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Bio Systems

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https://www.readbyqxmd.com/read/28344109/phylogenomic-proximity-and-metabolic-discrepancy-of-methanosarcina-mazei-go1-across-methanosarcinal-genomes
#1
M Bharathi, P Chellapandi
Methanosarcina mazei Go1 is a heterotrophic methanogenic archaean contributing a significant role in global methane cycling and biomethanation process. Phylogenomic relatedness and metabolic discrepancy of this genome were described herein by comparing its whole genome sequence, intergenomic distance, genome function, synteny homologs and origin of replication, and marker genes with very closely related genomes, Methanosarcina acetivorans and Methanosarcina barkeri. Phylogenomic analysis of this study revealed that genome functional feature and metabolic core of M...
March 23, 2017: Bio Systems
https://www.readbyqxmd.com/read/28300609/a-binary-representation-of-the-genetic-code
#2
Louis R Nemzer
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed...
March 11, 2017: Bio Systems
https://www.readbyqxmd.com/read/28263840/a-mathematical-model-predicting-host-mitochondrial-pyruvate-transporter-activity-to-be-a-critical-regulator-of-mycobacterium-tuberculosis-pathogenicity
#3
Parul Mehrotra, Kanury V S Rao, Samrat Chatterjee
Modulation of host metabolic machinery by Mycobacterium tuberculosis is a well established phenomenon. In our earlier study (Mehrotra et al., 2014), we observed a marked increase in acetyl-CoA levels in cells bearing virulent M. tuberculosis infections compared to host cells harbouring avirulent infections. The difference was observed inspite of similar levels of total host cellular pyruvate in both infection types. The present study aimed in capturing the cause for such a phenomenon that defines the pathogenicity of M...
March 2, 2017: Bio Systems
https://www.readbyqxmd.com/read/28254369/applying-attractor-dynamics-to-infer-gene-regulatory-interactions-involved-in-cellular-differentiation
#4
Ahmadreza Ghaffarizadeh, Gregory J Podgorski, Nicholas S Flann
The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort...
February 27, 2017: Bio Systems
https://www.readbyqxmd.com/read/28238940/dynamic-landscape-models-of-coevolutionary-games
#5
Hendrik Richter
Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use either birth-death (BD) or death-birth (DB) strategy updating. The main focus is on using dynamic fitness landscapes as a mathematical model of coevolutionary game dynamics. Hence, an alternative tool for analyzing coevolutionary games becomes available, and landscape measures such as modality, ruggedness and information content can be computed and analyzed...
February 24, 2017: Bio Systems
https://www.readbyqxmd.com/read/28238939/temporary-removal-unitary-circular-code-motifs-in-genomes-of-eukaryotes
#6
Karim El Soufi, Christian J Michel
The publisher regrets that this article has been temporarily removed. A replacement will appear as soon as possible in which the reason for the removal of the article will be specified, or the article will be reinstated. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
February 24, 2017: Bio Systems
https://www.readbyqxmd.com/read/28174135/a-system-of-recurrent-neural-networks-for-modularising-parameterising-and-dynamic-analysis-of-cell-signalling-networks
#7
S Samarasinghe, H Ling
In this paper, we show how to extend our previously proposed novel continuous time Recurrent Neural Networks (RNN) approach that retains the advantage of continuous dynamics offered by Ordinary Differential Equations (ODE) while enabling parameter estimation through adaptation, to larger signalling networks using a modular approach. Specifically, the signalling network is decomposed into several sub-models based on important temporal events in the network. Each sub-model is represented by the proposed RNN and trained using data generated from the corresponding ODE model...
February 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/28167098/what-if-houses-were-powered-by-milk
#8
Neil Phillips, Andrew Adamatzky, Richard Mayne
Living architectures and green energy are hot topics of the applied sciences. They aim to develop buildings that co-live with their environment and co-habit with people they house. An ultimate goal would be to make every block in a building capable of producing energy. We present results of scoping, and somewhat illustrative, experiments on generating electrical energy in modified aerated concrete blocks. These blocks are commonly used in modern building industry and therefore make an ideal candidate for 'inbuilt' microbial bio-reactors...
February 3, 2017: Bio Systems
https://www.readbyqxmd.com/read/28062323/biosystem-models-generated-from-a-complex-rule-reaction-influence-network-and-from-two-functionality-prototypes
#9
M Varga, A Prokop, B Csukas
In this work we have further developed the Direct Computer Mapping (DCM) based modelling and simulation methodology. A unified, transition-based representation of complex rule, reaction and influence networks has been introduced and two prototypes (one general state- and another general transition-prototype) have been developed for the unified functional modelling of the state and transition nodes. Starting from the network and from the functional prototypes, an automatic generation method of the graphically editable and extensible GraphML description of biosystem models has been elaborated...
February 2017: Bio Systems
https://www.readbyqxmd.com/read/28041845/inverse-bayesian-inference-as-a-key-of-consciousness-featuring-a-macroscopic-quantum-logical-structure
#10
Yukio-Pegio Gunji, Shuji Shinohara, Taichi Haruna, Vasileios Basios
To overcome the dualism between mind and matter and to implement consciousness in science, a physical entity has to be embedded with a measurement process. Although quantum mechanics have been regarded as a candidate for implementing consciousness, nature at its macroscopic level is inconsistent with quantum mechanics. We propose a measurement-oriented inference system comprising Bayesian and inverse Bayesian inferences. While Bayesian inference contracts probability space, the newly defined inverse one relaxes the space...
February 2017: Bio Systems
https://www.readbyqxmd.com/read/28034644/effects-of-size-refuge-specificity-on-a-predator-prey-model
#11
Hong Zhang, Feng Tian, Prince Harvim, Paul Georgescu
Predation is a major cause of early-stage mortality for prey individuals, which are often forced to use refuges in order to reduce the risk of being consumed. The ability of certain genotypes in a prey population to reach a size refuge from predation may contribute significantly to the preservation of community diversity. We investigate how the specificity of this behavior affects the evolution of a given population by using a modified Lotka-Volterra model, in which the proportion of each genotype available for predation consists of two components: an intrinsic part and a combination from all genotypes present in the population...
February 2017: Bio Systems
https://www.readbyqxmd.com/read/28027958/chasing-the-tail-the-emergence-of-autocatalytic-networks
#12
REVIEW
Wim Hordijk, Mike Steel
A ubiquitous feature of all living systems is their ability to sustain a biochemistry in which all reactions are coordinated by catalysts, and all reactants (along with the catalysts) are either produced by the system itself or are available from the environment. This led to the hypothesis that 'autocatalytic networks' play a key role in both the origin and the organization of life, which was first proposed in the early 1970s, and has been enriched in recent years by a combination of experimental studies and the application of mathematical and computational techniques...
February 2017: Bio Systems
https://www.readbyqxmd.com/read/27914944/an-efficient-finite-difference-strategy-for-sensitivity-analysis-of-stochastic-models-of-biochemical-systems
#13
Monjur Morshed, Brian Ingalls, Silvana Ilie
Sensitivity analysis characterizes the dependence of a model's behaviour on system parameters. It is a critical tool in the formulation, characterization, and verification of models of biochemical reaction networks, for which confident estimates of parameter values are often lacking. In this paper, we propose a novel method for sensitivity analysis of discrete stochastic models of biochemical reaction systems whose dynamics occur over a range of timescales. This method combines finite-difference approximations and adaptive tau-leaping strategies to efficiently estimate parametric sensitivities for stiff stochastic biochemical kinetics models, with negligible loss in accuracy compared with previously published approaches...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#14
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27894970/genome-wide-characterization-of-the-sidof-gene-family-in-foxtail-millet-setaria-italica
#15
Li Zhang, Baoling Liu, Gewen Zheng, Aiying Zhang, Runzhi Li
Dof (DNA binding with one finger) proteins, which constitute a class of transcription factors found exclusively in plants, are involved in numerous physiological and biochemical reactions affecting growth and development. A genome-wide analysis of SiDof genes was performed in this study. Thirty five SiDof genes were identified and those genes were unevenly distributed across nine chromosomes in the Seteria italica genome. Protein lengths, molecular weights, and theoretical isoelectric points of SiDofs all vary greatly...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27887904/a-new-integrated-symmetrical-table-for-genetic-codes
#16
Jian-Jun Shu
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature's coding processes...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27884620/effect-of-dispersal-in-two-patch-prey-predator-system-with-positive-density-dependence-growth-of-preys
#17
Sourav Kumar Sasmal, Dibakar Ghosh
Prey-predator systems in patchy environment, connected through dispersal between patches is a very common phenomenon observed in nature, which have a significant impact in ecology, species persistence and extinction, etc. In the present paper, we consider a two patch prey-predator system where the patches are connected through dispersal between preys populations only. We consider positive density dependence growth for preys population. In addition, we consider the time scale difference (different life span) between preys and predator populations...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27863978/predicting-the-physiological-response-of-tivela-stultorum-hearts-with-digoxin-from-cardiac-parameters-using-artificial-neural-networks
#18
Dora-Luz Flores, Claudia Gómez, David Cervantes, Alberto Abaroa, Carlos Castro, Rubén A Castañeda-Martínez
Multi-layer perceptron artificial neural networks (MLP-ANNs) were used to predict the concentration of digoxin needed to obtain a cardio-activity of specific biophysical parameters in Tivela stultorum hearts. The inputs of the neural networks were the minimum and maximum values of heart contraction force, the time of ventricular filling, the volume used for dilution, heart rate and weight, volume, length and width of the heart, while the output was the digoxin concentration in dilution necessary to obtain a desired physiological response...
January 2017: Bio Systems
https://www.readbyqxmd.com/read/27939914/corrigendum-to-dynamics-of-an-sir-model-with-vaccination-dependent-on-past-prevalence-with-high-order-distributed-delay-biosystems-129-2015-50-65
#19
John C Eckalbar, Walter L Eckalbar
No abstract text is available yet for this article.
December 7, 2016: Bio Systems
https://www.readbyqxmd.com/read/27784624/multiple-sequence-alignment-using-multi-objective-based-bacterial-foraging-optimization-algorithm
#20
R Ranjani Rani, D Ramyachitra
Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution...
December 2016: Bio Systems
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