JournalTOCs

Theory in Biosciences
Journal Prestige (SJR): 0.557

Citation Impact (citeScore): 1
Number of Followers: 0

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1611-7530 - ISSN (Online) 1431-7613
Published by Springer-Verlag

[2467 journals]

Path integral control of a stochastic multi-risk SIR pandemic model
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  Abstract: Abstract In this paper a Feynman-type path integral control approach is used for a recursive formulation of a health objective function subject to a fatigue dynamics, a forward-looking stochastic multi-risk susceptible–infective–recovered (SIR) model with risk-group’s Bayesian opinion dynamics toward vaccination against COVID-19. My main interest lies in solving a minimization of a policy-maker’s social cost which depends on some deterministic weight. I obtain an optimal lock-down intensity from a Wick-rotated Schrödinger-type equation which is analogous to a Hamiltonian–Jacobi–Bellman (HJB) equation. My formulation is based on path integral control and dynamic programming tools facilitates the analysis and permits the application of algorithm to obtain numerical solution for pandemic control model.
  PubDate: 2023-03-11
Evolutionary honing in and mutational replacement: how long-term directed
mutational responses to specific environmental pressures are possible
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  Abstract: Abstract Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the nonresistant but otherwise identical 20A \(\rightarrow\) T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here, we address this finding with the replacement hypothesis, according to which preexisting genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, an evolutionary process under selection can gradually hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A \(\rightarrow\) G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called interaction-based evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directed mutational responses to specific environmental pressures are possible. Such mutational phenomena need to be further tested by future studies in natural and artificial settings.
  PubDate: 2023-03-11
Wartime forced sex as a male mating strategy
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  Abstract: Abstract The aim of this study was an analytical justification of the emergence and presence of the phenomenon of war among hominins, taking into account males’ genetic benefits gained through war in the natural environment. Based on chimpanzee behavior, the analytical model of the primary warrior balance was explored, comparing the risk of a war expedition with the genetic profits from war rape—“life and death balance”. On the profits side, genetic gains possible to obtain in terms of permanent attractiveness of females (warrior status and abductions of females) were also included. Kin cooperation, parochial altruism, and “partisan strategy” have been defined as psychological mechanisms that enable effective group violence. Male genetic benefit from a war rape could exceed the risk of a warrior’s death in the chimpanzee–human LCA species; transition from the herd to the patriarchal tribal social system could increase warrior’s genetic gains from war. At the root of war lie sexual limitations of cooperating males, induced by female sexual preferences and lack of the permanent female sexual drive. War rape allows reproductive success for dominated and thus sexually restricted males. Tendencies for group aggression to gain access to out-group females (the war gene) are common among sexually restricted men. Resource-rich areas favor increase in human population density, this affects group territoriality and promotes intergroup conflicts, and thus patriarchy. Roots of conventional patriarchal marriage are strongly combined with war—“the right to land entails the right to a female”.
  PubDate: 2023-01-30
Biology as involving laws and inconceivable without them
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  Abstract: Abstract There is an old attempt to divide the sciences into sciences of laws and the historical sciences. More recently, John Beatty has drawn the distinction so that biology is a historical science and urged that there are no genuinely biological laws. This paper shows that there are indeed biological laws, specifically statistical ones, notably in evolutionary theory. Moreover, all or almost all other areas of biology involve laws as well. Even history involves laws. Finally, the paper shows that this pervasiveness of laws is compatible with the most basic commitments of those who, like Beatty, would claim that biology is only historical.
  PubDate: 2023-01-22
Descriptive versus causal morphology: gynandromorphism and intersexuality
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  Abstract: Abstract In animal species with separate sexes, abnormal individuals with a mix of phenotypically male and phenotypically female body parts are generally indicated as gynandromorphs, whereas individuals with intermediate sexual phenotypic traits are generally indicated as intersexes. However, this distinction, clear as it may seem, is neither universally agreed upon, nor free of critical issues. In consideration of the role of sex anomalies in understanding normal development, we reassess these phenomena of abnormal sexual development, taking into consideration the more recent advances in the study of sex determination and sexual differentiation. We argue that a distinction between gynandromorphism and intersexuality, although useful for descriptive purposes, is not always possible or sensible. We discuss the conceptual and terminological intricacies of the literature on this subject and provide reasons for largely, although not strictly, preferring a terminology based on descriptive rather than causal morphology, that is, on the observed phenotypic patterns rather on the causal process behind them.
  PubDate: 2023-01-12
  DOI: 10.1007/s12064-023-00385-1
Molecular characterization of chilli leaf curl Ahmedabad virus: homology
modelling and evaluation of viral proteins interacting with host protein
SnRK1 and docking against flavonoids—an in silico approach
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  Abstract: Abstract Chilli leaf curl Ahmedabad virus (ChiLCAV), a begomovirus belonging to the family Geminiviridae, has been reported for its occurrence in India, infecting chilli and tomato plants. The viral proteins associated with ChiLCAV involves in the primary pathogenesis and transmission of the virus by whitefly. Viral protein interactions with host proteins show the dynamics of structural binding and interaction in their infection cycle. At the same time, plants have multiple defence mechanisms against bacterial and viral infections. Secondary metabolites play a significant role in the inborne defence mechanism of plants. Host proteins are also the prime producers of secondary metabolites. In the present study, we evaluated the host protein SnRK1 interaction with all six viral proteins (V1, V2, C1, C2, C3 and C4). Apart from C4, all the other viral proteins showed appreciable binding and interaction with SnRK1. SnRK1 has the regulation mechanism for the accumulation of diterpenoids, secondary metabolites. Flavonoids are secondary metabolites produced by the plant under stress conditions. Further, we studied the binding and interaction of six selected flavonoids produced by Solanaceae family members with all the ChiLCAV proteins. All six selected flavonoids showed considerable binding energy with all viral proteins. Each flavonoid showed high binding energy with different viral proteins. Molecular docking is carried out for both flavonoids and the host protein SnRK1. These in silico interactions and docking studies could be useful for understanding the plants defence mechanism against viral infections at the molecular level.
  PubDate: 2023-01-06
  DOI: 10.1007/s12064-022-00383-9
Formal verification confirms the role of p53 protein in cell fate decision
mechanism
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  Abstract: Abstract The bio-cell cycle is controlled by a complex biochemical network of signaling pathways. Modeling such challenging networks accurately is imperative for the understanding of their detailed dynamical behavior. In this paper, we construct, analyze, and verify a hybrid Petri net (HPN) model of a complex biochemical network that captures the role of an important protein (namely p53) in deciding the fate of the cell. We model the behavior of the cell nucleus and cytoplasm as two stochastic and continuous Petri nets, respectively, combined together into a single HPN. We use simulative model checking to verify three different properties that capture the dynamical behavior of p53 protein with respect to the intensity of the ionizing radiation (IR) to which the cell is exposed. For each IR dose, 1000 simulation runs are carried out to verify each property. Our verification results showed that the fluctuations in p53, which relies on IR intensity, are compatible with the findings of the preceding simulation studies that have previously examined the role of p53 in cell fate decision.
  PubDate: 2022-12-12
  DOI: 10.1007/s12064-022-00381-x
Radioresistance and radiosensitivity: a biophysical approach on bacterial
cells robustness
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  Abstract: Abstract The study of radiosensitivity and radioresistance of organisms exposed to ionizing radiation has acquired additional relevance since a new bio-concept, coined as The primacy of Proteome over Genome, was proposed and demonstrated elsewhere a few years ago. According to that finding, genome integrity would require an actively functioning Proteome. However, when exposure to radiation takes place, Reactive Oxygen Species (ROS) from water radiolysis induce protein carbonylation (PC), an irreversible oxidative Proteome damage. The bio-models used in that study were the radiosensitive Escherichia coli and the extraordinarily robust Deinococcus radiodurans. The production of ROS induces protective reactions rendering them non-reactive forms. Protective entities present in the cytosol, moieties smaller than 3 kDa, shield the Proteome against ROS, yielding protection against carbonylation. Shown in the present study is the fact that the fate of proteins functionality is determined by the magnitude of the Protein Carbonylation Yield (YPC), a quantity here analytically defined using published YPC numerical results. Analytical YPC expressions for E. coli and D. radiodurans were the input for a phenomenological approach, where the radiobiological magnitudes PP and PN, the probabilities for production of protein damage and ROS neutralization, respectively, were also analytically deduced. These highly relevant magnitudes, associated with key radiosensitivity and radioresistance issues, are addressed and discussed in this study. Among the plethora of information and conclusions derived from the present study, those endowed with higher conceptual degree, vis-à-vis the “Primacy of Proteome over Genome” concept, are as follows: (1) the ROS neutralization process in D. radiodurans reaches a maximum at a dose interval corresponding to the repairing shoulder. Therefore, it is a signature of the higher efficiency of the PC neutralization process. (2) ROS neutralization in D. radiodurans is nearly one order of magnitude higher than in E. coli, thus accounting for its extraordinary radioresistance. (3) Both physical (ROS-induced carbonyl radicals) and biological (protein modifications) processes are imbedded in the Protein Carbonylation Yield. The amalgamation of these two processes was accomplished by means of a statistical formalism.
  PubDate: 2022-12-03
  DOI: 10.1007/s12064-022-00382-w
An almost periodic model to describe phenology mismatches in mutualistic
interactions
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  Abstract: Abstract We study seasonal mutualistic interactions between two species. The model takes into account the climate-mediated shifts that can change the phenologies of mutualistic species. We show conditions on the parameters of the model that guarantee global stability. Numerical simulations are performed for different scenarios associated with seasonal changes. They show that if periodic time-dependence is used to approximate an almost periodic one, then not only the densities of the mutualistic populations but also the overlapping intervals describing the interval of co-occurrence can be either underestimated or overestimated. Therefore, using an almost periodic model can be more adequate to design conservation strategies for asynchronous phenology.
  PubDate: 2022-10-12
  DOI: 10.1007/s12064-022-00380-y
Modeling the stochastic within-host dynamics SARS-CoV-2 infection with
discrete delay
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  Abstract: Abstract In this paper, a new mathematical model that describes the dynamics of the within-host COVID-19 epidemic is formulated. We show the stochastic dynamics of Target-Latent-Infected-Virus free within the human body with discrete delay and noise. Positivity and uniqueness of the solutions are established. Our study shows the extinction and persistence of the disease inside the human body through the stability analysis of the disease-free equilibrium \(E_0\) and the endemic equilibrium \(E^*\) , respectively. Moreover, we show the impact of delay tactics and noise on the extinction of the disease. The most interesting result is even if the deterministic system is inevitably pandemic at a specific point, extinction will become possible in the stochastic version of our model.
  PubDate: 2022-10-03
  DOI: 10.1007/s12064-022-00379-5
How much biology is in the product' Role and relevance of biological
evolution and function for bio-inspired design
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  Abstract: Abstract Bio-inspired design (BID) means the concept of transferring functional principles from biology to technology. The core idea driving BID-related work is that evolution has shaped functional attributes, which are termed “adaptations” in biology, to a high functional performance by relentless selective pressure. For current methods and tools, such as data bases, it is implicitly supposed that the considered biological models are adaptations and their functions already clarified. Often, however, the identification of adaptations and their functional features is a difficult task which is not yet accomplished for numerous biological structures, as happens to be the case also for various organismic features from which successful BID developments were derived. This appears to question the relevance of the much stressed importance of evolution for BID. While it is obviously possible to derive an attractive technical principle from an observed biological effect without knowing its original functionality, this kind of BID (“analog BID”) has no further ties to biology. In contrast, a BID based on an adaptation and its function (“homolog BID”) is deeply embedded in biology. It is suggested that a serious and honest clarification of the functional background of a biological structure is an essential first step in devising a BID project, to recognize possible problems and pitfalls as well as to evaluate the need for further biological analysis.
  PubDate: 2022-09-01
  DOI: 10.1007/s12064-022-00367-9
Network representation and analysis of energy coupling mechanisms in
cellular metabolism by a graph-theoretical approach
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  Abstract: Abstract Mechanisms coupling the chemical reactions of oxidation and ATP synthesis in cellular metabolism by the fundamental biological process of oxidative phosphorylation (OX PHOS) in mitochondria provide > 90% of the energy requirements in living organisms. Mathematical graph theory methods have been extensively used to characterize various metabolic, regulatory, and disease networks in biology. However, networks of energy coupling mechanisms in OX PHOS have not been represented and analyzed previously by these approaches. Here, the problem of biological energy coupling is translated into a graph-theoretical framework, and all possible coupling schemes between oxidation and ATP synthesis are represented as graphs connecting these processes by various intermediates or states. The problem is shown to be transformed into the hard problem of finding a Hamiltonian tour in the networks of possible constituent mechanisms, given the constraints of a cyclical nature of operation of enzymes and biological molecular machines. Accessible mathematical proofs of three theorems that guarantee sufficient conditions for the existence of a Hamiltonian cycle in simple graphs are provided. The results of the general theorems are applied to the set of possible coupling mechanisms in OX PHOS and shown to (1) unequivocally differentiate between the major theories and mechanisms of energy coupling, (2) greatly reduce the possibilities for detailed consideration, and (3) deduce the biologically selected mechanism using additional constraints from the cumulative experimental record. Finally, an algorithm is constructed to implement the graph-theoretical procedure. In summary, the enormous power and generality of mathematical theorems and approaches in graph theory are shown to help solve a fundamental problem in biology.
  PubDate: 2022-09-01
  DOI: 10.1007/s12064-022-00370-0
The shadow of “the Eclipse of Darwinism”: the problem of evolutionary
mechanisms in Republican China, 1910s–1930s
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  Abstract: Abstract How did Chinese scientific intellectuals react to the dispute over evolutionary mechanisms during the period of the “eclipse of Darwinism”' This is my focal question. To answer it, I survey the attitudes of three groups of people toward the debate in the early decades of the twentieth century: Chinese paleontologists and their general embrace of the anti-Darwinian position, a group of non-specialists (or semi-specialists) and their assertion of a “revival of Lamarckism,” and the American-trained Chinese biologists and their typical agnostic stance toward the antagonism between Darwinism and the mutation theory. Different concerns or motivations underlay these three different stances. There were also interesting attempts by biologists like Chen Zhen to exploit some recreational breeding traditions like goldfish breeding peculiar to China to participate in the dispute more directly.
  PubDate: 2022-09-01
  DOI: 10.1007/s12064-022-00378-6
Prebiotic chemical refugia: multifaceted scenario for the formation of
biomolecules in primitive Earth
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  Abstract: Abstract The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named “Prebiotic Chemical Refugia.” Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
  PubDate: 2022-08-30
  DOI: 10.1007/s12064-022-00377-7
Phenotypic plasticity in plasmodial slime molds and molecular phylogeny of
terrestrial vs. aquatic species
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  Abstract: Abstract Fifty years ago, the enigmatic Brazilian myxomycete-species Didymium aquatile was described and analyzed with respect to the structure of the plasmodium and its spores. In this study, we compare this rare plasmodial slime mold with another, temporarily aquatic taxon from Europe, Didymium nigripes. Phenotypic plasticity of D. nigripes was investigated under various environmental conditions. Large changes in the morphology of the plasmodia were observed. For species identification, characteristics of the fruiting bodies are key features. However, Didymium aquatile was only characterized by its “abnormal” plasmodia, but no molecular data were available. Here, we analyzed DNA-sequences of 22 species of the genera Didymium and Diderma with a focus on this South American taxon via molecular genetics. A comparison of 18S-rDNA-sequences from D. aquatile and 21 other Didymium (and Diderma)-species indicates that D. aquatile is a reproductively isolated morpho-species. Phenotypic plasticity of D. nigripes is documented with respect to plasmodium morphology and the formation of fruiting bodies, as an example of an adaptation of a terrestrial species to aquatic environments.
  PubDate: 2022-08-27
  DOI: 10.1007/s12064-022-00375-9
Goethe and Candolle: National forms of scientific writing'
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  Abstract: Abstract What role does nationality—or the image of a nation—play in how one thinks and receives scientific ideas' This paper investigates the commonly held ideas about “German science” and “French science” in early nineteenth-century France. During the politically turbulent time, the seemingly independent scientific community found itself in a difficult position: first, between the cosmopolitan ideals of scientific community and the invasive political reality, and second, between the popularized image of national differences and the actual comparisons of international scientific ideas. The tension between multiple sets of fictions and realities underscores the fragility of the concept of nationality as a scientific measure. A case study comparing morphological ideas, receptions in France, and the actual scientific texts of J. W. von Goethe and A. P. de Candolle further illustrates this fragility. Goethe and Candolle make an ideal comparative case because they were received in very different lights despite their similar concept of the plant type. Our sentence-classification and visualization methods are applied to their scientific texts, to compare the actual compositions and forms of the texts that purportedly represented German and French sciences. This paper concludes that there was a gap between what French readers assumed they read and what they really read, when it came to foreign scientific texts. The differences between Goethe’s and Candolle’s texts transcended the perceived national differences between German Romanticism and French Classicism.
  PubDate: 2022-08-11
  DOI: 10.1007/s12064-022-00376-8
Growth dynamics of breast cancer stem cells: effects of self-feedback and
EMT mechanisms
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  Abstract: Abstract Breast cancer stem cells (BCSCs) with the ability to self-renew and differentiate have been identified in primary breast cancer tissues and cell lines. The BCSCs are often resistant to traditional radiation and/or chemotherapies. Previous studies have also shown that successful therapy must eradicate cancer stem cells. The purpose of this paper is to develop a mathematical model with self-feedback mechanism to illustrate the issues regarding the difficulties of absolutely eliminating a breast cancer. In addition, we introduce the mechanism of the epithelial-mesenchymal transition (EMT) to investigate the influence of EMT on the effects of breast cancer growth and treatment. Results indicate that the EMT mechanism facilitates the growth of breast cancer and makes breast cancer more difficult to be cured. Therefore, targeting the signals involved in EMT can halt tumor progression in breast cancer. Finally, we apply the experimental data to carry out numerical simulations and validate our theoretical conclusions.
  PubDate: 2022-08-03
  DOI: 10.1007/s12064-022-00374-w
First principles of terrestrial life: exemplars for potential
extra-terrestrial biology
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  Abstract: The search for life elsewhere in the universe represents not only a potential expansion of our knowledge regarding life, but also a clarification of the first principles applicable to terrestrial life, which thus restrict the very search for extra-terrestrial life. Although there are no exact figures for how many species have existed throughout Earth's total history, we can still make inferences about how the distribution of this life has proceeded through a bell curve. This graph shows the totality of life, from its origin to its end. The system enclosing life contains a number of first principles designated the walls of minimal complexity and adaptive possibility, the fence of adaptation, and right-skewed extension. In this discussion of life, a framework will be formulated that, based on the dynamic relationship between mesophiles and extremophiles, will be imposed on exoworlds in order to utilize the graph's predictive power to analyze how extra-terrestrial life could unfold. In this framework the evolutionary variation does not depend on the specific biochemistry involved. Once life is ‘up and running,’ the various biochemical systems that can constitute terrestrial and extra-terrestrial life will have secondary significance. The extremophilic tail represents a range expansion in which all habitat possibilities are tested and occupied. This tail moves to the right not because of the biochemistry constitutions of organisms, but because it can do nothing else. Thus, it can be predicted that graphs of terrestrial and extra-terrestrial life will be similar overall. A number of other predictions can be made; for example, for worlds in which the atmospheric disequilibrium is approaching equilibrium, it is predicted that life may still be present because the extremophilic range expansion is stretched increasingly farther to the right. Because life necessarily arises at a left wall of minimal complexity, it is predicted that any origin of cellular life will have a close structural resemblance to that of the first terrestrial life. Thus, in principle, life may have originated more than once on Earth, and still exist. It is also predicted that there may be an entire subset of life existing among other domains that we do not see because, in an abstract sense, we are inside the graph. If we view the graph in its entirety, this subset appears very much like a vast supra-domain of life.
  PubDate: 2022-07-30
  DOI: 10.1007/s12064-022-00373-x
Thermodynamic principles for system biology and the patterns of flower
pigmentation
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  Abstract: Abstract The thermodynamic principles for system biology are reviewed and formulated, and then basic patterns of flower pigmentation are interpreted. Main thoughts: (1) any biological trait (color or function of a cell) is logically related to a thermodynamic system (or physiological system, signaling network of the cell), (2) the striped, speckled and circle are three basic patterns of flower pigmentation, the development of flowers is an irreversible process, (3) the patterns of flower pigmentation are formed in flower development, (4) the flower cells can change its color in a period of development and this process is controlled thermodynamically, (5) there is giant space of physiology within an organism and within its numerous thermal states can appear under different conditions. In this theory, the dominant inheritance means that a gene contributes great to the thermodynamic stability of a trait related system; different genes can be interacted or integrated thermodynamically according to their contribution to the stability of its related system. By combination of Turing theory and our views, complex patterns of pigmentation could be explained theoretically.
  PubDate: 2022-07-20
  DOI: 10.1007/s12064-022-00372-y
Mathematical modeling for mutator phenotype and clonal selection advantage
in the risk analysis of lung cancer
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  Abstract: Abstract Cancer is one of the leading diseases for human mortality. Although substantial research works have been conducted to investigate the initiation and progression of cancer disease, it is still an active debate regarding the function of mutations conferring a clone advantage and the importance of mutator phenotypes caused by the mutation of stability genes. To address this issue further, we develop a mathematical model based on the incidence data of non-small cell lung cancer and small cell lung cancer from the Surveillance Epidemiology and End Results registry in the USA. The key biological parameters have been analyzed to investigate the potential effective measures for inhibiting the risk of lung cancer. Although the first event is the gene mutation that leads to clonal expansion of cells for lung cancer, the simulation results show that the clonal advantage of cancer cells alone is insufficient to cause tumorigenesis. Our analysis suggests that mutations in genes that keep genetic stability are critical in the development of lung cancer. This implies that mutator phenotype is an important indicator for the diagnosis of lung cancer, which can enable early detection and treatment to reduce the risk of lung cancer effectively. Furthermore, the parameter analysis indicates that it would be highly effective to control the risk of lung cancer by inhibiting the transformation rate from the normal cells to mutated cells and the clonal expansion of cells with fewer gene mutations.
  PubDate: 2022-06-04
  DOI: 10.1007/s12064-022-00371-z