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Bio Systems

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https://www.readbyqxmd.com/read/30222993/on-symmetries-resonances-and-photonic-crystals-in-morphogenesis
#1
REVIEW
Zhengbing Hu, Sergey V Petoukhov, Elena S Petukhova
Biological symmetries, theories of the morphogenetic field, resonant interactions and the role of photons in morphogenetic processes represented the main fields of interest of Lev Beloussov and his followers. This review article includes some results of our study on the important role of resonances and photonic crystals in genetic informatics. Mathematical formalisms of differential Riemannian geometry and tensor analysis are used for modeling inherited curved surfaces in biomorphology and for understanding conformal bio-symmetries connected with the networks of curvature lines of surfaces...
September 14, 2018: Bio Systems
https://www.readbyqxmd.com/read/30222992/two-ways-for-interpreting-driesch-s-law-positional-information-and-morphogenetic-fields
#2
Lev V Beloussov, Richard Gordon
The late Lev V. Beloussov wrote a 2005 textbook The Foundations of General Embryology which is available in Russian. In 2003 he prepared an excellent, annotated translation of the part of his manuscript for this book on distinguishing positional information models from morphogenetic field models of embryogenesis, which is reproduced here verbatim. He concluded: "…the PI [positional information] concept has no predictive value, and cannot be thus regarded as a scientific theory".
September 14, 2018: Bio Systems
https://www.readbyqxmd.com/read/30205141/classification-of-riboswitch-sequences-using-k-mer-frequencies
#3
Hugo A Guillén-Ramírez, Israel M Martínez-Pérez
Riboswitches are non-coding RNAs that regulate gene expression by altering the structural conformation of mRNA transcripts. Their regulation mechanism might be exploited for interesting biomedical applications such as drug targets and biosensors. A major challenge consists in accurately identifying metabolite-binding RNA switches which are structurally complex and diverse. In this regard, we investigated the classification of 16 riboswitch families using supervised learning algorithms trained solely with sequence-based features...
September 8, 2018: Bio Systems
https://www.readbyqxmd.com/read/30184468/dynamics-of-trna-dissociation-in-early-and-later-cycles-of-translation-elongation-by-the-ribosome
#4
Xiao-Xuan Shi, Hong Chen, Ping Xie
Deacylated tRNA dissociation from E site and aminoacyl-tRNA binding to the A site of the ribosome play a critical role in repetitive cycles of protein synthesis. Available experimental data showed that in the small range of aminoacyl-tRNA concentrations, during the first few cycles of translation elongation (initiation phase of translation) the E-site tRNA can be dissociated either before or after the A-site tRNA binding, while during the later cycles of elongation (elongation phase) the E-site tRNA is mostly dissociated before the A-site tRNA binding...
September 2, 2018: Bio Systems
https://www.readbyqxmd.com/read/30179640/nonlinear-calcium-ion-waves-along-actin-filaments-control-active-hair-bundle-motility
#5
Jack A Tuszynski, Miljko V Sataric, Dalibor L Sekulic, Bogdan M Sataric, Slobodan Zdravkovic
Calcium ions (Ca2+ ) tune and control numerous diverse aspects of cochlear and vestibular physiological processes. This paper is focused on the Ca2+ control of mechanotransduction in sensory hair cells in the context of polyelectrolyte properties of actin filaments within the hair-bundles of inner ear. These actin filaments appear to serve as efficient pathways for the flow of Ca2+ ions inside stereocilia. We showed how this can be utilized for tuning of force-generating myosin motors. In an established model, we unified the Ca2+ nonlinear dynamics involved in the control of myosin adaptation motors with mechanical displacements of hair-bundles...
September 1, 2018: Bio Systems
https://www.readbyqxmd.com/read/30142359/integration-of-intracellular-signaling-biological-analogues-of-wires-processors-and-memories-organized-by-a-centrosome-3d-reference-system
#6
Nadezhda Barvitenko, Alfons Lawen, Muhammad Aslam, Antonella Pantaleo, Carlota Saldanha, Elisaveta Skverchinskaya, Marco Regolini, Jack A Tuszynski
BACKGROUND: Myriads of signaling pathways in a single cell function to achieve the highest spatio-temporal integration. Data are accumulating on the role of electromechanical soliton-like waves in signal transduction processes. Theoretical studies strongly suggest feasibility of both classical and quantum computing involving microtubules. AIM: A theoretical study of the role of the complex composed of the plasma membrane and the microtubule-based cytoskeleton as a system that transmits, stores and processes information...
August 22, 2018: Bio Systems
https://www.readbyqxmd.com/read/30134151/origins-of-the-embryo-self-organization-through-cybernetic-regulation
#7
Robert Stone, Tom Portegys, George Mikhailovsky, Bradly Alicea
The construction of an embryo from a single cell precursor is a highly complex process. Evolutionary emergence of the first embryos is even more complex, and involves both a transition to multicellularity along with the establishment of developmental mechanisms. We propose that embryogenesis relies on a community of cells conforming to a regulatory model of emergent multicellularity. This model draws together multiple threads in the scientific literature, from complexity theory to cybernetics, and from thermodynamic entropy to artificial life...
August 19, 2018: Bio Systems
https://www.readbyqxmd.com/read/30125625/reconstruction-and-analysis-of-a-genome-scale-metabolic-model-of-methylovorus-sp-mp688-a-high-level-pyrroloquinolone-quinone-producer
#8
Wei Zou, Xianghua Xiong, Jing Zhang, Kaizheng Zhang, Xingxiu Zhao, Changqing Zhao
Methylovorus sp. MP688 is a methylotrophic bacterium that can be used as a pyrroloquinolone quinone (PQQ) producer. To obtain a comprehensive understanding of its metabolic capabilities, we constructed a genome-scale metabolic model (iWZ583) of Methylovorus sp. MP688, based on its genome annotations, data from public metabolic databases, and literature mining. The model includes 772 reactions, 764 metabolites, and 583 genes. Growth of Methylovorus sp. MP688 was simulated using different carbon and nitrogen sources, and the results were consistent with experimental data...
August 18, 2018: Bio Systems
https://www.readbyqxmd.com/read/30114432/gamma-radiation-induced-in-vitro-hormetic-apogamy-in-the-fern-pityrogramma-calomelanos-l-link
#9
Sudha Sajeev, Jose Savio Melo, Smitha Hegde
Pityrogramma calomelanos (L.) Link, popularly known as "Silver fern" has significant importance as a medicinal plant used traditionally for its astringent, analgesic, anti-haemorrhagic, anti-hypertensive, anti-pyretic and anthelminthic properties. This fern demonstrates an increased morphogenetic potential towards sporophyte formation, upon exposure to low doses of gamma radiation. Young sporophytic leaf crosier cultures were established in vitro on agar based Knop's media with and without 20 g/l sucrose...
August 13, 2018: Bio Systems
https://www.readbyqxmd.com/read/30110600/multiple-roles-of-adenomatous-polyposis-coli-gene-in-wnt-signalling-a-computational-model
#10
Rejitha John Raji, Roschen Sasikumar, Elizabeth Jacob
The Adenomatous Polyposis Coli (APC) gene is a multifunctional gene that plays a major role in regulating the Wnt signalling pathway. The Wnt pathway, when activated by Wnt signalling molecules, initiates cell division. Mutation of APC disrupts the regulation and causes continuous activation of the Wnt pathway even in the absence of Wnt signals, thus causing uncontrolled cell proliferation. APC regulates the Wnt pathway by controlling the formation of the nuclear complex β-catenin/TCF that initiates the transcription of the Wnt target genes...
August 12, 2018: Bio Systems
https://www.readbyqxmd.com/read/30110599/pathway-based-gene-gene-interaction-network-modelling-to-predict-potential-biomarkers-of-essential-hypertension
#11
Le Wang, Fuhong Cheng, Jingbo Hu, Huan Wang, Nana Tan, Shaokang Li, Xiaoling Wang
Essential hypertension (EH) is a major risk factor for cardiovascular disease. Despite considerable efforts to elucidate the pathogenesis of EH, there is an imperious need for novel indicators of EH. This study aimed to develop a method to predict potential biomarkers of EH from the point of view of network. A pathway-based gene-gene interaction (GGI) network model was constructed and analyzed, containing 116 nodes and 1272 connections. The nodes represented EH-related genes, and that connections represented their interactions...
August 12, 2018: Bio Systems
https://www.readbyqxmd.com/read/30102933/towards-the-development-of-robot-immune-system-a-combined-approach-involving-innate-immune-cells-and-t-lymphocytes
#12
Maria Akram, Ali Raza
Mobile robots in uncertain and unstructuredenvironments frequently encounter faults. Therefore, an effective fault detection and recovery mechanism is required. One can possibly investigate natural systems to seek inspiration to develop systems that can handle such faults. Authors, in this pursuit, have explored the possibility of designing an artificial immune system, called Robot Immune System (RIS), to maintain a robot's internal health-equilibrium. This contrasts with existing approaches in which specific robotic tasks are performed instead of developing a self-healing robot...
August 10, 2018: Bio Systems
https://www.readbyqxmd.com/read/30099058/disease-probability-index-dpi-%C3%AF-a-new-alignment-free-scoring-method-to-evaluate-the-propensities-of-polypeptide-sequences-leading-to-disease-onset
#13
Ananya Ali, Angshuman Bagchi
The analyses of the amino acid sequences of proteins provide valuable information regarding the structure and function of the protein. A comparatively new approach is the alignment-free sequence comparisons. To-date most, if not all, sequence analysis techniques are used to find out the sequence homologies to measure the evolutionary relatedness among the species. However, a still untouched avenue in the field of sequence analyses is to build a comparative estimate of the sequence similarities between unrelated protein sequences from and within a single species...
August 9, 2018: Bio Systems
https://www.readbyqxmd.com/read/30092339/representational-fluidity-in-embodied-artificial-cognition
#14
David Windridge, Serge Thill
Theories of embodied cognition agree that the body plays some role in human cognition, but disagree on the precise nature of this role. While it is (together with the environment) fundamentally engrained in the so-called 4E (or multi-E) cognition stance, there also exists interpretations wherein the body is merely an input/output interface for cognitive processes that are entirely computational. In the present paper, we show that even if one takes such a strong computationalist position, the role of the body must be more than an interface to the world...
August 7, 2018: Bio Systems
https://www.readbyqxmd.com/read/30009873/a-general-framework-dedicated-to-computational-morphogenesis-part-ii-knowledge-representation-and-architecture
#15
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
#16
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/30055256/who-benefits-from-cellular-immune-response-during-the-chagas-disease
#17
S P Vega-Royero, G J Sibona
We extend our previous model for the dynamical interaction between a mammal's immune response and the Trypanosoma cruzi parasite during the acute phase of Chagas disease. The model here considers both humoral and cellular responses and the different stages of T. cruzi (intracellular and extracellular phases) inside the mammal host. We analyze the dynamical time evolution of the populations obtaining phase diagrams of the model results. The steady-state solution of the system yields two outcomes associated to Healing and Chronic stationary cases, the death case obtained when just the humoral immune response alone was considered is not being present...
September 2018: Bio Systems
https://www.readbyqxmd.com/read/30053414/tellurium-an-extensible-python-based-modeling-environment-for-systems-and-synthetic-biology
#18
Kiri Choi, J Kyle Medley, Matthias König, Kaylene Stocking, Lucian Smith, Stanley Gu, Herbert M Sauro
Here we present Tellurium, a Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source simulation environment composed of multiple libraries, plugins, and specialized modules and methods. Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution. Two interfaces are provided, one based on the Spyder IDE which has an accessible user interface akin to MATLAB and a second based on the Jupyter Notebook, which is a format that contains live code, equations, visualizations, and narrative text...
September 2018: Bio Systems
https://www.readbyqxmd.com/read/30048795/ferritin-and-neuromelanin-quantum-dot-array-structures-in-dopamine-neurons-of-the-substantia-nigra-pars-compacta-and-norepinephrine-neurons-of-the-locus-coeruleus
#19
REVIEW
Christopher John Rourk
In this review, the author shows that ferritin has documented quantum dot material properties that have been reported in numerous independent studies, and can enable quantum mechanical electron transport over substantial distances. In addition, neuromelanin is a pi-conjugated polymer, and quantum dot/pi-conjugated polymer combinations have been reported in numerous independent studies to facilitate electron transport for solar photovoltaic and other applications. Both ferritin and neuromelanin are present in large quantities in the dopamine neurons of the substantia nigra pars compactaand the norepinephrine neurons of the locus coeruleus...
September 2018: Bio Systems
https://www.readbyqxmd.com/read/30030162/genome-wide-analysis-of-h3k36me3-and-its-regulations-to-cancer-related-genes-expression-in-human-cell-lines
#20
Lu-Qiang Zhang, Qian-Zhong Li, Wen Jin, Yongchun Zuo, Shu-Chun Guo
H3K36me3 is a histone modification known to mark active genes. To further understand the effects of H3K36me3 on gene expression levels, we develop predictive models to compute the correlation between the binding signal of H3K36me3 in each bin and the gene expression levels. We find that the bins with stronger H3K36me3 averaged-binding signals present higher correlative strengths with the expression levels of gene. And the higher correlative strengths appear in the downstream regions of the transcription start site...
September 2018: Bio Systems
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