over a period of several decades it has been noticed that most astronauts, either orbiting the earth or on trips to the moon, have observed phosphenes or light flashes (LF) including streaks, spots and clouds of light when their eyes are closed or they are in a darkened cabin. Scientists suspect that two separate components of cosmic rays cause these flashes due to direct interaction with the retina. This phenomenon is not noticed on the ground because of cosmic ray interaction with the atmosphere. The argument is advanced that this effect may provide us with a new method of exploring the weak equivalence principle from the standpoint of Einstein's original thought experiment involving human subjects. This can be done, utilizing the retina only, as an animate quantu... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472817 Wed, 06 May 2009 04:00:00 +0100 2472817 http://www.medworm.com/index.php?rid=2472807&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%3D19426782%26dopt%3DAbstract Authors: Naldi A, Berenguier D, Fauré A, Lopez F, Thieffry D, Chaouiya C Many important problems in cell biology require the consideration of dense nonlinear interactions between functional modules. The requirement of computer simulation for the understanding of cellular processes is now widely accepted, and a variety of modelling frameworks have been designed to meet this need. Here, we present a novel public release of Gene Interaction Network simulation suite (GINsim), a software designed for the qualitative modelling and analysis of regulatory networks. The main functionalities of GINsim are illustrated through the analysis of a logical model for the core network controlling the fission yeast cell cycle. The last public release of GINsim (version 2.3), as well as development v... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472807 Wed, 06 May 2009 04:00:00 +0100 2472807 http://www.medworm.com/index.php?rid=2472827&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%3D19422876%26dopt%3DAbstract In conclusion, validation of the on-chip phosphorylation analysis for kinase inhibitors was achieved. This label-free method might be applied for discovery of kinase inhibitors. PMID: 19422876 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2472827 Tue, 05 May 2009 04:00:00 +0100 2472827 http://www.medworm.com/index.php?rid=2472848&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%3D19409445%26dopt%3DAbstract We describe this phenomenon with the distributed Selkov model that accounts for the reactions of phosphofructokinase, which is a key enzyme of the glycolytic reaction cascade. To describe the experimentally observed phase waves in an open spatial reactor we introduce a non-homogeneous flux of substrate in the model. The experimental observation that waves can change their direction of propagation during the experiment is considered in the model. The mechanism for such a change in wave direction is discussed. PMID: 19409445 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2472848 Sun, 03 May 2009 04:00:00 +0100 2472848 http://www.medworm.com/index.php?rid=2472838&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%3D19409956%26dopt%3DAbstract Authors: Alonso-Sanz R In the conventional spatial formulation of the iterated prisoner's dilemma only the results generated in the last round are taken into account in deciding the next choice. Historic memory can be implemented by featuring players with a summary of their previous winnings and moves. The effect of memory as a mechanism of supporting cooperation versus spatial disorder is assessed when the players are allowed for continuous degree of cooperation, not the mere binary cooperation/defection disjunctive. PMID: 19409956 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2472838 Sun, 03 May 2009 04:00:00 +0100 2472838 http://www.medworm.com/index.php?rid=2472781&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%3D19428979%26dopt%3DAbstract Authors: Molski M The Matsuno model of the muscle contraction is considered in the framework of the two-wave Corben's theory of composite objects built up of both time- and space-like components. It has been proved that during muscle contraction the locally coherent aggregates distributed along the actin filament interact by means of space-like fields, which are solutions of the relativistic Feinberg equation. The existence of such interactions and lack of decoherence are conditions sine qua non for appearance of the quantum entanglement between actin monomers in an ATP-activated filament. A possible role of a quantum potential in the muscle contraction is discussed and the mass of the carrier of space-like interactions is estimated m0' = 7.3 x 10(-32) g (46 eV). PMID: 19428979 [Pu... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472781 Fri, 01 May 2009 04:00:00 +0100 2472781 http://www.medworm.com/index.php?rid=2472766&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%3D19428980%26dopt%3DAbstract Authors: Kihara K, Mori K, Suzuki S, Ono N, Furusawa C, Yomo T Escherichia coli and the cellular slime mold Dictyostelium discoideum form stable viscous symbiotic colonies in the laboratory. To examine changes in E. coli gene expression during establishment of this symbiotic relationship, cells of symbiotic co-cultures and monocultures at various time points were subjected to microarrays analysis. Genes changed significantly over time compared to the initial gene expression level were determined as characteristics of GO function categories. The categories that appeared significantly at the same sampling time points between the two cultures were also identified. Up-regulation of genes from several GO categories associated with polysaccharide synthesis, cell wall degradation, and iron ac... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472766 Fri, 01 May 2009 04:00:00 +0100 2472766 http://www.medworm.com/index.php?rid=2472748&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%3D19428981%26dopt%3DAbstract Authors: Shang XF, Xu XF A series of artificial receptors, hydrazone derivatives containing anthracene, have been designed and synthesized. The interaction of these receptors with biologically important anions was determined by UV-vis, fluorescence and 1H NMR titration experiments and theoretical investigation. Results indicate that the receptor (1) without NO2 shows no binding ability for various anions. The other receptors (2 and 3) show the highest binding ability for acetate (AcO-) among studied anions (fluoride (F-), dihydrogen phosphate (H2PO4-), chloride (Cl-), bromide (Br-), iodide (I-)); and the binding ability for AcO- is not interfered by the existence of other anions. The additions of AcO-, F- and H2PO4- can arouse different degrees of fluorescence quenching. 1H NMR titrati... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472748 Fri, 01 May 2009 04:00:00 +0100 2472748 http://www.medworm.com/index.php?rid=2472729&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%3D19428982%26dopt%3DAbstract Authors: Gámez M, López I, Garay J, Varga Z The effect of radiation on a cell population is described by a two-dimensional nonlinear system of differential equations. If the radiation rate is not too high, the system is known to have an asymptotically stable equilibrium. First, for the monitoring of this effect, the concept of observability is applied. For the case when the total number of cells is observed, without distinction between healthy and affected cells, a so-called observer system is constructed, which, at least near the equilibrium state, makes it possible to recover the dynamics of both the healthy and the affected cells, from the observation of the total number of cells without distinction. Results of simulations with illustrative data are also presented. If we w... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472729 Fri, 01 May 2009 04:00:00 +0100 2472729 http://www.medworm.com/index.php?rid=2472711&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%3D19428983%26dopt%3DAbstract Authors: Bókkon I Here, we put forward a redox molecular hypothesis about the natural biophysical substrate of visual perception and visual imagery. This hypothesis is based on the redox and bioluminescent processes of neuronal cells in retinotopically organized cytochrome oxidase-rich visual areas. Our hypothesis is in line with the functional roles of reactive oxygen and nitrogen species in living cells that are not part of haphazard process, but rather a very strict mechanism used in signaling pathways. We point out that there is a direct relationship between neuronal activity and the biophoton emission process in the brain. Electrical and biochemical processes in the brain represent sensory information from the external world. During encoding or retrieval of information, elect... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472711 Fri, 01 May 2009 04:00:00 +0100 2472711 http://www.medworm.com/index.php?rid=2472693&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%3D19428984%26dopt%3DAbstract Authors: Cooper MB, Loose M, Brookfield JF Gene regulatory networks are shaped by selection for advantageous gene expression patterns. Can we use this fact to predict and explain the structure and properties of gene regulatory networks? Here we address this question with evolutionary simulations of small (two to four genes) transcriptional regulatory networks. Each modeled network is tested for the frequency with which it evolves to produce a bimodal spatial expression pattern of a target gene (the output), in response to a linear trigger gradient (the input). By including network features such as the organisation of binding sites that do not evolve in the model, we can compare the relative chances of evolutionary success between networks differing only in these features. Specifically,... Biosystems journals http://www.medworm.com/rss/comments.php?id=2472693 Fri, 01 May 2009 04:00:00 +0100 2472693 http://www.medworm.com/index.php?rid=2258744&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%3D19280687%26dopt%3DAbstract Passive competition between pairs of self-ordering proto-replicators and the effect of primitive membranes. Biosystems. 2009 Apr;96(1):44-57 Authors: Sayer RM Self-ordering proto-replicators provide an abstract, simulation based investigation of a possible intermediary step in the development of informational replicators. They involve the dynamic self-ordering of generalised subunits of at least two types into coherent and mobile structures, and do not require the preexistence of templates, replicators or functional catalysts. The following discussion naturally extends this approach to include pairs of such systems linked via a probabilistic, inter-system movement of structures. Initially for two specific forms of self-ordering proto-replicator, various types of probabilistic m... Biosystems journals http://www.medworm.com/rss/comments.php?id=2258744 Fri, 13 Mar 2009 13:28:27 +0100 2258744 http://www.medworm.com/index.php?rid=2104363&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%3D19138631%26dopt%3DAbstract Authors: Fogel GB PMID: 19138631 [PubMed - in process] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=2104363 Thu, 15 Jan 2009 08:00:36 +0100 2104363 http://www.medworm.com/index.php?rid=2086799&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%3D19124060%26dopt%3DAbstract Authors: Werner G In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as "Modern Critical Theory" [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest... Biosystems journals http://www.medworm.com/rss/comments.php?id=2086799 Thu, 11 Dec 2008 05:00:00 +0100 2086799 http://www.medworm.com/index.php?rid=2077651&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%3D19118597%26dopt%3DAbstract Authors: Jones D, McWilliam R, Purvis A Cellular automata (CA) have been used by biologists to study dynamic non-linear systems where the interaction between cell behaviour and end-pattern is investigated. It is difficult to achieve convergence of a CA towards a specific static pattern and a common solution is to use genetic algorithms and evolve a ruleset that describes cell behaviour. This paper presents an alternative means of designing CA to converge to specific static patterns. A matrix model is introduced and analysed then a design algorithm is demonstrated. The algorithm is significantly less computationally intensive than equivalent evolutionary algorithms, and not limited in scale, complexity or number of dimensions. PMID: 19118597 [PubMed - as supplied by publisher] (Sour... Biosystems journals http://www.medworm.com/rss/comments.php?id=2077651 Tue, 09 Dec 2008 05:00:00 +0100 2077651 http://www.medworm.com/index.php?rid=2073726&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%3D19111893%26dopt%3DAbstract Authors: Quinn T, Sinkala Z We develop a systems based model for prostate cancer, as a sub-system of the organism. We accomplish this in two stages. We first start with a general ODE that includes organism response terms. Then, to account for normally observed spatial diffusion of cell populations, the ODE is extended to a PDE that includes spatial terms. Numerical solutions of the full PDE are provided, and are indicative of traveling wave fronts. This motivates the use of a well known transformation to derive a canonically related (non-linear) system of ODEs for traveling wave solutions. For biological feasibility, we show that the non-negative cone for the traveling wave system is time invariant. We also prove that the traveling waves have a unique global attractor. Biologically, th... Biosystems journals http://www.medworm.com/rss/comments.php?id=2073726 Sat, 06 Dec 2008 05:00:00 +0100 2073726 http://www.medworm.com/index.php?rid=2055735&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%3D19095039%26dopt%3DAbstract Authors: Kun A, Scheuring I There are two key characteristic of animal and human societies: (1) degree heterogeneity, meaning that not all individual have the same number of associates; and (2) the interaction topology is not static, i.e. either individuals interact with different set of individuals at different times of their life, or at least they have different associations than their parents. Earlier works have shown that population structure is one of the mechanisms promoting cooperation. However, most studies had assumed that the interaction network can be described by a regular graph (homogeneous degree distribution). Recently there are an increasing number of studies employing degree heterogeneous graphs to model interaction topology. But mostly the interaction topology was ass... Biosystems journals http://www.medworm.com/rss/comments.php?id=2055735 Thu, 27 Nov 2008 05:00:00 +0100 2055735 http://www.medworm.com/index.php?rid=2046579&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%3D19070645%26dopt%3DAbstract Authors: Dawy Z, Morcos F, Weindl J, Mueller JC A model for the process of translation in gene expression is proposed. The model is based on the assumption that the ribosome decodes the mRNA sequences using consecutive subsequences of the 3(')-end of its 16S rRNA subunit. The biological consistency of the model is validated by successful detection of the Shine-Dalgarno signal and the start codon. Furthermore, implications on the role of the 3(')-end in the complete process of prokaryotic translation are presented and discussed. Interestingly, the results obtained support the possibility of an involvement of this part of the ribosome in the process of translation termination. Subsequently, results obtained via the proposed model are compared with published experimental results for diffe... Biosystems journals http://www.medworm.com/rss/comments.php?id=2046579 Tue, 25 Nov 2008 05:00:00 +0100 2046579 http://www.medworm.com/index.php?rid=2046578&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%3D19084574%26dopt%3DAbstract Authors: Zhan Y, Guo S, Kendrick KM, Feng J Novel approaches to effectively reduce noise in data recorded from multi-trial physiology experiments have been investigated using two-dimensional filtering methods, adaptive Wiener filtering and reduced update Kalman filtering. Test data based on signal and noise model consisting of different conditions of signal components mixed with noise have been considered with filtering effects evaluated using analysis of frequency coherence and of time-dependent coherence. Various situations that may affect the filtering results have been explored and reveal that Wiener and Kalman filtering can considerably improve the coherence values between two channels of multi-trial data and suppress uncorrelated components. We have extended our approach to exper... Biosystems journals http://www.medworm.com/rss/comments.php?id=2046578 Tue, 25 Nov 2008 05:00:00 +0100 2046578 http://www.medworm.com/index.php?rid=2026754&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%3D19063934%26dopt%3DAbstract Authors: Iwabuchi S, Kawahara K Waves of elevated intracellular free Ca(2+) that propagate between neighboring astrocytes (Ca(2+) waves) are important for the communication among astrocytes. We have previously revealed that focal photolysis of a caged calcium ionophore results in an increase in the concentration of intracellular Ca(2+) in the target astrocytes, then the increase propagates to neighboring astrocytes through gap junctions. The extracellular ATP-purinoceptors signaling pathways are not primarily responsible for the propagation of the photolytic flash-induced Ca(2+) waves. Here we examined whether and if so how the dynamics of Ca(2+) waves changed after treatment with sublethal simulated ischemia; oxygen-glucose deprivation (OGD). OGD treatment increased the astrocytic exp... Biosystems journals http://www.medworm.com/rss/comments.php?id=2026754 Fri, 21 Nov 2008 05:00:00 +0100 2026754 http://www.medworm.com/index.php?rid=2026753&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%3D19063935%26dopt%3DAbstract Authors: Xie P The translocation of tRNA coupled with mRNA in the ribosome is one of important steps during protein synthesis. Despite extensive experimental studies, the detailed mechanism of the translocation remains undetermined. Here, based on previous biochemical, cryo-electron microscopic and X-ray crystallographic studies, a thermal ratchet model is presented for this translocation. In the model, during one elongation cycle of the protein synthesis, two large conformational transitions of the ribosome are involved, with one being the relative rotation between the two ribosomal subunits following the peptide transfer, which is facilitated by the EF-G.GTP binding, and the other one being the reverse relative rotation between the two ribosomal subunits upon EF-G.GTP hydrolysis. The... Biosystems journals http://www.medworm.com/rss/comments.php?id=2026753 Fri, 21 Nov 2008 05:00:00 +0100 2026753 http://www.medworm.com/index.php?rid=2026755&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%3D19059458%26dopt%3DAbstract Authors: Tanimoto J In donor-recipient games (DRG), one of the sub-classes of Prisoner's Dilemma (PD), it is well-known that a game structure is described by two parameters benefit (b) and cost (c) of cooperation. By means of a series of numerical experiments, we proved that the effectiveness of supporting mutual cooperation in DRG by various reciprocity mechanisms can be expressed in a single game structural parameter, b/c. This also implies that the dilemma strength in various donor-recipient games with various reciprocity mechanisms can be evaluated only by b/c, which is consistent with the previous novel finding by Nowak. It was also discussed whether this kind of parameterization idea can be extended to general games in PD game class. PMID: 19059458 [PubMed - as supplied by pu... Biosystems journals http://www.medworm.com/rss/comments.php?id=2026755 Wed, 19 Nov 2008 05:00:00 +0100 2026755 http://www.medworm.com/index.php?rid=2026756&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%3D19059304%26dopt%3DAbstract Authors: Hatori K, Matsui M, Omote Y An actin filament sliding on myosin molecules exhibits fluctuating or staggered movements as responding to changes in the ATP concentration. We previously observed that fluctuations in the sliding velocity enhanced in a manner being independent of the magnitude of the velocity. The present study focused upon a single actin filament bound to a glass surface through avidin-biotin bonding to examine those fluctuations inherent to the filament in the presence of heavy meromyosin. The auto-correlation analysis revealed that the relaxation time of fluctuations in the filamental displacement obtains its maximum value at about 100muM of the ATP concentration in the ambient, while the magnitude of the fluctuations gradually increased with an increase of the ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2026756 Tue, 18 Nov 2008 05:00:00 +0100 2026756 http://www.medworm.com/index.php?rid=2017409&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%3D19056460%26dopt%3DAbstract Authors: Pal R, Basu D, Banerjee M In this paper, a three-tier model of phytoplankton, zooplankton and nutrient is considered and stability of different equilibrium points is analyzed along with Hopf-bifurcation around coexisting equilibrium point. Here, we have assumed toxication process as the guiding factor for bloom formation as well as its termination and this process is incorporated into our model by choosing the zooplankton grazing function as a Monod-Haldane function due to the phytoplankton toxicity. Extensive numerical simulations have been performed to validate the analytical findings and these simulation work reveal the chaotic oscillation exhibited by the model system for certain choice of the parameter values. PMID: 19056460 [PubMed - as supplied by publisher] (Source... Biosystems journals http://www.medworm.com/rss/comments.php?id=2017409 Fri, 14 Nov 2008 05:00:00 +0100 2017409 http://www.medworm.com/index.php?rid=2017408&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%3D19056461%26dopt%3DAbstract Authors: Chen LL, Zhang L, Yoon J, Deisboeck TS Aberrantly regulated cell motility is a hallmark of cancer cells. A hybrid agent-based model has been developed to investigate the synergistic and antagonistic cell motility-impacting effects of three microenvironment variables simultaneously: chemoattraction, haptotactic permission, and biomechanical constraint or resistance. Reflecting distinct cell-specific intracellular machinery, the cancer cells are modeled as processing a variety of spatial search strategies that respond to these three influencing factors with differential weights attached to each. While responding exclusively to chemoattraction optimizes cell displacement effectiveness, incorporating permission and resistance components becomes increasingly important with greater ... Biosystems journals http://www.medworm.com/rss/comments.php?id=2017408 Fri, 14 Nov 2008 05:00:00 +0100 2017408 http://www.medworm.com/index.php?rid=1998822&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%3D19038306%26dopt%3DAbstract Authors: Annila A, Kuismanen E Hierarchical organization of 'systems within systems' is an apparent characteristic of nature. For many biotic and abiotic systems it is known how the nested structural and functional order builds up, yet the general principle why matter evolves to hierarchies has remained unfamiliar to many. We clarify that increasingly larger integrated systems result from the quest to decrease free energy according to the 2nd law of thermodynamics. The argumentation is based on the recently derived equation of motion for natural processes. Hierarchically organized energy transduction machinery emerges naturally when it provides increased rates of energy dispersal. Likewise, a hierarchical system will dismantle into its constituents when they as independent systems will... Biosystems journals http://www.medworm.com/rss/comments.php?id=1998822 Thu, 06 Nov 2008 05:00:00 +0100 1998822 http://www.medworm.com/index.php?rid=1990482&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%3D19026711%26dopt%3DAbstract Authors: Gerlee P, Anderson AR In this paper, we present a modelling framework for cellular evolution that is based on the notion that a cell's behaviour is driven by interactions with other cells and its immediate environment. We equip each cell with a phenotype that determines its behaviour and implement a decision mechanism to allow evolution of this phenotype. This decision mechanism is modelled using feed-forward neural networks, which have been suggested as suitable models of cell signalling pathways. The environmental variables are presented as inputs to the network and result in a response that corresponds to the phenotype of the cell. The response of the network is determined by the network parameters, which are subject to mutations when the cells divide. This approach is vers... Biosystems journals http://www.medworm.com/rss/comments.php?id=1990482 Wed, 05 Nov 2008 05:00:00 +0100 1990482 http://www.medworm.com/index.php?rid=1990481&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%3D19026712%26dopt%3DAbstract Authors: Rodrigues J, Hans du Buf JM In this paper we present an improved model for line and edge detection in cortical area V1. This model is based on responses of simple and complex cells, and it is multi-scale with no free parameters. We illustrate the use of the multi-scale line/edge representation in different processes: visual reconstruction or brightness perception, automatic scale selection and object segregation. A two-level object categorization scenario is tested in which pre-categorization is based on coarse scales only and final categorization on coarse plus fine scales. We also present a multi-scale object and face recognition model. Processing schemes are discussed in the framework of a complete cortical architecture. The fact that brightness perception and object recogn... Biosystems journals http://www.medworm.com/rss/comments.php?id=1990481 Wed, 05 Nov 2008 05:00:00 +0100 1990481 http://www.medworm.com/index.php?rid=1968592&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%3D19010382%26dopt%3DAbstract Authors: Nacher JC, Hayashida M, Akutsu T Recent analyses of biological and artificial networks have revealed a common network architecture, called scale-free topology. The origin of the scale-free topology has been explained by using growth and preferential attachment mechanisms. In a cell, proteins are the most important carriers of function, and are composed of domains as elemental units responsible for the physical interaction between protein pairs. Here, we propose a model for protein-protein interaction networks that reveals the emergence of two possible topologies. We show that depending on the number of randomly selected interacting domain pairs, the connectivity distribution follows either a scale-free distribution, even in the absence of the preferential attachment, or a norm... Biosystems journals http://www.medworm.com/rss/comments.php?id=1968592 Sat, 01 Nov 2008 04:00:00 +0100 1968592 http://www.medworm.com/index.php?rid=1968591&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%3D19010383%26dopt%3DAbstract Authors: Khrennikov A In this paper we offer the quantum-like (QL) representation of the Shafir-Tversky statistical effect which is well known in cognitive psychology. We apply the so-called contextual approach. We consider the Shafir-Tversky effect to result from mixing statistical data obtained in incompatible contexts which are involved, e.g. in Prisoner's Dilemma or in more general games in which the disjunction effect can be found. As a consequence, the law of total probability is violated for the experimental data obtained in experiments on cognitive psychology by Shafir and Tversky [Shafir, E., Tversky, A., 1992. Thinking through uncertainty: nonconsequential reasoning and choice. Cogn. Psychol. 24, 449-474] as well as Tversky and Shafir [Tversky, A., Shafir, E., 1992. The disju... Biosystems journals http://www.medworm.com/rss/comments.php?id=1968591 Sat, 01 Nov 2008 04:00:00 +0100 1968591 http://www.medworm.com/index.php?rid=1968590&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%3D19010384%26dopt%3DAbstract Authors: Das KP, Roy S, Chattopadhyay J We propose and analyze a simple mathematical model for susceptible prey (S)-infected prey (I)-predator (P) interaction, where the susceptible prey population (S) is infected directly from external sources as well as through contact with infected class (I) and the predator completely avoids consuming the infected prey. The model is analyzed to obtain different thresholds of the key parameters under which the system exhibits stability around the biologically feasible equilibria. Through numerical simulations we display the effects of external infection and the infection through contact on the system dynamics in the absence as well as in the presence of the predator. We compare the system dynamics when infection occurs only through contact, with tha... Biosystems journals http://www.medworm.com/rss/comments.php?id=1968590 Sat, 01 Nov 2008 04:00:00 +0100 1968590 http://www.medworm.com/index.php?rid=1951718&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%3D18996435%26dopt%3DAbstract Authors: Roy S A small group of phytoplankton species that produce toxic or allelopathic chemicals has a significant effect on plankton dynamics in marine ecosystems. The species of non-toxic phytoplankton, which are large in number, are affected by the toxin-allelopathy of those species. By analysis of the abundance data of marine phytoplankton collected from the North-West coast of the Bay of Bengal, an empirical relationship between the abundance of the potential toxin-producing species and the species diversity of the non-toxic phytoplankton is formulated. A change-point analysis demonstrates that the diversity of non-toxic phytoplankton increases with the increase of toxic species up to a certain level. However, for a massive increase of the toxin-producing species the diversity o... Biosystems journals http://www.medworm.com/rss/comments.php?id=1951718 Sat, 18 Oct 2008 04:00:00 +0100 1951718 http://www.medworm.com/index.php?rid=1951719&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%3D18992786%26dopt%3DAbstract Authors: Darehmiraki M In this paper, we use stickers to construct a solution space of DNA for the maximal clique problem (MCP). Simultaneously, we also apply the DNA operation in the sticker-based model to develop a DNA algorithm. The results of the proposed algorithm show that the MCP is resolved with biological operations in the sticker-based model for the solution space of the sticker. Moreover, this work presents clear evidence of the ability of DNA computing to solve the NP-complete problem. The potential of DNA computing for the MCP is promising given the operational time complexity of O(nxk). PMID: 18992786 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1951719 Fri, 17 Oct 2008 04:00:00 +0100 1951719 http://www.medworm.com/index.php?rid=1938840&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%3D18983888%26dopt%3DAbstract Authors: Pizzi RM, Rossetti D, Cino G, Marino D, A L Vescovi , Baer W The development of bio-electronic prostheses, hybrid human-electronics devices and bionic robots has been the aim of many researchers. Although neurophysiologic processes have been widely investigated and bio-electronics has developed rapidly, the dynamics of a biological neuronal network that receive sensory inputs, store and control information is not yet understood. Toward this end, we have taken an interdisciplinary approach to study the learning and response of biological neural networks to complex stimulation patterns. This paper describes the design, execution, and results of several experiments performed in order to investigate the behavior of complex interconnected structures found in biological neural netwo... Biosystems journals http://www.medworm.com/rss/comments.php?id=1938840 Fri, 17 Oct 2008 04:00:00 +0100 1938840 http://www.medworm.com/index.php?rid=1933961&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%3D18977406%26dopt%3DAbstract Authors: Murakoshi K, Saito M We propose a neural circuit model of emotional learning using two pathways with different granularity and speed of information processing. In order to derive a precise time process, we utilized a spiking model neuron proposed by Izhikevich and spike-timing-dependent synaptic plasticity (STDP) of both excitatory and inhibitory synapses. We conducted computer simulations to evaluate the proposed model. We demonstrate some aspects of emotional learning from the perspective of the time process. The agreement of the results with the previous behavioral experiments suggests that the structure and learning process of the proposed model are appropriate. PMID: 18977406 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1933961 Tue, 14 Oct 2008 04:00:00 +0100 1933961 http://www.medworm.com/index.php?rid=1917845&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%3D18955106%26dopt%3DAbstract Authors: Silveira M, Monteiro A A favorite wing pattern element in butterflies that has been the focus of intense study in evolutionary and developmental biology, as well as in behavioral ecology, is the eyespot. Because the pace of research on these bull's eye patterns is accelerating we sought to develop a tool to automatically detect and measure butterfly eyespot patterns in digital images of the wings. We used a machine learning algorithm with features based on circularity and symmetry to detect eyespots on the images. The algorithm is first trained with examples from a database of images with two different labels (eyespot and non-eyespot), and subsequently is able to provide classification for a new image. After an eyespot is detected the radius measurements of its color rings are... Biosystems journals http://www.medworm.com/rss/comments.php?id=1917845 Sun, 05 Oct 2008 04:00:00 +0100 1917845 http://www.medworm.com/index.php?rid=1888049&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%3D18926874%26dopt%3DAbstract Authors: Newth D, Cornforth D Over the past 50 years, much attention has been given to the Prisoner's Dilemma as a metaphor for problems surrounding the evolution and maintenance of cooperative and altruistic behavior. The bulk of this work has dealt with the successfulness and robustness of various strategies. Nowak and May [Nowak, M.A., May, R.M., 1992. Evolutionary games and spatial chaos. Nature 359, 826-829] considered an alternative approach to studying evolutionary games. They assumed that players were distributed across a two-dimensional (2D) lattice, interactions between players occurred locally, rather than at long range as in the well mixed situation. The resulting spatial evolutionary games display dynamics not seen in their well-mixed counterparts. An assumption underlying... Biosystems journals http://www.medworm.com/rss/comments.php?id=1888049 Wed, 24 Sep 2008 04:00:00 +0100 1888049 http://www.medworm.com/index.php?rid=1852470&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%3D18832007%26dopt%3DAbstract Authors: Wojciechowski M, Cieplak M We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are studied by placing several identical proteins within the sphere, denaturing them, and then by monitoring refolding. If the interactions between the proteins are dominated by the excluded volume effects, the net folding times are essentially like for a single protein. An introduction of inter-proteinic attractive contacts hinders folding when the strength of the attraction exceeds about a half of the value of the strength of the single pro... Biosystems journals http://www.medworm.com/rss/comments.php?id=1852470 Thu, 11 Sep 2008 04:00:00 +0100 1852470 http://www.medworm.com/index.php?rid=1840862&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%3D18822342%26dopt%3DAbstract Authors: Mori K, Kashiwagi A, Urabe I, Yomo T We performed a series of evolution experiments, the results of which illustrated the relationship between mutations and increased carrying capacity (K). Performing an evolution experiment with repeated cycles of mutation by PCR and selection makes it possible to obtain results over shorter culture durations than in methods reported previously relying on spontaneous mutation and selection. We constructed random mutant populations of Escherichia coli in which members differed only in part of the genomic copy of the glutamine synthetase gene and performed daily serial transfer culture where the populations were in K-selected environments. The value of K in this system was increased by 10(5)- to 10(8)-fold relative to the parent clone, which wa... Biosystems journals http://www.medworm.com/rss/comments.php?id=1840862 Sat, 06 Sep 2008 04:00:00 +0100 1840862 http://www.medworm.com/index.php?rid=1802588&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%3D18793694%26dopt%3DAbstract Authors: Masuda T Myosins are molecular motors that convert the chemical energy of ATP into mechanical work called a power stroke. Class II myosin engaged in muscle contraction is reported to show a "loose coupling phenomenon", in which the number of power strokes is greater than the number of ATP hydrolyses. This phenomenon cannot be explained by the lever-arm hypothesis, which is currently accepted as a standard theory for myosin motility. In this paper, a model is proposed to reproduce the loose coupling phenomenon. The model is based on a mechanochemical process called "Driven by Detachment (DbD)" mechanism, which assumes that the energy of the power strokes originates from the potential energy generated by the attractive force between myosin and actin. During the docking process, ... Biosystems journals http://www.medworm.com/rss/comments.php?id=1802588 Wed, 27 Aug 2008 04:00:00 +0100 1802588 http://www.medworm.com/index.php?rid=1779091&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%3D18773936%26dopt%3DAbstract Authors: Dudek G, Grzywna ZJ, Willcox ML Using fuzzy set theory, we created a system, that assesses a herb's usefulness for the treatment of tuberculosis, based on ethnobotanical data. We analysed two systems which contain different amount of inputs. The first system contains four inputs, the second one contains six inputs. We used the Takagi-Sugeno-Kanga model. Mamdani model is poor at representation as it needs more fuzzy rules than that of TSK to model a real world system where accuracy is demanded. It has been employed a fuzzy controller, and a fuzzy model, in successfully solving difficult control and modelling problems in practice. It is implemented in the Fuzzy Logic Toolbox in Matlab. The data for inputs are gathered in the database named SOPAT (selection of plants against tube... Biosystems journals http://www.medworm.com/rss/comments.php?id=1779091 Tue, 19 Aug 2008 04:00:00 +0100 1779091 http://www.medworm.com/index.php?rid=1779090&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%3D18773937%26dopt%3DAbstract Authors: Guo Y, Tan J In this research, we demonstrated that the plastoquinone-related electron-transport kinetics in photosynthesis could be sufficiently described with as few as three state variables, Q(A)(-), Q(B)(-), and Q(B)(2-). A third-order kinetic model structure was developed with delayed fluorescence as the measurable output. Delayed fluorescence emissions from drought-stressed, DCMU-treated, or healthy plants were measured with a photon-counting system and used to verify the model structure through nonlinear least-squares optimization. While there were no visible differences between the healthy and the stressed plants, the model showed an obvious decrease of Q(A) reduction rate in the drought-stressed samples and a clear decline of functional Q(A)Q(B) pairs in the DCMU-trea... Biosystems journals http://www.medworm.com/rss/comments.php?id=1779090 Tue, 19 Aug 2008 04:00:00 +0100 1779090 http://www.medworm.com/index.php?rid=1754551&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%3D18761392%26dopt%3DAbstract Authors: Dockendorf KP, Park I, He P, Príncipe JC, Demarse TB In vitro neural networks of cortical neurons interfaced to a computer via multichannel microelectrode arrays (MEA) provide a unique paradigm to create a hybrid neural computer. Unfortunately, only rudimentary information about these in vitro network's computational properties or the extent of their abilities are known. To study those properties, a liquid state machine (LSM) approach was employed in which the liquid (typically an artificial neural network) was replaced with a living cortical network and the input and readout functions were replaced by the MEA-computer interface. A key requirement of the LSM architecture is that inputs into the liquid state must result in separable outputs based on the liquid's response (... Biosystems journals http://www.medworm.com/rss/comments.php?id=1754551 Wed, 13 Aug 2008 04:00:00 +0100 1754551 http://www.medworm.com/index.php?rid=1745924&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%3D18722502%26dopt%3DAbstract Authors: Gadomski A Structure versus property (small-scale) relationship enters when something interesting is going to happen in a biosystem. This special-type "happening" is actually appearing to be manifested at both micro- and mesoscopic levels of always productive soft-matter organization under dynamic response, especially the one characteristic of the articular cartilage-an efficient, designed-by-nature multi-membrane, and virtually, with-ion-channels equipped, shock absorber and load relaxor. PMID: 18722502 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1745924 Tue, 05 Aug 2008 04:00:00 +0100 1745924 http://www.medworm.com/index.php?rid=1745925&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%3D18722501%26dopt%3DAbstract Authors: Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot MF, Stougie L Constraint-based approaches recently brought new insight into our understanding of metabolism. By making very simple assumptions such as that the system is at steady-state and some reactions are irreversible, and without requiring kinetic parameters, general properties of the system can be derived. A central concept in this methodology is the notion of an elementary mode (EM for short). The computation of EMs still forms a limiting step in metabolic studies and several algorithms have been proposed to address this problem leading to increasingly faster methods. However, although a theoretical upper bound on the number of elementary modes that a network may possess has been established, surpris... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745925 Sun, 03 Aug 2008 04:00:00 +0100 1745925 http://www.medworm.com/index.php?rid=1745923&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%3D18723072%26dopt%3DAbstract Authors: Crumière A, Sablik M We discuss a rule proposed by the biologist Thomas according to which the possibility for a genetic network (represented by a signed directed graph called a regulatory graph) to have several stable states implies the existence of a positive circuit. This result is already known for different models, differential or discrete formalism, but always with a network of genes contained in a single cell. Thus, we can ask about the validity of this rule for a system containing several cells and with intercellular genetic interactions. In this paper, we consider the genetic interactions between several cells located on a d-dimensional lattice, i.e., each point of lattice represents a cell to which we associate the expression level of n genes contained in this c... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745923 Sun, 03 Aug 2008 04:00:00 +0100 1745923 http://www.medworm.com/index.php?rid=1745936&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%3D18721848%26dopt%3DAbstract In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic-hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic (E(HH)) aminoacids were chosen from the well-known HP-type models (E(HH)in[-4,-3,-2.3,-1]), whereas interaction energies between hydrophobic and hydrophilic aminoacids (E(HP)) as well as interaction energies between hydrophilic aminoacids (E(PP)) were chosen from the range: <-1,1>, but not all values from this range fulfiled limitations resulting from the exploration of the Miyazawa-Jernigan matrix. Exploring every positively vetted combinations of energy interactions a polymorphism of the unit cell was observed... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745936 Thu, 31 Jul 2008 04:00:00 +0100 1745936 http://www.medworm.com/index.php?rid=1745935&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%3D18721849%26dopt%3DAbstract Authors: Machura L, Kostur M, Luczka J Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically studied with respect to its energetic efficiency and quality expressed by an effective diffusion coefficient. We demonstrate the role of friction and non-equilibrium driving on the transport quantifiers and identify regions of a parameter space where motors are optimally transported. PMID: 18721849 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1745935 Thu, 31 Jul 2008 04:00:00 +0100 1745935 http://www.medworm.com/index.php?rid=1745934&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%3D18721850%26dopt%3DAbstract Authors: Nicolini C, Bruzzese D, Sivozhelezov V, Pechkova E Proteins represent versatile building blocks for realization of nanostructured materials of unique structure-function relationship to be applied in nanobiotechnology. Following a recent work [Bruzzese, D., Pastorino, L., Pechkova, E., Sivozhelezov, Nicolini, V., Nicolini, C., Increase of catalytic activity of lipase towards olive oil by Langmuir-Film Immobilization of Lipase, Enzyme and Microbial Technology, submitted for publication.], the Langmuir-Blodgett technique was utilized to develop nanostructured crystal materials based on enzymes interfacially activated with olive oil as substrate. Particularly, thin films of lipase from both Mucor miehei and Candida rugosa were fabricated and characterized by UV-vis spectroscopy, A... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745934 Thu, 31 Jul 2008 04:00:00 +0100 1745934 http://www.medworm.com/index.php?rid=1745933&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%3D18721851%26dopt%3DAbstract Authors: Pawlak Z, Oloyede A Phospholipid (PL) molecules form the main structure of the membrane that prevents the direct contact of opposing articular cartilage layers. In this paper we conceptualise articular cartilage as a giant reverse micelle (GRM) in which the highly hydrated three-dimensional network of phospholipids is electrically charged and able to resist compressive forces during joint movement, and hence loading. Using this hypothetical base, we describe a hydrophilic-hydrophilic (HL-HL) biopair model of joint lubrication by contacting cartilages, whose mechanism is reliant on lamellar cushioning. To demonstrate the viability of our concept, the electrokinetic properties of the membranous layer on the articular surface were determined by measuring via microelectrophoresis,... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745933 Thu, 31 Jul 2008 04:00:00 +0100 1745933 http://www.medworm.com/index.php?rid=1745932&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%3D18721852%26dopt%3DAbstract In this study the postural control system is modeled in terms of two counteracting bio-subsystems. Their activities are described by two Ornstein-Uhlenbeck processes with different-in-magnitude noise sources. The model is constructed as a sum of these processes, where in each of them the same noise source with opposite sign of the noise coefficients was introduced. Since the friction coefficients are also different for these processes, the delay of a crossover from ballistic to diffusive motion for one of the subsystems is greater than for its counterpart. It turns out that for smaller time intervals a superdiffusive behavior is observed, whereas, counteraction of subsystem is called into play for a larger time interval, which for investigated range of data, is exhibited as a slow, subdiff... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745932 Thu, 31 Jul 2008 04:00:00 +0100 1745932 http://www.medworm.com/index.php?rid=1745931&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%3D18721853%26dopt%3DAbstract Authors: Borys P, Grzywna ZJ The ball and chain mechanism is a widely accepted theory for the inactivation of the Shaker K(+)channel. In this paper we propose a diffusive model that predicts a rate of inactivation that is comparable to the experimental measurements. PMID: 18721853 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1745931 Thu, 31 Jul 2008 04:00:00 +0100 1745931 http://www.medworm.com/index.php?rid=1745930&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%3D18721854%26dopt%3DAbstract Authors: Borys P, Krasowska M, Grzywna ZJ, Djamgoz MB, Mycielska ME An important goal in many branches of science, especially in molecular biology and medicine is the quantitative analysis of the structures and their morphology. The morphology can be analyzed in many ways, in particular by the fractal analysis. Apart from the fractal dimension, an important part of the fractal analysis is the lacunarity measurement which, roughly speaking, characterizes the distribution of gaps in the fractal: a fractal with high lacunarity has large gaps. In this paper, we present an extension of the lacunarity measure to objects with nonregular shapes that enables us to provide a successful discrimination of cancer cell lines. The cell lines differ in the shape of vacuole (the gaps in their body) whi... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745930 Thu, 31 Jul 2008 04:00:00 +0100 1745930 http://www.medworm.com/index.php?rid=1745929&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%3D18721855%26dopt%3DAbstract Authors: Pawlak Z, Pai R, Bayraktar E, Kaldonski T, Oloyede A Phospholipid molecules (PLs) in vivo and graphite, molybdenum disulfide, tungsten disulfide and hexagonal boron nitride (h-BN) in vitro are good examples of frictionless lubricants. PLs and solid materials have the ability to form multi-bilayer or layered structures similar to lamellate solid. It has been confirmed experimentally that PLs as lamellar lubricants protect the surface of joints against wear while acting as frictionless lubricant. An experimental study has been conducted on the friction properties of h-boron nitride on porous non-full journal bearings. The porous non-full journal bearings were a mixture of 97.5wt.% Fe and 2.5wt.% Cu powder, and compressed to a density of 5.9g/cm(3). The porosity of non-full journ... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745929 Thu, 31 Jul 2008 04:00:00 +0100 1745929 http://www.medworm.com/index.php?rid=1745928&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%3D18721856%26dopt%3DAbstract Authors: Wybranowski T, Cyrankiewicz M, Ziomkowska B, Kruszewski S The determination of affinity of warfarin and flurbiprofen to human serum albumin (HSA) by fluorescence anisotropy measurements of carboxylate form of camptothecin (CPT-C) is the subject of this paper. A simple method based on measurements of fluorescence anisotropy of CPT-C allows to determine the affinity constant of CPT-C to HSA by computation of the fraction of bound CPT-C molecules with HSA It was observed, that adding of competing drug to plasma significant reduces the rate of increase of CPT-C fluorescence anisotropy with increase of albumin concentration and, the affinity constant of CPT-C to HSA decreases. The hypothesis of interactions between competing drug and CPT-C is presented. The results of these studies... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745928 Thu, 31 Jul 2008 04:00:00 +0100 1745928 http://www.medworm.com/index.php?rid=1745927&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%3D18721857%26dopt%3DAbstract Authors: Pechkova E, Tripathi S, Spera R, Nicolini C Single crystals of ribosomal proteins obtained for the first time by Langmuir-Blodget (LB) nanotemplate confirm earlier findings (Pechkova et al., 2008), pointing to a new generation of bionanomaterials of unique structure-function relationship. The ribosomal protein phage GroEL was overexpressed in E. coli. Since these protein's samples have some difficulties by classical vapour diffusion method to yield optimal diffraction quality and order (GroEL), the LB nanotemplate method has been applied and compared to the classical method. With the thin film nanotemplate method large phage GroEL crystals appeared in few days and were subsequently characterized by MALDI-TOF Mass Spectroscopy and by a very preliminary X-ray diffraction. PM... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745927 Thu, 31 Jul 2008 04:00:00 +0100 1745927 http://www.medworm.com/index.php?rid=1745926&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%3D18721858%26dopt%3DAbstract Authors: Beldiman M, Xiao Y, Crawford RW, Oloyede A Osteoarthritis (OA), the most common form of arthritis is a degenerative joint disease, which causes severe long-term pain and physical disability. It is becoming more important to improve diagnosis and understanding of the disease process and subsequently develop new intervention to delay or even reverse the disease progress. Our study was designed to combine two relatively novel treatment techniques, autologous chondrocyte transplantation (ACT) and proposed application of medical remedies based on surface-active phospholipids. To this end we exposed chondrocyte to culture environments with mixtures of culture medium and phospholipid solutions. Following various culture periods, cell survival and well-being were determined by measuri... Biosystems journals http://www.medworm.com/rss/comments.php?id=1745926 Thu, 31 Jul 2008 04:00:00 +0100 1745926 http://www.medworm.com/index.php?rid=1729318&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%3D18718500%26dopt%3DAbstract Authors: Orlowski S, Nowak W The physiological role of recently discovered human neuroglobin (Ngb) is still unknown. Sound hypothesis says that it protects brain during hypoxia. In this paper the advanced potential of mean force by implicit ligand sampling (PMF/ILS) method is used to study the free energy landscape of Ngb for O(2), NO and CO ligands. The multiple diffusion paths are discovered and four ligand binding cavities are determined. The data show that certain regions are easily accessible by O(2) and NO but are protected from CO. Free energy landscapes provide realistic data for stochastic models of ligand diffusion in proteins. PMID: 18718500 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1729318 Thu, 31 Jul 2008 04:00:00 +0100 1729318 http://www.medworm.com/index.php?rid=1729317&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%3D18718501%26dopt%3DAbstract Authors: Pugno NM, Lepore E In this letter we report experimental observations on the times of adhesion of living Tokay geckos (Gekko geckos) on polymethylmethacrylate (PMMA) inverted surfaces. Two different geckos (male and female) and three surfaces with different root mean square (RMS) roughness (RMS=42, 618 and 931nm) have been considered, for a total of 72 observations. The measured data are proved to be statistically significant, following the Weibull Statistics with coefficients of correlation between 0.781 and 0.955. The unexpected result is the observation of a maximal gecko adhesion on the surface with intermediate roughness of RMS=618nm, that we note has waviness comparable to the seta size. PMID: 18718501 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1729317 Thu, 31 Jul 2008 04:00:00 +0100 1729317 http://www.medworm.com/index.php?rid=1729316&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%3D18718502%26dopt%3DAbstract Authors: Kruszewski S, Ziomkowska B, Cyrankiewicz M, Wybranowski T Fluorescence spectroscopy methods are applied to the study of camptothecin analogue DB-67 and its ester DB-67-4ABTFA (trifluoroacetic acid salt of 20(S)-aminobutyrate substituted DB-67). Camptothecin and many of its analogues exhibit anticancer properties. They are fluorescent compounds, so using the method of fluorescence anisotropy measurements and fluorescence spectra recording many biophysical properties can be determined including affinity to proteins and membranes. One can also observe the process of conversion of the ester into DB-67. Active lactone form of camptothecin in fluids at pH 7.4 hydrolyses and converts into inactive carboxylate. Process of camptothecin deactivation is accelerated in plasma and after ab... Biosystems journals http://www.medworm.com/rss/comments.php?id=1729316 Thu, 31 Jul 2008 04:00:00 +0100 1729316 http://www.medworm.com/index.php?rid=1729315&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%3D18718503%26dopt%3DAbstract Authors: Gadomski A The spherical prototype of a crystalline and/or disorderly formation may help in understanding the final stages of many complex biomolecular arrangements. These stages are important for both naturally organized simple biosystems, such as protein (or, other amphiphilic) aggregates in vivo, as well as certain their artificial counterparts, mimicking either in vitro or in silico their structure-property principal relationship. For our particular one-seed based realization of a protein crystal/aggregate late-stage nucleus grown from nearby environment, it turns out that the (osmotic-type) pressure could be, due to local inhomogeneities, and their dynamics shown up in the double layer tightly surrounding the growing object, still an appreciably detectable quantity. This ... Biosystems journals http://www.medworm.com/rss/comments.php?id=1729315 Thu, 31 Jul 2008 04:00:00 +0100 1729315 http://www.medworm.com/index.php?rid=1717053&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%3D18708118%26dopt%3DAbstract Authors: Gadomski A PMID: 18708118 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1717053 Wed, 30 Jul 2008 04:00:00 +0100 1717053 http://www.medworm.com/index.php?rid=1717055&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%3D18706969%26dopt%3DAbstract Authors: Karnani M, Annila A The ideas of the Gaia hypothesis from the 1960s are today largely included in global ecology and Earth system sciences. The interdependence between biosphere, oceans, atmosphere and geosphere is well-established by data from global monitoring. Nevertheless the theory underlying the holistic view of the homeostatic Earth has remained obscure. Here the foundations of Gaia theory are examined from the recent formulation of the 2nd law of thermodynamics as an equation of motion. According to the principle of increasing entropy, all natural processes, inanimate just as animate, consume free energy, the thermodynamic driving force. All species, abiotic just as biotic are viewed as mechanisms of energy transduction for the global system to evolve toward a stationa... Biosystems journals http://www.medworm.com/rss/comments.php?id=1717055 Tue, 29 Jul 2008 04:00:00 +0100 1717055 http://www.medworm.com/index.php?rid=1717054&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%3D18706970%26dopt%3DAbstract Authors: Ouifki R, Witten G We consider a model of HIV-1 infection with a reverse transcriptase inhibitor (RTI) therapy and three delays: the first delay is defined as the time from the virus entry into the target cell to the reverse transcriptase step, the second delay represents the time from the virus entry to the production of new viruses and the third delay corresponds to the time necessary for a newly produced virus to become infectious. We analyse the stability of the steady states and determine a threshold value for the first delay at which the system exhibits a Hopf bifurcation. This might explain the clinically observed transient elevated viremia called viral blips. The frequency of the bifurcating periodic solution as well as the threshold value is approximated numerically u... Biosystems journals http://www.medworm.com/rss/comments.php?id=1717054 Fri, 25 Jul 2008 04:00:00 +0100 1717054 http://www.medworm.com/index.php?rid=1708817&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%3D18703113%26dopt%3DAbstract Authors: Zhdanov VP The author proposes a kinetic model describing the interplay of messenger ribonucleic acid (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA). The model includes association of mRNA and ncRNA and regulation of the ncRNA production by protein. In the case of positive feedback between the production of protein and ncRNA, the steady state of the system is found to be unique. For negative feedback, the model predicts in the mean-field case either unique steady state or bistable kinetics. With incorporation of fluctuations, the bistability is manifested in the form of kinetic bursts provided that the number of reactants is low. Basically, the model describes the simplest biological switch operating with participation of ncRNA. Althou... Biosystems journals http://www.medworm.com/rss/comments.php?id=1708817 Fri, 25 Jul 2008 04:00:00 +0100 1708817 http://www.medworm.com/index.php?rid=1700547&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%3D18692544%26dopt%3DAbstract This article presents a number of computer simulations of the evolution of fimbriae to scrutinize the evolutionary plausibility of this orthodox view. It turns out that these simulations suggest a revised interpretation of the fimbriae mediated parasite-host interaction. Rather than being a passive victim the host is actively providing a niche that evolutionary favors less virulent parasites. The article closes with a number of testable predictions of this model. PMID: 18692544 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1700547 Tue, 22 Jul 2008 04:00:00 +0100 1700547 http://www.medworm.com/index.php?rid=1682863&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%3D18675880%26dopt%3DAbstract Authors: Zhou W, Li X, Liu M, Zhao Y, Zhu G, Luo Q Homeostatic plasticity plays a critical role in the stability of neuronal activities. Here, with high-density hippocampal networks cultured on multi-electrode arrays (MEAs), the transformation of spontaneous neuronal firing patterns induced by 1muM tetrodotoxin was clarified. Once tetrodotoxin was washed out after a 4-h treatment, spontaneous activities rose significantly with spike rate increasing approximately three times, and synchronized burst oscillations appeared throughout the network, with the cross-correlation coefficient between the active sites rising from 0.06+/-0.03 to 0.27+/-0.05. The long-term recording showed that the oscillations lasted for more than 4h before the network recovered. These results suggest that short-ter... Biosystems journals http://www.medworm.com/rss/comments.php?id=1682863 Tue, 15 Jul 2008 04:00:00 +0100 1682863 http://www.medworm.com/index.php?rid=1682864&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%3D18675311%26dopt%3DAbstract Authors: Ibrahim B, Dittrich P, Schmitt E, Diekmann S Eukaryotic cells rely on a surveillance mechanism, the "Spindle Assembly Checkpoint"SACM in order to ensure accurate chromosome segregation by preventing anaphase initiation until all chromosomes are correctly attached to the mitotic spindle. In different organisms, a mitotic checkpoint complex (MCC) composed of Mad2, Bub3, BubR1/Mad3, and Cdc20 inhibits the anaphase promoting complex (APC/C) to initiate promotion into anaphase. The mechanism of MCC formation and its regulation by the kinetochore are unclear. Here, we constructed dynamical models of MCC formation involving different kinetochore control mechanisms including amplification as well as inhibition effects, and analysed their quantitative properties. In particular, in this... Biosystems journals http://www.medworm.com/rss/comments.php?id=1682864 Sat, 12 Jul 2008 04:00:00 +0100 1682864 http://www.medworm.com/index.php?rid=1645797&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%3D18640237%26dopt%3DAbstract In this study, we introduce an algorithm for readjusting the boundaries of clusters by adopting the advantages of both k-means and singular value decomposition (SVD). In addition, we suggest a methodology for searching the principal genes that can be the most crucial genes in regulation of clusters. We found 34 principal genes from 171 clusters having strong concentratedness in their expression patterns and distinct ranges of oscillatory phases, by using a time-series microarray dataset of mouse embryonic stem (ES) cells after induction of dopaminergic neural differentiation. The biological significance of the principal genes examined in the literature supports the feasibility of our algorithms in that the hierarchy of clusters may lead the manifestation of the phenotypes, e.g., the develo... Biosystems journals http://www.medworm.com/rss/comments.php?id=1645797 Wed, 02 Jul 2008 04:00:00 +0100 1645797 http://www.medworm.com/index.php?rid=1645798&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%3D18639609%26dopt%3DAbstract Authors: Mandal S, Ray S, Roy SK The ascendancy concept aims at quantitatively describing the growth and development of an ecosystem as whole. Growth is an increase in the total system throughflow, while development is taken to be a rise in the average mutual information inherent in the network flow structure. As an ecosystem matures and goes through a series of successional stages, its ascendancy exhibits a propensity to increase. In any ecosystem the equilibrium condition may gradually turn into a chaotic situation for different reasons. In this paper a model is proposed of an aquatic ecosystem comprising of three groups, viz., phytoplankton, zooplankton and fish. Rate parameters are changed according to the change of the size of the organisms. The model is run in different condition... Biosystems journals http://www.medworm.com/rss/comments.php?id=1645798 Tue, 01 Jul 2008 04:00:00 +0100 1645798 http://www.medworm.com/index.php?rid=1638989&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%3D18634976%26dopt%3DAbstract Authors: Buonocore A, Pirozzi E, Ricciardi LM, Sato S PMID: 18634976 [PubMed - in process] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1638989 Tue, 01 Jul 2008 04:00:00 +0100 1638989 http://www.medworm.com/index.php?rid=1630883&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%3D18619513%26dopt%3DAbstract Authors: Smith SL, Timmis J This paper presents a novel evolutionary algorithm inspired by protein/substrate binding exploited in enzyme genetic programming (EGP) and artificial immune networks. The immune network-inspired evolutionary algorithm has been developed in direct response to an application in clinical neurology, the diagnosis of Parkinson's disease. The inspiration for, and implementation of the algorithm is described and its performance to the application area considered. PMID: 18619513 [PubMed - as supplied by publisher] (Source: Biosystems) Biosystems journals http://www.medworm.com/rss/comments.php?id=1630883 Fri, 20 Jun 2008 04:00:00 +0100 1630883 http://www.medworm.com/index.php?rid=1630882&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%3D18619514%26dopt%3DAbstract Authors: Boyle JH, Cohen N Over the past four decades, one of the simplest nervous systems across the animal kingdom, that of the nematode worm Caenorhabditis elegans, has drawn increasing attention. This system is the subject of an intensive concerted effort to understand the behaviour of an entire living animal, from the bottom up and the top down. C. elegans locomotion, in particular, has been the subject of a number of models, but there is as yet no general agreement about the key (rhythm generating) elements. In this paper we investigate the role of one component of the locomotion subsystem, namely the body wall muscles, with a focus on the role of inter-muscular gap junctions. We construct a detailed electrophysiological model which suggests that these muscles function, to a firs... Biosystems journals http://www.medworm.com/rss/comments.php?id=1630882 Fri, 20 Jun 2008 04:00:00 +0100 1630882