Mixed-monolayer functionalized gold nanoparticles for cancer treatment: Atomistic molecular dynamics simulations study.
Abstract Gold nanoparticles (AuNPs) are employed as drug carriers due to their inertness, non-toxicity, and ease of synthesis. An experimental search for the optimal AuNP design would require a systematic variation of physico-chemical properties which is time-consuming and expensive. Computational methods provide quicker and cheaper approach to complement experiments and provide useful guidelines. In this paper, we performed atomistic molecular dynamics simulations to study how the size, hydrophobicity, and concentration of the drug affect the structure of functionalized AuNPs in the aqueous environment. We simula...
Source: Biosystems - January 11, 2021 Category: Biotechnology Authors: Kovacevic M, Balaz I, Marson D, Laurini E, Jovic B Tags: Biosystems Source Type: research

The emergence of a fractal structure of formal logic via the spatiotemporal reflexive self-identification.
Abstract In this paper, we aim to unravel the structure of formal logic in relation to its emergence as a universal tool for understanding and description of reality. There are some extended variations of logic that treat time and/or space (e.g. temporal logic), however in general, formal logic is regarded as universal. This universality makes formal logic neither spatial nor temporal. Nevertheless, the emergence of formal logic takes place in time and space and its operation is characterized by the simultaneous temporal and spatial features. We realize these aspects of formal logic along the line of the previousl...
Source: Biosystems - January 5, 2021 Category: Biotechnology Authors: Sawa K, Igamberdiev AU Tags: Biosystems Source Type: research

Protein-DNA target search relies on quantum walk.
Abstract Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researchers for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena...
Source: Biosystems - December 30, 2020 Category: Biotechnology Authors: D'Acunto M Tags: Biosystems Source Type: research

Incorporating antagonistic pleiotropy into models for molecular replicators.
Abstract In modern cells, chromosomal genes composed of DNA encode multi-subunit protein/RNA complexes that catalyze the replication of the chromosome and cell. One prevailing theory for the origin of life posits an early stage involving self-replicating macromolecules called replicators, which can be considered genes capable of self-replication. One prevailing theory for the genetics of aging in humans and other organisms is antagonistic pleiotropy, which posits that a gene can be beneficial in one context, and detrimental in another context. We previously reported that the conceptual simplicity of molecular repl...
Source: Biosystems - December 24, 2020 Category: Biotechnology Authors: Qu T, Calabrese P, Singhavi P, Tower J Tags: Biosystems Source Type: research

The effect of noise and harmonic excitation in growing Bacillus subtilis biofilms.
Abstract We study the dynamic growth behaviors of Bacillus subtilis biofilms by using a stochastic delay differential equation similar to the Mackey-Glass equation. We observe a wealth of dynamic behavior from a mathematical perspective. Firstly, the change of the time delay (i.e. the time that the growth state of the periphery to affect the stress of the interior cells needs and the time required for the stress signal coming from the interior to reach the peripheral cells) and the external excitation (i.e. the change in temperature) frequency will influence the size of Bacillus subtilis biofilm and the collective...
Source: Biosystems - December 23, 2020 Category: Biotechnology Authors: Wang Q, Zhang X, Yang Y Tags: Biosystems Source Type: research

High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net.
Abstract Dynamic simulation promises a deeper understanding of complex molecular mechanisms of biological pathways. How to determine the reaction kinetic parameters which govern the simulation results is still an open question in the field of systems biology. (1) Background: To execute simulation experiments, it is an essential first step to search effective values of model parameters. The complexity of biological systems and the experimental measurement technology severely limit the acquirement of accurate kinetic parameters. Previously proposed genomic data assimilation (GDA) approach enables users to handle par...
Source: Biosystems - December 22, 2020 Category: Biotechnology Authors: Li C, Qin J, Kuroyanagi K, Lu L, Nagasaki M, Satoru M Tags: Biosystems Source Type: research

A protein folding robot driven by a self-taught agent.
Abstract This paper presents a computer simulation of a virtual robot that behaves as a peptide chain of the Hemagglutinin-Esterase protein (HEs) from human coronavirus. The robot can learn efficient protein folding policies by itself and then use them to solve HEs folding episodes. The proposed robotic unfolded structure inhabits a dynamic environment and is driven by a self-taught neural agent. The neural agent can read sensors and control the angles and interactions between individual amino acids. During the training phase, the agent uses reinforcement learning to explore new folding forms that conduce toward m...
Source: Biosystems - December 21, 2020 Category: Biotechnology Authors: Chang O, Gonzales-Zubiate FA, Zhinin-Vera L, Valencia-Ramos R, Pineda I, Diaz-Barrios A Tags: Biosystems Source Type: research

Cell and extracellular matrix growth theory and its implications for tumorigenesis.
The objective of the present theory is to predict the increase in the size of the cell cluster as a function of its structure, and also to predict the critical cluster sizes that mark the transitions from one distinct cluster configuration to the next. This amounts to predicting the timing and the main features of the transitions from single cell to clusters with two, four, eight and more cells, including larger clusters with cells organized on its outer surface. The predicted evolution of the size and configuration of the cell cluster is validated successfully by comparison with measurements from several independent studi...
Source: Biosystems - December 21, 2020 Category: Biotechnology Authors: Sauer TJ, Samei E, Bejan A Tags: Biosystems Source Type: research

The late appearance of DNA, the nature of the LUCA and ancestors of the domains of life.
Abstract It has been firmly observed that replicative DNA polymerases of bacteria, archaea and eukaryotes are not homologous proteins. This lack of homology in the replication apparatus among the domains of life is not only compatible with but would seem to imply the view that the emergence of DNA occurred in the fundamental cellular lineages. In consequence, this diversity of DNA polymerase would go back to the level of ancestors of the domains of life and to the evolutionary time in which the DNA emerged. Therefore, the presumed evolutionary stage linked to the RNA- > DNA transition would have occurred on...
Source: Biosystems - December 19, 2020 Category: Biotechnology Authors: Di Giulio M Tags: Biosystems Source Type: research

Quantum-like modeling in biology with open quantum systems and instruments.
We present the novel approach to mathematical modeling of information processes in biosystems. It explores the mathematical formalism and methodology of quantum theory, especially quantum measurement theory. This approach is known as quantum-like and it should be distinguished from study of genuine quantum physical processes in biosystems (quantum biophysics, quantum cognition). It is based on quantum information representation of biosystem's state and modeling its dynamics in the framework of theory of open quantum systems. This paper starts with the non-physicist friendly presentation of quantum measurement theory, from ...
Source: Biosystems - December 18, 2020 Category: Biotechnology Authors: Basieva I, Khrennikov A, Ozawa M Tags: Biosystems Source Type: research

Non-genetic inheritance: Evolution above the organismal level.
Abstract The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less on community system traits (synergetic/organizational traits) that characterize transgenerational biological, ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of interacting populations that occupy the same place in ...
Source: Biosystems - December 11, 2020 Category: Biotechnology Authors: Sukhoverkhov AV, Gontier N Tags: Biosystems Source Type: research

The role of the "Thiodendron" consortium in the Postulation of the karyomastigont chimaera of the endosymbiosis theory by Lynn Margulis.
The role of the "Thiodendron" consortium in the Postulation of the karyomastigont chimaera of the endosymbiosis theory by Lynn Margulis. Biosystems. 2020 Dec 10;:104322 Authors: Grabovich MY, Gureeva MV, Dubinina GA Abstract The endosymbiosis theory of the origin of eukaryotic cell was first proposed more than a hundred years ago. In the second half of the 20th century, Lynn Margulis suggested a new interpretation of the origin of the nucleus in modern eukaryotes. The background was the study of the consortium "Thiodendron", a symbiotic bacterial community, which includes anaerobic...
Source: Biosystems - December 10, 2020 Category: Biotechnology Authors: Grabovich MY, Gureeva MV, Dubinina GA Tags: Biosystems Source Type: research

KatzDriver: A network based method to cancer causal genes discovery in gene regulatory network.
In this study, we proposed KatzDriver, as a network-based approach, in order to detect CDGs. This method is able to calculate the relative impact of each gene in the spread of abnormality in the gene regulatory network. In this approach, we firstly create the studied networks using gene expression and regulatory interaction data. Then by combining the topological and biological data, the weights of edges (regulatory interactions) and nodes (genes) are calculated. Afterward, based on the KATZ approach, the receiving and broadcasting powers of each gene were calculated to find the relative impact of each gene. At the end, th...
Source: Biosystems - December 10, 2020 Category: Biotechnology Authors: Safar MA, Teimourpour B Tags: Biosystems Source Type: research

A novel mathematical model of AIDS-associated Kaposi sarcoma: Analysis and optimal control.
Abstract Kaposi sarcoma (KS) has been the most common HHV-8 virus-induced neoplasm associated with HIV infection. Although the standard KS therapy has not changed in 20 years, not all cases of KS will respond to the same therapy. The goal of current AIDS-KS treatment modalities is to reconstitute the immune system and suppress HIV-1 replication, but newer treatment modalities are on horizon. There are very few mathematical models that have included HIV-1 viral load (VL) measures, despite VL being a key determinant of treatment outcome. Here we introduce a mathematical model that consolidates the effect of both HIV...
Source: Biosystems - December 9, 2020 Category: Biotechnology Authors: Kaondera-Shava RF, Lungu E, Szomolay B Tags: Biosystems Source Type: research

PDE based geometry model for BCG immunotherapy of bladder cancer.
We present a model describing a BCG immunotherapy dynamic taking into consideration an approximation of the bladder's geometry using PDE. We show that the proposed model takes into account the initial distribution of the cancer cells in the geometry of the bladder and as such can provide more customized treatment by providing tumor polyp depth in the urothelium. In addition, time optimal treatment protocol for the average case and recover-rate optimal, personalized treatment protocol based on initial tumor distribution have been analyzed. PMID: 33309555 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - December 9, 2020 Category: Biotechnology Authors: Lazebnik T, Aaroni N, Bunimovich-Mendrazitsky S Tags: Biosystems Source Type: research

A systems-biology view of viruses explains why they are not alive.
Abstract Whether or not viruses are alive remains unsettled. Discoveries of giant viruses with translational genes and large genomes have kept the debate active. Here, a fresh approach is introduced, based on the organisational definition of life from within systems biology. It views living as a circular process of self-organisation and self-construction which is 'closed to efficient causation'. How information combines with force to fabricate and organise environmentally obtained materials, given an energy source, is here explained as a physical embodiment of informational constraint. Comparing a general virus re...
Source: Biosystems - December 8, 2020 Category: Biotechnology Authors: Farnsworth KD Tags: Biosystems Source Type: research

Lynn Margulis and Boris Kozo-Polyansky: How the Symbiogenesis was translated from Russian.
Abstract This contribution details the complex history of the early work by Boris Kozo-Polyansky (1924) that became available in English translation 86 years after it was published in Russian. The great American naturalist Lynn Margulis-whose serial endosymbiosis theory was presciently predated by Kozo-Polyansky by four decades-was instrumental in organizing this resurrection and 'horizontal transfer' of knowledge, forgotten by that time even in Russia. PMID: 33285250 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - December 4, 2020 Category: Biotechnology Authors: Fet V Tags: Biosystems Source Type: research

Stability analysis and optimal control of HPV infection model with early-stage cervical cancer.
Abstract Cervical cancer cells may develop from any cell infected by human papillomavirus (HPV). The aim of this paper is to study whether an optimal control of HPV infection can reduce those resulting cancer cells. To this end, the problem will be modelled by five differential equations that describe the interactions between healthy cells, infected cells, free virus, precancerous cells and cancer cells. A saturated infection rate and two treatments are incorporated into the model. The first therapy stands for the efficacy of drug treatment in blocking new infections, whereas the second serves as the drug effectiv...
Source: Biosystems - December 4, 2020 Category: Biotechnology Authors: Allali K Tags: Biosystems Source Type: research

The theory of two plasma lineages as the basis of symbiogenesis, a new principle for the origin of organisms.
Abstract In 1910, the Russian biologist Konstantin Sergejewitch Mereschkowsky (Константин Сергеевич Мережковский, in standard transliterations also written as Konstantin Sergeevič Merežkovskij and Konstantin Sergeevich Merezhkovsky) published a notable synthesis of observations and inferences concerning the origin of life and the origin of nucleated cells. His theory was based on physiology and leaned heavily upon the premise that thermophilic autotrophs were ancient. The ancestors of plants and animals were inferred as ancestrally mesophilic anucleate heterotrophs (Monera) that be...
Source: Biosystems - December 3, 2020 Category: Biotechnology Authors: Kowallik KV, Martin WF Tags: Biosystems Source Type: research

Identification of breast cancer prognostic modules via differential module selection based on weighted gene Co-expression network analysis.
Abstract Breast cancer is a complex cancer which includes many different subtypes. Identifying prognostic modules, i.e., functionally related gene networks that play crucial roles in cancer development is essential in breast cancer study. Different subtypes of breast cancer correspond to different treatment methods. The purpose of this study is to use a new method to divide breast cancer into different prognostic modules, so as to provide scientific basis for improving clinical management. The method is based on comparing similarities between modules detected from different weighted gene co-expression networks. Th...
Source: Biosystems - December 3, 2020 Category: Biotechnology Authors: Guo L, Mao L, Lu W, Yang J Tags: Biosystems Source Type: research

Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions.
Abstract The field of evolutionary algorithms (EAs) emerged in the area of computer science due to transfer of ideas from biology and developed independently for several decades, enriched with techniques from probability theory, complexity theory and optimization methods. In this paper, we consider some recent results form the EAs theory transferred back into biology. The well-known biotechnological procedure SELEX (Systematic Evolution of Ligands by EXponential enrichment) is viewed as an experimental implementation of an evolutionary algorithm. Theoretical bounds on EAs runtime are applied to model SELEX search ...
Source: Biosystems - December 2, 2020 Category: Biotechnology Authors: Eremeev AV, Spirov AV Tags: Biosystems Source Type: research

Beyond planetary-scale feedback self-regulation: Gaia as an autopoietic system.
Abstract The Gaia hypothesis states that the Earth is an instance of the living phenomenon. However, appraisals of it tend to focus on the claim that life is a feedback self-regulator that controls Earth's chemistry and climate dynamics, yet, self-regulation by feedbacks is not a definitive characteristic of living systems. Here, we consider the characterization of biological systems as autopoietic systems (causally organized to self-produce through metabolic closure) and then ask whether the Gaia hypothesis is a tractable question from this standpoint. A proof-of-concept based on Chemical Organization Theory (COT...
Source: Biosystems - November 30, 2020 Category: Biotechnology Authors: Rubin S, Veloz T, Maldonado P Tags: Biosystems Source Type: research

Extraction of the molecular level biomedical event trigger based on gene ontology using radial belief neural network techniques.
Abstract Detection of molecular level biomedical event extraction plays a vital role in creating and visualizing the applications related to natural language processing. Cystic Fibrosis is an inherited genetic and debilitating pathology involving the respiratory and digestive systems. The excessive production of thick sticky mucus on the outside of the cells is the main consequence of such disease. This includes disease prevention and medical search to signify the occurrence and detection of event triggers, which is regarded as a proper step in an event extraction of molecular level in biomedical applications. In ...
Source: Biosystems - November 28, 2020 Category: Biotechnology Authors: Devendra Kumar RN, Chakrapani A, Srihari K Tags: Biosystems Source Type: research

On multistep tumor growth models of fractional variable-order.
Abstract Fractional mathematical oncology is a research topic that applies non-integer order calculus to tackle cancer problems such as tumor growth analysis or its optimal treatment. This work proposes a multistep exponential model with a fractional variable-order representing the evolution history of a tumor. Model parameters are tuned according to variable fractional order profiles while assessing their capability of fitting a clinical time series. The results point to the superiority of the proposed model in describing the experimental data, thus providing new perspectives for modeling tumor growth. PMID:...
Source: Biosystems - November 25, 2020 Category: Biotechnology Authors: Valentim CA, Rabi JA, David SA, Tenreiro Machado JA Tags: Biosystems Source Type: research

Dynamical diversity of mitochondrial BK channels located in different cell types.
Abstract Mitochondrial large-conductance voltage- and Ca2+-activated potassium channels (mitoBK) exhibit substantial similarities in their physiology regardless of the channel's location. Nevertheless, depending on the cell type, composition of membranes can vary, and mitoBK channels can be expressed in different splice variants as well as they can be co-assembled with different types of auxiliary β subunits. These factors can modulate their voltage- and Ca2+-sensitivity, and single-channel current kinetics. It is still an open question to what extent the mentioned factors can affect the complexity of the con...
Source: Biosystems - November 25, 2020 Category: Biotechnology Authors: Wawrzkiewicz-Jałowiecka A, Trybek P, Machura Ł, Bednarczyk P Tags: Biosystems Source Type: research

Reactive fungal wearable.
Abstract Smart wearables sense and process information from the user's body and environment and report results of their analysis as electrical signals. Conventional electronic sensors and controllers are commonly, sometimes augmented by recent advances in soft electronics. Organic electronics and bioelectronics, especially with living substrates, offer a great opportunity to incorporate parallel sensing and information processing capabilities of natural systems into future and emerging wearables. Nowadays fungi are emerging as a promising candidate to produce sustainable textiles to be used as ecofriendly bioweara...
Source: Biosystems - November 24, 2020 Category: Biotechnology Authors: Adamatzky A, Nikolaidou A, Gandia A, Chiolerio A, Dehshibi MM Tags: Biosystems Source Type: research

Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky.
Abstract We analyze evolutionary views of Boris Kozo-Polyansky (1890-1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on the symbiotic origin of chloroplasts and mitochondria appeared earlier, the book of Kozo-Polyansky presented symbiogenesis as the main factor of complexification in the course of evolution, not only in relation to the origin of eukaryotic cell. Kozo-Polyansky i...
Source: Biosystems - November 20, 2020 Category: Biotechnology Authors: Agafonov VA, Negrobov VV, Igamberdiev AU Tags: Biosystems Source Type: research

MRWMDA: A novel framework to infer miRNA-disease associations.
Abstract MicroRNAs (miRNAs) are widely involved in a series of significant biological processes, which have been revealed and verified by accumulating experimental studies. The computational inference of the correlation between miRNAs and diseases is essential to facilitate the detection of disease biomarkers for disease diagnosis, prevention, treatment and prognosis. In this paper, a model with Multiple use of Random Walk with restart algorithm was introduced for the prediction of the MiRNA-Disease Association (MRWMDA). Based on diverse similarity measures, the model first implemented the random walk with restart...
Source: Biosystems - November 19, 2020 Category: Biotechnology Authors: Wang M, Zhu P Tags: Biosystems Source Type: research

Cell-to-cell diversification in ERBB-RAS-MAPK signal transduction that produces cell-type specific growth factor responses.
Abstract Growth factors regulate cell fates, including their proliferation, differentiation, survival, and death, according to the cell type. Even when the response to a specific growth factor is deterministic for collective cell behavior, significant levels of fluctuation are often observed between single cells. Statistical analyses of single-cell responses provide insights into the mechanism of cell fate decisions but very little is known about the distributions of the internal states of cells responding to growth factors. Using multi-color immunofluorescent staining, we have here detected the phosphorylation of...
Source: Biosystems - November 19, 2020 Category: Biotechnology Authors: Miyagi H, Hiroshima M, Sako Y Tags: Biosystems Source Type: research

Harnessing adaptive novelty for automated generation of cancer treatments.
Abstract Nanoparticles have the potential to modulate both the pharmacokinetic and pharmacodynamic profiles of drugs, thereby enhancing their therapeutic effect. The versatility of nanoparticles allows for a wide range of customization possibilities. However, it also leads to a rich design space which is difficult to investigate and optimize. An additional problem emerges when they are applied to cancer treatment. A heterogeneous and highly adaptable tumour can quickly become resistant to primary therapy, making it inefficient. To automate the design of potential therapies for such complex cases, we propose a comp...
Source: Biosystems - November 17, 2020 Category: Biotechnology Authors: Balaz I, Petrić T, Kovacevic M, Tsompanas MA, Stillman N Tags: Biosystems Source Type: research

p-Adic mathematics and theoretical biology.
NŽ Abstract The principal objective of this article is a brief overview of the main parts of p-adic mathematics, which have already had valuable applications and may have a significant impact in the near future on the further development of some fields of theoretical and mathematical biology. In particular, we present the basics of ultrametrics, p-adic numbers and p-adic analysis, as well as insight into their applications for modeling some cognitive processes, genetic code and protein dynamics. We also argue that ultrametric concepts and p-adic mathematics are natural tools for the viable description of biolog...
Source: Biosystems - November 11, 2020 Category: Biotechnology Authors: Dragovich B, Khrennikov AY, Kozyrev SV, Mišić NŽ Tags: Biosystems Source Type: research

Surface contraction waves or cell proliferation waves in the presumptive neurectoderm during amphibian gastrulation: Mexican axolotl versus African clawed frog.
Abstract This essay represents a critical analysis of the literary data on various types of waves occurring in the amphibian embryos during gastrulation. A surface contraction wave travels through the presumptive neurectoderm during Mexican axolotl gastrulation. This wave coincides temporally and spatially with involution of the inducing chordomesoderm and with the prospective neural plate. By contrast, there is no similar surface contraction wave during African clawed frog gastrulation. However, the clawed frog displays the waves of DNA synthesis and mitosis in the presumptive neurectoderm during gastrulation, wh...
Source: Biosystems - November 9, 2020 Category: Biotechnology Authors: Desnitskiy AG Tags: Biosystems Source Type: research

Modeling inherited physiological structures based on hyperbolic numbers.
Abstract The article is devoted to using the mathematics of multi-dimensional hyperbolic numbers and their matrix representations for modeling of different inherited biosystems, which are parts of the holistic body. The list of considered models includes phyllotaxis sequences; Punnet squares of the Mendelian genetics; the main psychophysical Weber-Fechner law, and some others. This modeling approach reveals hidden structural interconnections among different biosystems and leads a deeper understanding of their commonality related to the commonality of their genetic basis. At the same time, it shows the structural c...
Source: Biosystems - November 6, 2020 Category: Biotechnology Authors: Petoukhov SV Tags: Biosystems Source Type: research

Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach.
Abstract In this paper, we identify all possible Gray Code and Partitioned Gray Code representations of the Universal Genetic Code for n = 2-bit and 3-bit binary numbers. We analyse the Hamming Distance matrices of all these Gray code and Partitioned Gray Code possibilities for which we obtain the Toeplitz and Partitioned Toeplitz Matrices, respectively. We use this Gray Code and Partitioned Gray Code representations of the Universal Genetic Code combined with the novel Toeplitz matrix approach to generate many Never Born Protein (NBP) Sequences, which exhibit intrinsic structural stability. In general, Never ...
Source: Biosystems - November 5, 2020 Category: Biotechnology Authors: Muthugobal BKN, Ramesh G, Parthasarathy S, Suvaithenamudhan S, Prasath KM Tags: Biosystems Source Type: research

Evaluating the effectiveness of several synchronization control methods applying to the electrically and the chemically coupled hindmarsh-rose neurons.
This study focuses on the synchronization control between the coupled neurons. The achievements of several synchronization control methods have been checked by evaluating the effects of the synaptic coupling weight alteration on the synchronization. Here, a neural ensemble has been constructed by utilizing the Hindmarsh Rose (HR) Neuron Model. The HR neurons have been linked to each other with the bidirectional coupling. The synchrony or the asynchrony states between these coupled neurons have been observed by using the standard deviation results. Here, firstly, the electrically and the chemically coupled HR neurons have b...
Source: Biosystems - November 4, 2020 Category: Biotechnology Authors: Çimen Z, Korkmaz N, Altuncu Y, Kılıç R Tags: Biosystems Source Type: research

Exploring the complexity and chaotic behavior in plankton-fish system with mutual interference and time delay.
Abstract Anti-predator defense is an important mechanism that preys use to reduce the stress of constant struggle in a high concentration of predator and commonly established through evolution that supports prey organisms against predators. In the current study, we explore a three-tier plankton-fish interaction model using two kinds of function form, Monod-Haldane and Beddington-DeAngelis type. We introduce a discrete-time delay in the top predator population due to gestation. Our main objective persuades in this article is to address the role of inhibitory effect, mutual interference and gestation delay on the sy...
Source: Biosystems - November 3, 2020 Category: Biotechnology Authors: Ojha A, Thakur NK Tags: Biosystems Source Type: research

D'Arcy W. Thompson's On Growth and Form: A landmark for the mathematical foundations of epigenetics.
Abstract The celebrated 1917 work "On Growth and Form" of D'Arcy W. Thompson has established a landmark for mathematical biology, introducing new perspectives of study and research in biology, providing mathematical methods to morphology of biological systems. In this brief historical essay, we recall the novelties and relevance of the work from a retrospective stance, above all pointing out the crucial role played by it in the dawning of epigenetic standpoint. The role of underlying epigenetic processes in generation of biological forms via similarity transformations is analyzed within the framework of ...
Source: Biosystems - October 24, 2020 Category: Biotechnology Authors: Iurato G, Igamberdiev AU Tags: Biosystems Source Type: research

A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details.
Abstract Waddington's epigenetic landscape is a classic metaphor for describing the cellular dynamics during the development modulated by gene regulation. Quantifying Waddington's epigenetic landscape by mathematical modeling would be useful for understanding the mechanisms of cell fate determination. A few computational methods have been proposed for quantitative modeling of landscape; however, to model and visualize the landscape of a high dimensional gene regulatory system with realistic details is still challenging. Here, we propose a Monte Carlo method for modeling the Waddington's epigenetic landscape of a g...
Source: Biosystems - October 17, 2020 Category: Biotechnology Authors: Zhang X, Chong KH, Zhu L, Zheng J Tags: Biosystems Source Type: research

Contribution of AMPA and NMDA receptors in the spontaneous firing patterns of single neurons in autaptic culture.
Abstract Single neurons in an autaptic culture exhibit various types of firing pattern with different firing durations and rhythms. However, a neuron with autapses has often been modeled as an oscillator providing a monotonic firing pattern with a constant periodicity because of the lack of a mathematical model. In the work discribed in this study, we use computational simulation and whole-cell patch-clamp recording to elucidate and model the mechanism by which such neurons generate various firing pattens. In the computational simulation, three types of spontaneous firing pattern, i.e., short, long-lasting, and pe...
Source: Biosystems - October 16, 2020 Category: Biotechnology Authors: Hattori K, Hayakawa T, Nakanishi A, Ishida M, Yamamoto H, Hirano-Iwata A, Tanii T Tags: Biosystems Source Type: research

Simulation of multiple microenvironments shows a pivot role of RPTPs on the control of epithelial-to-mesenchymal transition.
Abstract Epithelial-to-Mesenchymal Transition (EMT) is a natural and reversible process involved in embryogenesis, wound healing and thought to participate in the process of metastasis. Multiple signals from the microenvironment have been reported to drive EMT. However, the tight control of this process on physiological scenarios and how it is disrupted during cancer progression is not fully understood. Here, we analysed a regulatory network of EMT accounting for 10 key microenvironment signals focusing on the impact of two cell contact signals on the reversibility of EMT and the stability of resulting phenotypes....
Source: Biosystems - October 14, 2020 Category: Biotechnology Authors: Pais RJ Tags: Biosystems Source Type: research

The rise of languaging.
Abstract In this paper, we turn to languaging, defined here as activity in which wordings play a part. On such a view, while activity is paramount, people also orient to acts of vocalization as wordings. These physical wordings can be used as tools that shape attending, with recourse to neither mental representations nor symbols that store and transmit information. The view is consistent with macroevolutionary continuity and will be used to challenge appeal to a major evolutionary transition to 'language'. On the languaging view, like many modern social primates, hominins have long undertaken encultured activities...
Source: Biosystems - October 14, 2020 Category: Biotechnology Authors: Cowley SJ, Kuhle A Tags: Biosystems Source Type: research

Implementing logical inference based on DNA assembly.
We describe mechanisms for finding the successful solutions among the many parallel assemblies. A whole tile assembly system is established on the base of a seed configuration and three subsystems. This prototype is the first programming language to implement deduction operations based on two-dimensional DNA assembly. It is demonstrated that algorithmic DNA tile assembly system can be treated as an important way to implement logic inference, which will shed light on aspects of applications in the field of artificial intelligence in the future. PMID: 33068673 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - October 14, 2020 Category: Biotechnology Authors: Huang Y, Xu Y Tags: Biosystems Source Type: research

Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes.
Abstract The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for the cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence ...
Source: Biosystems - October 13, 2020 Category: Biotechnology Authors: Petoukhov SV Tags: Biosystems Source Type: research

Asynchronous time-space model for evolutionary market.
Abstract An economic system is thought to be evolutionary growing. Economists investigate human decision-making by monetary value. However, the emergent property of the economy has not been explained. A model considering the extent of the monetary value is required. In this paper, a time-space model is proposed to elucidate the economic evolution of a market. Since the market activities are always open and realtime, the model of time and space is complicated. For the complexity, the probabilistic boundary and expectations under a low-possibility are introduced. Then, time and space cannot be separated and are defi...
Source: Biosystems - October 10, 2020 Category: Biotechnology Authors: Sasai K Tags: Biosystems Source Type: research

An integrative explanation of action.
Abstract The Predictive Processing Theory (PP) and its foundational Free Energy Principle (FEP) provide a unifying theoretical groundwork that subsumes theories of perception, cognition, and action. Recently Colin Klein (2018) contends that PP-FEP cannot explain adaptive action with the same force that they deal with perceptions. In his answer to the objection, Clark (2020) points out that FEP explains action, desire and motivation on the basis of minimisation of energy. I argue that this answer begs the question of the unifying framework of FEP. I assume that FEP-PP alone cannot provide an ultimately compelling e...
Source: Biosystems - October 10, 2020 Category: Biotechnology Authors: Beni MD Tags: Biosystems Source Type: research

The evolutionary dynamics of social systems - Looking for a new dialog.
ev AU PMID: 33038462 [PubMed - as supplied by publisher] (Source: Biosystems)
Source: Biosystems - October 7, 2020 Category: Biotechnology Authors: Marijuán PC, Igamberdiev AU Tags: Biosystems Source Type: research

The common misuse of noise decomposition as applied to genetic systems.
Abstract The noise-decomposition technique is applied in several fields, including genetic systems, optical images, recording, and navigation. In genetic systems, noise decomposition is usually achieved by using two reporters [Elowitz M.B., Levine A.J., Siggia E.D., Swain P·S., 2002. Stochastic gene expression in a single cell. Science 297, 1183-6.]. A reporter is a protein with fluorescence, an RNA hybridized with a fluorescent probe, or any other detectable intracellular component. If a reporter is constructed in addition to the original reporter, the system's stochasticity may change. Such phenomena beca...
Source: Biosystems - October 7, 2020 Category: Biotechnology Authors: Chen BR, You CX, Shu CC Tags: Biosystems Source Type: research

Morphogenetic systems: Models and experiments.
M, Sosík P Abstract M systems are mathematical models of morphogenesis developed to gain insights into its relations to phenomena such as self-assembly, self-controlled growth, homeostasis, self-healing and self-reproduction, in both natural and artificial systems. M systems rely on basic principles of membrane computing and self-assembly, as well as explicit emphasis on geometrical structures (location and shape) in 2D, 3D or higher dimensional Euclidean spaces. They can be used for principled studies of these phenomena, both theoretically and experimentally, at a computational level abstracted from their ...
Source: Biosystems - October 7, 2020 Category: Biotechnology Authors: Smolka V, Drastík J, Bradík J, Garzon M, Sosík P Tags: Biosystems Source Type: research

Feedback enrichment analysis for transcription factor-target genes in signaling pathways.
In this study, I focused on the feedback regulation of signal molecules like transcription factor (TF)-associated target genes controlled after transcription (named TF-target feedback genes). I statistically analyzed the static network of signal transduction pathways and TF-target feedbacks to investigate their presence in upstream signal molecules of TFs in 394 different cell types, including 146 primary cells, 111 tissues, and 137 cell lines. The directed network of signal transduction utilized pathways annotated in KEGG, and the TF-target genes estimated per individual cells were used. Feedback enrichment analysis of ...
Source: Biosystems - September 27, 2020 Category: Biotechnology Authors: Inoue K Tags: Biosystems Source Type: research

Modeling a cancerous tumor development in a virtual patient suffering from a depressed state of mind: Simulation of somatic evolution with a customized genetic algorithm.
Abstract Cancer is a disease of evolutionary origin in which a group of cells in the body initiate evolutionary changes under certain circumstances that can lead to the formation of a tumor. It is currently believed that a hostile cell environment can lead to the cells of an organ or tissue initiating a whole series of physiological changes that will lead to the transformation of healthy cells into cancerous ones. During the process of transformation, cells evolve under a paradigm known as somatic evolution. In this work the first stages of the formation of a cancerous tumor have been simulated assuming that the c...
Source: Biosystems - September 27, 2020 Category: Biotechnology Authors: Lahoz-Beltra R, Rodriguez RJ Tags: Biosystems Source Type: research