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Bio Systems

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https://www.readbyqxmd.com/read/29758243/mechanisms-of-directed-evolution-of-morphological-structures-and-the-problems-of-morphogenesis
#1
REVIEW
Alexey V Melkikh, Andrei Khrennikov
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. This model shows that the evolution of morphological structures essentially depends on the availability of a priori information on these structures...
May 11, 2018: Bio Systems
https://www.readbyqxmd.com/read/29742459/amino-acid-content-of-beta-strands-and-alpha-helices-depends-on-their-flanking-secondary-structure-elements
#2
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Victor Vitoldovich Poboinev
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...
May 6, 2018: Bio Systems
https://www.readbyqxmd.com/read/29733888/molecular-motor-translocation-kinetics-application-of-monte-carlo-computer-simulations-to-determine-microscopic-kinetic-parameters
#3
Sarah E LeGresley, Koan Briggs, Christopher J Fischer
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. The associated kinetic time courses are often analyzed using a simple sequential uniform n-step mechanism to estimate the macroscopic kinetic parameters (e.g., translocation rate and processivity) and the microscopic kinetic parameters (e...
May 4, 2018: Bio Systems
https://www.readbyqxmd.com/read/29729294/a-solution-to-the-problem-of-proper-segment-positioning-in-the-course-of-digit-formation
#4
László Pecze
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. In this study, a process called "French-flag driven Turing patterning" is presented that takes the advantages of both previous systems. Four components have been considered: I) a short-range activator (diffusion factor), II.) a long-range inhibitor (diffusion factor) and III) a very-long acting diffusing inhibitor or "French-flag factor", as well as IV) a non-diffusing, cell-autonomous transcription factor...
May 2, 2018: Bio Systems
https://www.readbyqxmd.com/read/29715506/similar-bowtie-structures-and-distinct-largest-strong-components-are-identified-in-the-transcriptional-regulatory-networks-of-arabidopsis-thaliana-during-photomorphogenesis-and-heat-shock
#5
Shitao Luo, Fengming Zhang, Yingfei Ruan, Jie Li, Zheng Zhang, Yan Sun, Shixiong Deng, Rui Peng
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. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis...
April 28, 2018: Bio Systems
https://www.readbyqxmd.com/read/29634993/-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
#6
Naoki Sato
"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. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life...
April 7, 2018: Bio Systems
https://www.readbyqxmd.com/read/29621569/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
#7
Hervé Seligmann
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...
April 2, 2018: Bio Systems
https://www.readbyqxmd.com/read/29608931/hybrid-randomized-and-high-capacity-conservative-mutations-dna-based-steganography-for-large-sized-data
#8
Ghada Hamed, Mohammed Marey, Safaa Amin El-Sayed, Mohamed Fahmy Tolba
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. The DNA conservative mutations are utilized in a way that allows a DNA base to be substituted by another base to allow carrying two bits...
March 30, 2018: Bio Systems
https://www.readbyqxmd.com/read/29605248/metabolism-is-the-tie-the-bertalanffy-type-cancer-growth-model-as-common-denominator-of-various-modelling-approaches
#9
Hans H Diebner, Thomas Zerjatke, Max Griehl, Ingo Roeder
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...
March 29, 2018: Bio Systems
https://www.readbyqxmd.com/read/29526816/elastic-dipole-dipole-interaction-and-viscosity-impact-on-vibrational-properties-of-anisotropic-hexagonal-microtubule-lattice
#10
S Eh Shirmovsky, D V Shulga
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. Calculations have been performed for various directions of wave front propagation: helix, along the protofilament, and anti-helix. Three different wave polarization directions have been considered. It has been shown that the direction of the wave polarization influences the frequency and wave group velocity values in the lattice considerably...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29505794/characterizing-isi-and-sub-threshold-membrane-potential-distributions-ensemble-of-if-neurons-with-random-squared-noise-intensity
#11
Sanjeev Kumar, Karmeshu
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 σ2 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...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29501731/a-limit-in-the-dynamic-increase-in-the-accuracy-of-group-migration
#12
Vladimir N Binhi
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. Orientation accuracy of a group may be significantly higher as the errors caused by a variety of casual factors are averaged due to social interactions. This idea, called the "many wrongs principle," has been confirmed both in behavioral experiments and numerical simulations...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29486901/corrigendum-to-slime-mould-the-fundamental-mechanisms-of-biological-cognition-biosystems-165-2018-57-70
#13
Jordi Vallverdú, Oscar Castro, Richard Mayne, Max Talanov, Michael Levin, Frantisek Baluška, Yukio Gunji, Audrey Dussutour, Hector Zenil, Andrew Adamatzky
No abstract text is available yet for this article.
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29476802/a-model-of-optimal-protein-allocation-during-phototrophic-growth
#14
Marjan Faizi, Tomáš Zavřel, Cristina Loureiro, Jan Červený, Ralf Steuer
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. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29428618/robustness-of-expression-pattern-formation-due-to-dynamic-equilibrium-in-gap-gene-system-of-an-early-drosophila-embryo
#15
Ekaterina Myasnikova, Alexander Spirov
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. We propose an approach based on the observation that for the formation of a pattern with well-established domain borders it is necessary that there exist a stationary nucleus in which the gene expression level is almost constant in time...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29408296/gnc-app-a-new-cytoscape-app-to-rate-gene-networks-biological-coherence-using-gene-gene-indirect-relationships
#16
Juan J Díaz-Montaña, Francisco Gómez-Vela, Norberto Díaz-Díaz
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. RESULTS: In this paper, we present the new GNC-app for Cytoscape. GNC-app implements the GNC methodology for assessing the biological coherence of gene association networks and integrates it into Cytoscape...
April 2018: Bio Systems
https://www.readbyqxmd.com/read/29409799/self-organization-in-aggregating-robot-swarms-a-dw-knn-topological-approach
#17
Belkacem Khaldi, Fouzi Harrou, Foudil Cherif, Ying Sun
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...
March 2018: Bio Systems
https://www.readbyqxmd.com/read/29408212/interaction-between-the-immune-system-and-acute-myeloid-leukemia-a-model-incorporating-promotion-of-regulatory-t-cell-expansion-by-leukemic-cells
#18
Yoshiaki Nishiyama, Yutaka Saikawa, Nobuaki Nishiyama
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...
March 2018: Bio Systems
https://www.readbyqxmd.com/read/29407383/logic-of-two-antagonizing-intra-species-quorum-sensing-systems-in-bacteria
#19
Mahendra Kumar Prajapat, Supreet Saini
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. This density-dependent control of gene expression and physiology is called quorum sensing (QS). Quorum sensing controls a wide variety of functions in bacteria, including those related to motility, growth, virulence etc...
March 2018: Bio Systems
https://www.readbyqxmd.com/read/29337084/a-graph-based-approach-to-analyze-flux-balanced-pathways-in-metabolic-networks
#20
Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed-Amir Marashi
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. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions...
March 2018: Bio Systems
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