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Bio Systems

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https://www.readbyqxmd.com/read/29331630/mrna-function-after-intracellular-delivery-and-release
#1
Vladimir P Zhdanov
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. Assuming the release to be rapid on the time scale of other steps, the author shows theoretically the mRNA-related transient features of gene expression occurring in stable, bistable, and oscillatory regimes in a single cell...
January 10, 2018: Bio Systems
https://www.readbyqxmd.com/read/29326068/slime-mould-the-fundamental-mechanisms-of-biological-cognition
#2
Jordi Vallverdú, Oscar Castro, Richard Mayne, Max Talanov, Michael Levin, Frantisek Baluška, Yukio Gunji, Audrey Dussutour, Hector Zenil, Andrew Adamatzky
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 rather as an active living substrate yet the slime mould is a self-consistent living creature which evolved for millions of years and occupied most part of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" the slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P...
January 8, 2018: Bio Systems
https://www.readbyqxmd.com/read/29317314/phi-in-physiology-psychology-and-biomechanics-the-golden-ratio-between-myth-and-science
#3
REVIEW
Marco Iosa, Giovanni Morone, Stefano Paolucci
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. Nevertheless, recent scientific results often fall between two extremes: those of a priori sceptic researchers accusing the artificial emergence of ϕ in many studies, and those of researchers that find a mystic meaning in the presence of ϕ in human physiology...
January 6, 2018: Bio Systems
https://www.readbyqxmd.com/read/29317313/the-role-of-fenton-reaction-in-ros-induced-toxicity-underlying-atherosclerosis-modeled-and-analyzed-using-a-petri-net-based-approach
#4
Dorota Formanowicz, Marcin Radom, Agnieszka Rybarczyk, Piotr Formanowicz
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. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated...
January 6, 2018: Bio Systems
https://www.readbyqxmd.com/read/29278731/a-test-of-the-adaptive-network-explanation-of-functional-disorders-using-a-machine-learning-analysis-of-symptoms
#5
Christos Melidis, Susan L Denham, Michael E Hyland
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., irritable bowel syndrome (IBS), fibromyalgia syndrome (FMS), and chronic fatigue syndrome (CFS)). Two network models (symptom network and adaptive network) can explain the specificity and covariation of symptomatology, but only the adaptive network model can explain the covariation of the somatic symptoms of functional disorders...
December 23, 2017: Bio Systems
https://www.readbyqxmd.com/read/29278730/cm-viewer-visualizing-interaction-network-of-co-mutated-and-mutually-exclusively-mutated-cancer-genes
#6
Nan Zhou, Zongyue Hu, Chuanfang Wu, Jinku Bao
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. Although cancer genes with co-occurring and mutually exclusive mutations have already been studied on different scales, there is no timely updated interaction network available for co-mutated and mutually exclusively mutated cancer genes...
December 23, 2017: Bio Systems
https://www.readbyqxmd.com/read/29274363/unique-features-of-nucleotide-and-codon-usage-patterns-in-mycoplasmas-revealed-by-information-entropy
#7
Yi-Ning Wang, Wen-Heng Ji, Xue-Rui Li, Yong-Sheng Liu, Jian-Hua Zhou
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...
December 20, 2017: Bio Systems
https://www.readbyqxmd.com/read/29258888/the-first-special-issue-on-code-biology-a-bird-s-eye-view
#8
REVIEW
Jan-Hendrik S Hofmeyr
No abstract text is available yet for this article.
December 16, 2017: Bio Systems
https://www.readbyqxmd.com/read/29248539/modeling-of-decision-making-process-for-moving-straight-using-inverse-bayesian-inference
#9
Youichi Horry, Ai Yoshinari, Yurina Nakamoto, Yukio-Pegio Gunji
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. In the experiment, subjects viewed a three-dimensional space displayed on a computer display in the first person's perspective and were instructed to go straight from the start to the goal position. Results showed that unreasonable selections that strayed from the centerline connecting the start and goal positions were frequently made...
December 14, 2017: Bio Systems
https://www.readbyqxmd.com/read/29246781/modular-assembling-process-of-an-in-silico-protocell
#10
Eugenia Schneider, Michael Mangold
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...
December 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/29233730/cyclic-concatenated-genetic-encoder-a-mathematical-proposal-for-biological-inferences
#11
M E Duarte-González, O Y Echeverri, J M Guevara, R Palazzo
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...
December 9, 2017: Bio Systems
https://www.readbyqxmd.com/read/29233729/prediction-of-replication-sites-in-saccharomyces-cerevisiae-genome-using-dna-segment-properties-multi-view-ensemble-learning-mel-approach
#12
Vinod Kumar Singh, Vipin Kumar, Annangarachari Krishnamachari
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. We considered a few properties of DNA segments and divided them into multiple subsets (views) for computational prediction of ARS sequences...
December 9, 2017: Bio Systems
https://www.readbyqxmd.com/read/29229425/dynamic-analysis-on-the-calcium-oscillation-model-considering-the-influences-of-mitochondria
#13
Xiang Li, Suxia Zhang, Xijun Liu, Xiaojing Wang, Anqi Zhou, Peng Liu
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. Third, β (representing calcium leak) is introduced and it can be found that with the increase of β, the Hopf bifurcation points of system move towards the decreasing direction of μ (representing stimulus intensity) and calcium oscillations region gradually decreases...
December 8, 2017: Bio Systems
https://www.readbyqxmd.com/read/29199093/evolutionary-epistemology-reviewing-and-reviving-with-new-data-the-research-programme-for-distributed-biological-intelligence
#14
REVIEW
Predrag Slijepcevic
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...
November 30, 2017: Bio Systems
https://www.readbyqxmd.com/read/29174696/corrigendum-to-mathematical-analysis-of-a-cholera-model-with-public-health-interventions-biosystems-105-3-2011-190-200
#15
A Mwasa, J M Tchuenche
No abstract text is available yet for this article.
November 22, 2017: Bio Systems
https://www.readbyqxmd.com/read/29174790/towards-measuring-the-semantic-capacity-of-a-physical-medium-demonstrated-with-elementary-cellular-automata
#16
Peter Dittrich
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). The semantic capacity is measured by counting the number of ways codes can be implemented...
November 21, 2017: Bio Systems
https://www.readbyqxmd.com/read/29158132/deciphering-the-histone-code-to-build-the-genome-structure
#17
Kirti Prakash, David Fournier
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. Next, we present evidence for the association among different histone modifications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replication and cell division...
November 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/29157987/corrigendum-to-a-biophysical-approach-to-cancer-dynamics-quantum-chaos-and-energy-turbulence-biosystems-156-157-june-july-2017-1-22
#18
Abicumaran Uthamacumaran
No abstract text is available yet for this article.
November 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/29129822/a-hyperbolastic-type-i-diffusion-process-parameter-estimation-by-means-of-the-firefly-algorithm
#19
Antonio Barrera, Patricia Román-Román, Francisco Torres-Ruiz
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. Some examples based on simulated sample paths and real data illustrate this development.
November 9, 2017: Bio Systems
https://www.readbyqxmd.com/read/29122587/the-splicing-code
#20
REVIEW
Marco Baralle, Francisco Ernesto Baralle
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. A degree of ambiguity is possible if mutations are introduced in the tRNAs in a way that the anticodon reads one amino acid but the aminoacyl-transferase attaches a different one onto the tRNA...
November 6, 2017: Bio Systems
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