Theory in Biosciences

In this work, we formulate the following question: How the distribution of aminoacyl-tRNA synthetases (aaRSs) went from an ancestral bidirectional gene (mirror symmetry) to the symmetrical distribution of aaRSs in a six-dimensional hypercube of the Standard Genetic Code (SGC)? We assume a primeval RNY code, two Extended Genetic RNA codes type 1 and 2, and the SGC. We outline the types of symmetries of the distribution of aaRSs in each code. The symmetry groups of aaRSs in each code are described, until the symmetries of the SGC display a mirror symmetry...

This paper addresses the relationship between information and structure of the genetic code. The code has two puzzling anomalies: First, when viewed as 64 sub-cubes of a [Formula: see text] cube, the codons for serine (S) are not contiguous, and there are amino acid codons with zero redundancy, which goes counter to the objective of error correction. To make sense of this, the paper shows that the genetic code must be viewed not only on stereochemical, co-evolution, and error-correction considerations, but also on two additional factors of significance to natural systems, that of an information-theoretic dimensionality of the code data, and the principle of maximum entropy...

Adaptive mimicry in animals is a well-known phenomenon. Here, we propose that a similarly adaptive strategy in humans is using kin terms for people who are not closely genetically related. Irrespective of the initiator attributing a kin term to a non-kin, we call this kin term mimicry (KTM). The emergence of human sociality and language allowed not only easy kin recognition, but also led to strong positive emotions related to such kin names as "mother," "father," "brother," "sister," "aunt" or "uncle." Although the phenomenon of using kin terms of genetically unrelated people is well known in the social sciences, here we discuss it in the light of evolution...

In this article, we study the dynamical properties of susceptible-vaccinated-infected-susceptible (SVIS) epidemic system with saturated incidence rate and vaccination strategies. By constructing the suitable Lyapunov function, we examine the existence and uniqueness of the stochastic system. With the help of Khas'minskii theory, we set up a critical value [Formula: see text] with respect to the basic reproduction number [Formula: see text] of the deterministic system. A unique ergodic stationary distribution is investigated under the condition of [Formula: see text]...

In this study, we proposed a biological model explaining the progress of autoimmune activation along different stages of systemic lupus erythematosus (SLE). For any upcoming stage of SLE, any new component is introduced, when it is added to the model. Particularly, the interaction of mesenchymal stem cells, with the components of the model, is specified in a way that both the inflammatory and anti-inflammatory functions of these cells would be covered. The biological model is then recapitulated to a model with less complexity that explains the main features of the problem...

In biological processes involving gene networks, genes regulate other genes that determine the phenotypic traits. Gene regulation plays an important role in evolutionary dynamics. In a genetic algorithm, a trans-gene regulatory mechanism was shown to speed up adaptation and evolution. Here, we examine the effect of cis-gene regulation on an adaptive system. The model is haploid. A chromosome is partitioned into regulatory loci and structural loci. The regulatory genes regulate the expression and functioning of structural genes via the cis-elements in a probabilistic manner...

Autosomal dominant diseases typically have an age-related onset. Here, I focus on genetic prion disease (gPrD), caused by various mutations in the PRNP gene. While gPrD typically occurs at or after middle age, there can be considerable variability in the specific age of onset. This variability can occur among patients with the same PRNP mutation; in some cases, these differences occur not only between families but even within the same family. It is not known why gPrD onset is typically delayed for decades when the causative mutation is present from birth...

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[Formula: see text]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...

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...

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...

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...

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...

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...

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...

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...

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...

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 [Formula: see text] and the endemic equilibrium [Formula: see text], respectively...

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...

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 (H2 O), hydrogen (H2 ) and hydrogen sulfide (H2 S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins...

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...