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Bio Systems

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https://www.readbyqxmd.com/read/30009873/a-general-framework-dedicated-to-computational-morphogenesis-part-ii-knowledge-representation-and-architecture
#1
Pridi Siregar, Nathalie Julen, Peter Hufnagl, George Mutter
In our previous paper we introduced morphogenesis and post-embryonic life as arising from cells interacting via coupled chemical, electrical and mechanical processes occurring across multiple organization levels. We reviewed these processes from the perspectives of developmental biology and how they relate to physics-based constitutive equations that are well suited to model intercellular interactions' fields. In this paper we will describe a knowledge representation and architectural design strategy that can organize and encode the biochemical, biological and biophysical data necessary to represent and model the highly specialized and diversified cells that constitute living tissues...
July 13, 2018: Bio Systems
https://www.readbyqxmd.com/read/30005999/a-general-framework-dedicated-to-computational-morphogenesis-part-i-constitutive-equations
#2
Pridi Siregar, Nathalie Julen, Peter Hufnagl, George Mutter
In order to understand living organisms, considerable experimental efforts and resources have been devoted to correlate genes and their expressions with cell, tissue, organ and whole organisms' phenotypes. This data driven approach to knowledge discovery has led to many breakthrough in our understanding of healthy and diseased states, and is paving the way to improve the diagnosis and treatment of diseases. Complementary to this data-driven approach, computational models of biological systems based on first principles have been developed in order to deepen our understanding of the multi-scale dynamics that drives normal and pathological biological functions...
July 10, 2018: Bio Systems
https://www.readbyqxmd.com/read/30005998/matesim-monte-carlo-simulation-for-the-generation-of-mating-tables
#3
A Carvajal-Rodríguez
In species with sexual reproduction, the mating pattern is an important element for understanding evolutionary and speciation processes. Given a mating pool where individuals can encounter each other randomly, the individual mating preferences define the mating frequencies in the population. However, in every mating process we can distinguish two different steps. First, the encounter between partners, and second, the actual mating once the encounter has occurred. Yet, we cannot always assume that the observed population patterns accurately reflect the individuals' preferences...
July 10, 2018: Bio Systems
https://www.readbyqxmd.com/read/30008425/integrated-constraints-based-analysis-of-an-engineered-violacein-pathway-in-escherichia-coli
#4
Selva Rupa Christinal Immanuel, Deepanwita Banerjee, Mayooreshwar P Rajankar, Anu Raghunathan
Strategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Δpgi & ΔpheA were validated using in silico gene deletion analysis...
July 3, 2018: Bio Systems
https://www.readbyqxmd.com/read/29953912/threshold-dynamics-of-the-transmission-of-antibiotic-resistant-infections
#5
Zinabu Teka Melese, S M Mwalili, G O Orwa
Despite numerous studies conducted, multidrug-resistant infections such as methicillin-resistant Staphylococcus aureus (MRSE) and vancomycin-resistant enterococci (VRE) are still increasing in hospitals, and yet continued to be the important challenges of worldwide health. Mathematical modeling gives an insightful information in policy and decision making to control the transmission and spread of these infections globally. We formulated and analyse a mathematical model to characterise the transmission co-dynamics of hospital-acquired MRSE (HA-MRSA) and community-acquired MRSE (CA-MRSA) and to investigate the long run competitiveness of the two strains in hospital...
June 25, 2018: Bio Systems
https://www.readbyqxmd.com/read/29935230/estimation-of-plasma-insulin-concentration-under-glycemic-variability-using-nonlinear-filtering-techniques
#6
Luis Omar Avila, Mariano De Paula, Carlos Roberto Sanchez-Reinoso
The ultimate goal of an artificial pancreas is finding the optimal insulin rates that can effectively reduce high blood glucose (BG) levels in type 1 diabetic patients. To achieve this, most closed-loop control strategies need to compute the optimal insulin action on the basis of precedent glucose and insulin levels. Unlike glucose levels which can be measured in real-time, unavailability of insulin sensors makes it essential the use of mathematical models to estimate plasma insulin concentrations. Between others, filtering techniques based on a generalization of the Kalman filter (KF) have been the most widely applied in the estimation of hidden states in nonlinear dynamic systems...
June 20, 2018: Bio Systems
https://www.readbyqxmd.com/read/29870756/the-cipher-of-the-genetic-code
#7
Miloje M Rakočević
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...
June 2, 2018: Bio Systems
https://www.readbyqxmd.com/read/29859208/intracellular-mirna-or-sirna-delivery-and-function
#8
Vladimir P Zhdanov
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. Bearing in mind such applications, the author shows the specifics of the corresponding transient kinetics by using three generic models without and with feedback resulting in bistability in the gene expression. In the absence of feedback, the suppression of the mRNA and protein population is transient...
May 30, 2018: Bio Systems
https://www.readbyqxmd.com/read/29729294/a-solution-to-the-problem-of-proper-segment-positioning-in-the-course-of-digit-formation
#9
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/29859767/the-dynamics-of-a-harvested-predator-prey-system-with-holling-type-iv-functional-response
#10
Xinxin Liu, Qingdao Huang
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. The boundedness of solutions, the existence and stability of equilibrium points of the system are further studied...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29859766/computational-morphogenesis-embryogenesis-cancer-research-and-digital-pathology
#11
REVIEW
Pridi Siregar, Nathalie Julen, Peter Hufnagl, George L Mutter
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...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29857031/a-portable-structural-analysis-library-for-reaction-networks
#12
Yosef Bedaso, Frank T Bergmann, Kiri Choi, Kyle Medley, Herbert M Sauro
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. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29803620/spiking-neural-p-systems-with-multiple-channels-and-anti-spikes
#13
Xiaoxiao Song, Jun Wang, Hong Peng, Guimin Ning, Zhang Sun, Tao Wang, Fan Yang
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. At last, a small universal system using 65 neurons for computing any Turing computable function is given...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29800627/prediction-of-antimicrobial-activity-of-large-pool-of-peptides-using-quasi-smiles
#14
Alla P Toropova, Andrey A Toropov, Emilio Benfenati, Danuta Leszczynska, Jerzy Leszczynski
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. This approach provides the possibility to involve different eclectic conditions related to analyzed endpoint in the modelling process...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29787790/a-discriminative-test-among-the-different-theories-proposed-to-explain-the-origin-of-the-genetic-code-the-coevolution-theory-finds-additional-support
#15
Massimo Di Giulio
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 χ2 value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories...
July 2018: Bio Systems
https://www.readbyqxmd.com/read/29758243/mechanisms-of-directed-evolution-of-morphological-structures-and-the-problems-of-morphogenesis
#16
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...
June 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
#17
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...
June 2018: Bio Systems
https://www.readbyqxmd.com/read/29733888/molecular-motor-translocation-kinetics-application-of-monte-carlo-computer-simulations-to-determine-microscopic-kinetic-parameters
#18
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...
June 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
#19
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...
June 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
#20
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...
May 2018: Bio Systems
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