3,093 results match your criteria BioSystems [Journal]


The Cipher of the Genetic Code.

Biosystems 2018 Jun 2. Epub 2018 Jun 2.

Department of Chemistry, Faculty of Science, University of Niš, Serbia. Electronic address:

In the paper is presented a new approach to understanding of the genetic code. In order to overcome the key paradox (and Darwinian selection problem) that the highly complex amino acid Phe is encoded by the simplest codons (UUY), and the simplest Gly encoded by the most complex codons (GGN); as well as the paradox of the duplication of some amino acids in the encoding process (Leu, Ser, Arg), we proposed an extension of the notion (and concept) of genetic code. For a better (and lighter) understanding of genetic coding, we proposed a hypothesis after that (under the conditions of allowed metaphoricity and modeling in biology) genetic code has to be understood, analogously to understanding in cryptology, as the unity of the three entities: the code, the cipher of the code and the key of the cipher. Read More

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The dynamics of a harvested predator-prey system with Holling type IV functional response.

Biosystems 2018 May 31;169-170:26-39. Epub 2018 May 31.

College of Mathematics, Jilin University, Changchun 130012, China. Electronic address:

The paper aims to investigate the dynamical behavior of a predator-prey system with Holling type IV functional response in which both the species are subject to capturing. We mainly consider how the harvesting affects equilibria, stability, limit cycles and bifurcations in this system. We adopt the method of qualitative and quantitative analysis, which is based on the dynamical theory, bifurcation theory and numerical simulation. Read More

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Computational morphogenesis - Embryogenesis, cancer research and digital pathology.

Biosystems 2018 May 31;169-170:40-54. Epub 2018 May 31.

Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.

Overall survival benefits of cancer therapies have, in general, fallen short of what was expected from them. By examining the many parallels that exist between embryogenesis and carcinogenesis, we discuss how clinical and fundamental cancer research can benefit from computational morphogenesis (CM) insofar as carcinogenesis is causally related to altered mechanisms underlying embryogenesis and post-embryonic tissue homeostasis. We also discuss about the critical role played by digital pathology (DP) since it constitutes the main source of data for the model-fitting and validation of CM-generated virtual tissues. Read More

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Intracellular miRNA or siRNA delivery and function.

Biosystems 2018 May 30. Epub 2018 May 30.

Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia. Electronic address:

Nanocarrier-mediated delivery and release of short non-coding RNA (e.g., miRNA or siRNA) into the cells with subsequent suppression of the populations of some of the mRNAs and proteins is of interest in the context of the development of a new generation of drugs. Read More

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A portable structural analysis library for reaction networks.

Biosystems 2018 May 30;169-170:20-25. Epub 2018 May 30.

Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address:

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Read More

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Spiking neural P systems with multiple channels and anti-spikes.

Biosystems 2018 May 24;169-170:13-19. Epub 2018 May 24.

School of Electrical Engineering and Electronic Information, Xihua University, Chengdu 610039, PR China; Key Laboratory of Fluid and Power Machinery, Ministry of Education, Xihua University, Chengdu 610039, PR China.

Spiking neural P systems (SN P systems) with multiple channels are a variant of SN P systems presented recently. By introducing anti-spikes in neurons, SN P systems with multiple channels and anti-spikes are constructed in this work, where both spikes and anti-spikes are used in rules with channel labels. The Turing universality as number generating and accepting devices is proved at first, and then a universal SN P systems with multiple channels and anti-spikes for computing functions is investigated. Read More

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May 2018
1 Read

Prediction of antimicrobial activity of large pool of peptides using quasi-SMILES.

Biosystems 2018 May 22;169-170:5-12. Epub 2018 May 22.

Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.

The purpose of this study was the estimation of ability of the so-called optimal descriptors calculated to be a tool to predict the antimicrobial activity of large pool of peptides. Traditional simplified molecular input-line entry system (SMILES) is an efficient tool to represent the molecular structure of different compounds. Quasi-SMILES represents an extension of traditional SMILES. Read More

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A discriminative test among the different theories proposed to explain the origin of the genetic code: The coevolution theory finds additional support.

Biosystems 2018 May 19;169-170:1-4. Epub 2018 May 19.

Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino, 111, 80131 Naples, Italy. Electronic address:

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. Read More

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Mechanisms of directed evolution of morphological structures and the problems of morphogenesis.

Biosystems 2018 Jun 19;168:26-44. Epub 2018 May 19.

International Center for Mathematical Modelling in Physics and Cognitive Sciences, Linnaeus University, Växjö, S-35195, Sweden; National Research University of Information Technologies, Mechanics and Optics (ITMO), St. Petersburg 197101, Russia. Electronic address:

Morphogenesis mechanisms are considered from the point of view of complexity. It has been shown that the presence of long-range interactions between biologically important molecules is a necessary condition for the formation and stable operation of morphological structures. A quantum model of morphogenesis based on non-Archimedean analysis and the presence of long-range interactions between biologically important molecules has been constructed. Read More

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Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements.

Biosystems 2018 Jun 6;168:45-54. Epub 2018 May 6.

Department of General Chemistry, Belarusian State Medical University, Minsk, Dzerzinskogo, 83, Belarus.

The influence of flanking structures (alpha helices and beta strands in the primary sequence) on amino acid content of the elements of secondary structure has been analyzed in seven sets of nonhomologous proteins. Elevated usage of beta structural amino acid residues and pentapeptides in beta strands between two alpha helices can be explained by the stabilization of secondary structure of those beta strands by natural selection. High usage of alpha helical amino acids and pentapeptides in beta strands situated between two other beta strands is an evidence of the relaxation of natural selection: "passive" beta strands in these fragments of polypeptide chains are frequently formed due to the influence of flanking "active" beta strands. Read More

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June 2018
1 Read

Molecular motor translocation kinetics: Application of Monte Carlo computer simulations to determine microscopic kinetic parameters.

Biosystems 2018 Jun 4;168:8-25. Epub 2018 May 4.

Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA. Electronic address:

Methods for studying the translocation of motor proteins along a filament (e.g., nucleic acid and polypeptide) typically monitor the total production of ADP, the arrival/departure of the motor protein at/from a particular location (often one end of the filament), or the dissociation of the motor protein from the filament. Read More

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A solution to the problem of proper segment positioning in the course of digit formation.

Authors:
László Pecze

Biosystems 2018 May 2. Epub 2018 May 2.

Independent Scientist, Marly 1723, Switzerland. Electronic address:

Digit formation requires a robust process. Both digit number and digit identity are precisely controlled. Alan Turing and Lewis Wolpert proposed two different mathematical processes for digit formation, yet neither of them is completely satisfactory. Read More

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May 2018
2 Reads

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

Biosystems 2018 Jun 30;168:1-7. Epub 2018 Apr 30.

Department of Bioinformatics, Chongqing Medical University, Chongqing, China. Electronic address:

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. Read More

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June 2018
5 Reads

"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

Authors:
Naoki Sato

Biosystems 2018 May 7;167:24-32. Epub 2018 Apr 7.

Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan. Electronic address:

"What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. Read More

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May 2018
1 Read

Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

Authors:
Hervé Seligmann

Biosystems 2018 May 3;167:33-46. Epub 2018 Apr 3.

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; The National Natural History Collections, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel. Electronic address:

Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Read More

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May 2018
1 Read

Hybrid, randomized and high capacity conservative mutations DNA-based steganography for large sized data.

Biosystems 2018 May 30;167:47-61. Epub 2018 Mar 30.

Department of Scientific Computing, Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt.

In this paper, a well secured, high capacity, preserved algorithm is proposed through integrating the cryptography and steganography concepts with the molecular biology concepts. We achieved this by first encrypting the confidential data using the DNA Playfair cipher to avoid extra information sent to the receiver and it consequently acts as a trap for an attacker. Second, it achieves a randomized steganography process by exploiting the DNA conservative mutations. Read More

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May 2018
1 Read

Metabolism is the tie: The Bertalanffy-type cancer growth model as common denominator of various modelling approaches.

Biosystems 2018 May 29;167:1-23. Epub 2018 Mar 29.

Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany.

Cancer or tumour growth has been addressed from a variety of mathematical modelling perspectives in the past. Examples are single variable growth models, reaction diffusion models, compartment models, individual cell-based models, clonal competition models, to name only a few. In this paper, we show that the so called Bertalanffy-type growth model is a macroscopic model variant that can be conceived as an optimal condensed modelling approach that to a high degree preserves complexity with respect to the aforementioned more complex modelling variants. Read More

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May 2018
3 Reads

Elastic, dipole-dipole interaction and viscosity impact on vibrational properties of anisotropic hexagonal microtubule lattice.

Biosystems 2018 Apr 8;166:1-18. Epub 2018 Mar 8.

Theoretical and Nuclear Physics Chair, Far Eastern Federal University, 8 Sukhanov St., Vladivostok 690950, Russia. Electronic address:

The paper investigates microtubules lattice properties taking into consideration elastic, dipole-dipole interaction of tubulins and viscosity. A microtubule is modeled as a system of bound tubulins, forming a skewed hexagonal two-dimensional lattice. Wave frequencies and group velocities have been calculated. Read More

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April 2018
1 Read

Characterizing ISI and sub-threshold membrane potential distributions: Ensemble of IF neurons with random squared-noise intensity.

Biosystems 2018 Apr 26;166:43-49. Epub 2018 Mar 26.

Department of Computer Science and Engineering, Shiv Nadar University, Gautam Budh Nagar, India. Electronic address:

A theoretical investigation is presented that characterizes the emerging sub-threshold membrane potential and inter-spike interval (ISI) distributions of an ensemble of IF neurons that group together and fire together. The squared-noise intensity σ of the ensemble of neurons is treated as a random variable to account for the electrophysiological variations across population of nearly identical neurons. Employing superstatistical framework, both ISI distribution and sub-threshold membrane potential distribution of neuronal ensemble are obtained in terms of generalized K-distribution. Read More

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April 2018
1 Read

A limit in the dynamic increase in the accuracy of group migration.

Authors:
Vladimir N Binhi

Biosystems 2018 Apr 1;166:19-25. Epub 2018 Mar 1.

A.M. Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., Moscow 119991, Russian Federation. Electronic address:

Many migratory animals regularly travel thousands of kilometers, exactly finding their seasonal destinations. The nature of this ability is still not fully understood. The aggregation of animals in groups and their socially coordinated movement is considered a way to eliminate navigational errors. Read More

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April 2018
5 Reads

A model of optimal protein allocation during phototrophic growth.

Biosystems 2018 Apr 21;166:26-36. Epub 2018 Feb 21.

Humboldt-Universität zu Berlin, Institut für Biologie, Fachinstitut für Theoretische Biologie (ITB), 10115 Berlin, Germany. Electronic address:

Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function typically reduces the proteome available for other cellular functions. Here, we develop a semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. Read More

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April 2018
1 Read

Robustness of expression pattern formation due to dynamic equilibrium in gap gene system of an early Drosophila embryo.

Biosystems 2018 Apr 8;166:50-60. Epub 2018 Feb 8.

I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, 44 Thorez Pr., St.-Petersburg, 194223, Russia; Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, 11794, NY, USA.

The first manifestation of a segmentation pattern in the early Drosophila development is the formation of expression domains of genes belonging to the gap class. In our previous research the phenomenon of the gap system's robustness, exhibited as the ability to reduce highly variable gene expression in the course of development, was explained as a result of gene cross-regulation. In this paper we formulate the rigorous robustness conditions using the inherent properties of gap gene family. Read More

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April 2018
1 Read

Self-organization in aggregating robot swarms: A DW-KNN topological approach.

Biosystems 2018 Mar 2;165:106-121. Epub 2018 Feb 2.

King Abdullah University of Science and Technology (KAUST) Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia.

In certain swarm applications, where the inter-agent distance is not the only factor in the collective behaviours of the swarm, additional properties such as density could have a crucial effect. In this paper, we propose applying a Distance-Weighted K-Nearest Neighbouring (DW-KNN) topology to the behaviour of robot swarms performing self-organized aggregation, in combination with a virtual physics approach to keep the robots together. A distance-weighted function based on a Smoothed Particle Hydrodynamic (SPH) interpolation approach, which is used to evaluate the robot density in the swarm, is applied as the key factor for identifying the K-nearest neighbours taken into account when aggregating the robots. Read More

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March 2018
2 Reads

GNC-app: A new Cytoscape app to rate gene networks biological coherence using gene-gene indirect relationships.

Biosystems 2018 Apr 14;166:61-65. Epub 2018 Feb 14.

Intelligent Data Analysis (DATAi), Division of Computer Science, Pablo de Olavide University, ES-41013 Seville, Spain. Electronic address:

Motivation: Gene networks are currently considered a powerful tool to model biological processes in the Bioinformatics field. A number of approaches to infer gene networks and various software tools to handle them in a visual simplified way have been developed recently. However, there is still a need to assess the inferred networks in order to prove their relevance. Read More

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April 2018
1 Read

Interaction between the immune system and acute myeloid leukemia: A model incorporating promotion of regulatory T cell expansion by leukemic cells.

Biosystems 2018 Mar 6;165:99-105. Epub 2018 Feb 6.

Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Ishikawa, 9201192, Japan; Institute of Liberal Arts and Science, Kanazawa University, Kakuma, Ishikawa, 9201192, Japan. Electronic address:

Population dynamics of regulatory T cells (Treg) are crucial for the underlying interplay between leukemic and immune cells in progression of acute myeloid leukemia (AML). The goal of this work is to elucidate the dynamics of a model that includes Treg, which can be qualitatively assessed by accumulating clinical findings on the impact of activated immune cell infusion after selective Treg depletion. We constructed an ordinary differential equation model to describe the dynamics of three components in AML: leukemic blast cells, mature regulatory T cells (Treg), and mature effective T cells (Teff), including cytotoxic T lymphocytes. Read More

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March 2018
5 Reads

Logic of two antagonizing intra-species quorum sensing systems in bacteria.

Biosystems 2018 Mar 5;165:88-98. Epub 2018 Feb 5.

Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. Electronic address:

Bacteria release signaling molecules into the surrounding environment and sense them when present in their proximity. Using this strategy, a cell estimates the number of neighbors in its surrounding. Upon sensing a critical number of individuals, bacteria coordinate a number of cellular processes. Read More

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March 2018
1 Read

A graph-based approach to analyze flux-balanced pathways in metabolic networks.

Biosystems 2018 Mar 12;165:40-51. Epub 2018 Jan 12.

Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran. Electronic address:

An elementary flux mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. Read More

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March 2018
2 Reads

mRNA function after intracellular delivery and release.

Biosystems 2018 Mar 11;165:52-56. Epub 2018 Jan 11.

Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia. Electronic address:

Nanocarrier-mediated mRNA delivery and release into the cells with subsequent translation to protein is of interest in the context of the development of a new generation of drugs. In particular, this protein can play a role of a transcription factor and be used as a tool to regulate temporarily the genetic networks. The corresponding transient kinetics of gene expression are expected to depend on the mechanism and duration of mRNA release. Read More

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March 2018
1 Read

Slime mould: The fundamental mechanisms of biological cognition.

Biosystems 2018 Mar 8;165:57-70. Epub 2018 Jan 8.

Unconventional Computing Centre, University of the West of England, Bristol, UK.

The slime mould Physarum polycephalum has been used in developing unconventional computing devices for in which the slime mould played a role of a sensing, actuating, and computing device. These devices treated the slime mould as an active living substrate, yet it is a self-consistent living creature which evolved over millions of years and occupied most parts of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P. Read More

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March 2018
2 Reads

Phi in physiology, psychology and biomechanics: The golden ratio between myth and science.

Biosystems 2018 Mar 6;165:31-39. Epub 2018 Jan 6.

Clinical Laboratory of Experimental Neurorehabilitation, IRCCS Fondazione Santa Lucia, Rome, Italy.

In recent years, there has been a renewed interest in the use of the so-called golden ratio (Phi, ϕ), an irrational number with fractal properties, used in artworks since V century BC. and now for modelling complex biological structures and functions. This number, in fact, recursively pops-up in human history, from Ancient Greeks to Renaissance, and to contemporary scientific studies. Read More

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March 2018
2 Reads

The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach.

Biosystems 2018 Mar 6;165:71-87. Epub 2018 Jan 6.

Institute of Computing Science, Poznan University of Technology, Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland. Electronic address:

The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. Read More

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March 2018
2 Reads

A test of the adaptive network explanation of functional disorders using a machine learning analysis of symptoms.

Biosystems 2018 Mar 24;165:22-30. Epub 2017 Dec 24.

School of Psychology, United Kingdom; University of Plymouth, United Kingdom. Electronic address:

The classification and etiology of functional disorders is controversial. Evidence supports both psychological and biological (disease) models that show, respectively, that functional disorders should be classified as one (bodily distress syndrome) and many (e.g. Read More

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March 2018
4 Reads

CM-viewer: Visualizing interaction network of co-mutated and mutually exclusively mutated cancer genes.

Biosystems 2018 Apr 24;166:37-42. Epub 2017 Dec 24.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China. Electronic address:

Cancer genes usually play a crucial role in regulating cell growth. Normal cells transform into malignant tumors by the acquisition of accumulated genetic mutations that enable them to evade normal growth control. It is therefore important to understand the relationships between mutations during cancer development and progression. Read More

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April 2018
8 Reads

Unique features of nucleotide and codon usage patterns in mycoplasmas revealed by information entropy.

Biosystems 2018 Mar 20;165:1-7. Epub 2017 Dec 20.

State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China. Electronic address:

Currently, the comparison between GC usage pattern at the 3rd codon position and codon usage index is commonly used to estimate the roles of evolutionary forces in shaping synonymous codon usages, however, this kind of analysis often losses the information about the role of A/T usage bias in shaping synonymous codon usage bias. To overcome this limitation and better understand the interplay between nucleotide and codon usages for the evolution of bacteria at gene levels, in this study, we employed the information entropy method with some modification to estimate roles of nucleotide compositions in the overall codon usage bias for 18 mycoplasma species in combination with Davies-Bouldin index. At gene levels, the overall nucleotide usage bias represents A content as the highest, followed by T, G and C for mycoplasmas, resulting in a low GC content. Read More

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March 2018
4 Reads

The first Special Issue on code biology - A bird's-eye view.

Biosystems 2018 02 16;164:11-15. Epub 2017 Dec 16.

Centre for Complex Systems in Transition and Dept. of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Electronic address:

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February 2018
3 Reads

Modeling of decision-making process for moving straight using inverse Bayesian inference.

Biosystems 2018 Jan 14;163:70-81. Epub 2017 Dec 14.

Department of Intermedia Art and Science, Waseda University, Japan.

Humans sometimes make unreasonable decisions when viewed in objective terms. Even in the real world, we may lose sense of direction by turning around the corner several times or mistaking the estimation of travel distance. We experimented in virtual space how we lose sense of direction under what circumstances. Read More

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January 2018
3 Reads

Modular assembling process of an in-silico protocell.

Biosystems 2018 Mar 13;165:8-21. Epub 2017 Dec 13.

Technische Hochschule Bingen, University of applied sciences, 55411 Bingen am Rhein, Germany. Electronic address:

The bottom-up approach of synthetic biology is driven by the need for a deepened understanding of the interaction of functional modules in living or artificial systems. The hope is that the gained knowledge will help to optimize existing systems, or, as one long-term goal of synthetic biology, to build up artificial cell-like entities from single building blocks. This article focuses on a system theoretic approach to synthetic biology, and in particular on the construction of a protocell model by the modular assembling process. Read More

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March 2018
3 Reads

Cyclic Concatenated Genetic Encoder: A mathematical proposal for biological inferences.

Biosystems 2018 Jan 9;163:47-58. Epub 2017 Dec 9.

Department of Electrical Engineering, Universidade Estadual de Campinas, Campinas, SP, Brazil.

The organization of the genetic information and its ability to be conserved and translated to proteins with low error rates have been the subject of study by scientists from different disciplines. Recently, it has been proposed that living organisms display an intra-cellular transmission system of genetic information, similar to a model of digital communication system, in which there is the ability to detect and correct errors. In this work, the concept of Concatenated Genetic Encoder is introduced and applied to the analysis of protein sequences as a tool for exploring evolutionary relationships. Read More

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January 2018
3 Reads

Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: Multi-view ensemble learning (MEL) approach.

Biosystems 2018 Jan 9;163:59-69. Epub 2017 Dec 9.

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address:

Autonomous replication sequences (ARS) are essential for the replication of Saccharomyces cerevisiae genome. The content and context of ARS sites are distinct from other segments of the genome and these factors influence the conformation and thermodynamic profile of DNA that favor binding of the origin recognition complex proteins. Identification of ARS sites in the genome is a challenging task because of their organizational complexity and degeneracy present across the intergenic regions. Read More

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January 2018
4 Reads

Dynamic analysis on the calcium oscillation model considering the influences of mitochondria.

Biosystems 2018 Jan 8;163:36-46. Epub 2017 Dec 8.

Department of Mechanics, School of Mechanical Engineering, Tianjin University, Tianjin 300354, PR China; Tianjin Key Laboratory of Nonlinear Dynamics and Chaos Control, Tianjin 300354, PR China.

Based on the model considering the influences of mitochondria, a further theoretical study on the dynamic behaviors of calcium signals is made. First of all, the reason for the generation and disappearance of calcium oscillations is verified in theory. Second, an analysis on the model considering the influences of mitochondria and the model neglecting the influences of mitochondria is carried out. Read More

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January 2018
7 Reads

Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence.

Biosystems 2018 Jan 2;163:23-35. Epub 2017 Dec 2.

Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom. Electronic address:

Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research. Read More

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January 2018
4 Reads

Towards measuring the semantic capacity of a physical medium demonstrated with elementary cellular automata.

Authors:
Peter Dittrich

Biosystems 2018 Feb 22;164:177-185. Epub 2017 Nov 22.

Bio Systems Analysis Group, Institute for Computer Science, Friedrich Schiller University Jena, 07745 Jena, Germany. Electronic address:

The organic code concept and its operationalization by molecular codes have been introduced to study the semiotic nature of living systems. This contribution develops further the idea that the semantic capacity of a physical medium can be measured by assessing its ability to implement a code as a contingent mapping. For demonstration and evaluation, the approach is applied to a formal medium: elementary cellular automata (ECA). Read More

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February 2018
4 Reads

Corrigendum to "Mathematical analysis of a cholera model with public health interventions" [Biosystems, 105 (3) (2011), 190-200].

Biosystems 2018 Jan 23;163:83-84. Epub 2017 Nov 23.

School of Computer Science and Applied Mathematics, University of the Witwatersrand, Johannesburg, South Africa. Electronic address:

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January 2018
3 Reads

Evidence for the implication of the histone code in building the genome structure.

Biosystems 2018 Feb 20;164:49-59. Epub 2017 Nov 20.

Faculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany. Electronic address:

Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Read More

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February 2018
4 Reads

Corrigendum to "A biophysical approach to cancer dynamics: Quantum chaos and energy turbulence" [BioSystems 156-157 (June-July) (2017) 1-22].

Biosystems 2018 Jan 20;163:82. Epub 2017 Nov 20.

Concordia University, Montreal, Canada, Canada. Electronic address:

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January 2018
11 Reads

A hyperbolastic type-I diffusion process: Parameter estimation by means of the firefly algorithm.

Biosystems 2018 Jan 9;163:11-22. Epub 2017 Nov 9.

Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, s/n, Campus de Fuentenueva, Universidad de Granada, 18071 Granada, Spain. Electronic address:

A stochastic diffusion process, whose mean function is a hyperbolastic curve of type I, is presented. The main characteristics of the process are studied and the problem of maximum likelihood estimation for the parameters of the process is considered. To this end, the firefly metaheuristic optimization algorithm is applied after bounding the parametric space by a stagewise procedure. Read More

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January 2018
4 Reads

The splicing code.

Biosystems 2018 Feb 6;164:39-48. Epub 2017 Nov 6.

International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Italy.

This issue dedicated to the code of life tackles very challenging and open questions in Biology. The genetic code, brilliantly uncovered over 50 years ago is an example of a univocal biological code. In fact, except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5' GUGUUC 3' reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human. Read More

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February 2018
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The evolutionary dynamics of language.

Biosystems 2018 Feb 7;164:128-137. Epub 2017 Nov 7.

Parmenides Center for the Conceptual Foundations of Science, Pullach, Munich, Germany, Germany; Evolutionary Systems Research Group, MTA Ecological Research Centre, the Hungarian Academy of Sciences, Tihany, Hungary. Electronic address:

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Read More

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February 2018
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Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data.

Biosystems 2018 Jan 4;163:1-10. Epub 2017 Nov 4.

Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh.

The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of the cell. In this paper, we propose gene ontology (GO) annotations based semi-supervised clustering algorithm called GO fuzzy relational clustering (GO-FRC) where one gene is allowed to be assigned to multiple clusters which are the most biologically relevant behavior of genes. Read More

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January 2018
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