Acta Biotheoretica最新文献

The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics.

The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given the set of elements, the reactions between them (chemical or otherwise), and with various elements catalysing certain reactions, a Reflexively Autocatalytic F-generated (RAF) set is a subset R(') of reactions that is self-generating from a given food set, and with each reaction in R(') being catalysed from within R('). RAF theory has been applied to various phenomena in theoretical biology, and a key feature of the approach is that it is possible to efficiently identify and classify RAFs within large systems. This is possible because RAFs can be described as the (nonempty) subsets of the reactions that are the fixed points of an (efficiently computable) interior map that operates on subsets of reactions. Although the main generic results concerning RAFs can be derived using just this property, we show that for systems with at least 12 reactions there are generic results concerning RAFs that cannot be proven using the interior operator property alone.

Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.

The variance effective population size ((N_{eV})) is frequently used to quantify the expected rate at which a population’s allele frequencies change over time. The purpose of this paper is to find expressions for the global (N_{eV}) of a spatially structured population that are of interest for conservation of species. Since (N_{eV}) depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (I) and a second component mainly due to migration between subpopulations (II). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of II is eliminated, and (N_{eV}) of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal (N_{eV}) is the sought for global effective size, since it approximates the gene diversity effective size (N_{eGD}), a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of (N_{eV}), one of which (the backward version of (N_{eV})) is most stable, exists for most populations, and is closer to (N_{eGD}) than the classical notion of (N_{eV}). Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of (N_{eV}) with maximal accuracy.

Let the individuals of a population be divided into two groups with different personal habits. The core group is associated with health risk behaviors; the non-core group avoids unhealthy activities. Assume that the infected individuals of the core group can spread a contagious disease to the whole population. Also, assume that cure does not confer immunity. Here, an epidemiological model written as a set of ordinary differential equations is proposed to investigate the infection propagation in this population. In the model, migrations between these two groups are allowed; however, the transitions from the non-core group into the core group prevail. These migrations can be either spontaneous or stimulated by social pressure. It is analytically shown that, in the scenario of spontaneous migration, the disease is either naturally eradicated or chronically persists at a constant level. In the scenario of stimulated migration, in addition to eradication and constant persistence, self-sustained oscillations in the number of sick individuals can also be found. These analytical results are illustrated by numerical simulations and discussed from a public health perspective.

The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene.

Cyanolichens are symbiotic organisms involving cyanobacteria and fungi (bipartite) or with the addition of an algal partner (tripartite). Cyanolichens are known for their heightened susceptibility to environmental pollution. We focus here on the impacts on cyanolichens due to rising air pollution; we are especially interested in the role of sulfur dioxide on cyanolichen biology. Cyanolichens due to air pollution including sulfur dioxide exposure, show symptomatic changes including degradation of chlorophyll, lipid membrane peroxidation, decrease in ATP production, changes in respiration rate, and alteration of endogenous auxins and ethylene production, although symptoms are known to vary with species and genotype. Sulfur dioxide has been shown to be damaging to photosynthesis but is relatively benign on nitrogen fixation which proposes as a hypothesis that the algal partner may be more in harm’s way than the cyanobiont. In fact, the Nostoc cyanobiont of sulfur dioxide-susceptible Lobaria pulmonaria carries a magnified set of sulfur (alkane sulfonate) metabolism genes capable of alkane sulfonate transport and assimilation, which were only unraveled by genome sequencing, a technology unavailable in the 1950–2000 epoch, where most physiology- based studies were performed. There is worldwide a growing corpus of evidence that sulfur has an important role to play in biological symbioses including rhizobia-legumes, mycorrhizae-roots and cyanobacteria-host plants. Furthermore, the fungal and algal partners of L. pulmonaria appear not to have the sulfonate transporter genes again providing the roles of ambient-sulfur (alkanesulfonate metabolism etc.) mediated functions primarily to the cyanobacterial partner. In conclusion, we have addressed here the role of the atmospheric pollutant sulfur dioxide to tripartite cyanolichen viability and suggest that the weaker link is likely to be the photosynthetic algal (chlorophyte) partner and not the nitrogen-fixing cyanobiont.

It is common to say that the origin of the membrane potential is attributed to transmembrane ion transport, but it is theoretically possible to explain its generation by the mechanism of ion adsorption. It has been previously suggested that the ion adsorption mechanism even leads to potential formulae identical to the famous Nernst equation or the Goldman-Hodgkin-Katz equation. Our further analysis, presented in this paper, indicates that the potential formula based on the ion adsorption mechanism leads to an equation that is a function of the surface charge density of the material and the surface potential of the material. Furthermore, we have confirmed that the equation holds in all the different experimental systems that we have studied. This equation appears to be a key equation that governs the characteristics of the membrane potential in all systems.

Nitric oxide (NO) is involved in synaptic long-term potentiation (LTP) by multiple signaling pathways. Here, we show that LTP of synaptic transmission can be explained as a feature of signal transduction—bistable behavior in a chain of biochemical reactions with positive feedback, formed by diffusion of NO to the presynaptic site and facilitating the release of glutamate (Glu). The dynamics of Glu, calcium (Ca²⁺) and NO is described by a system of nonlinear reaction–diffusion equations with modified Michaelis–Menten (MM) kinetics. Numerical investigation reveals that the chain of biochemical reactions analyzed can exhibit a bistable behavior under physiological conditions when production of Glu is described by MM kinetics and decay of NO is modeled by means of two enzymatic pathways with different kinetic properties. Our finding extends understanding of the role of NO in LTP: a short high-intensity stimulus is “memorized” as a long-lasting elevation of NO concentration. The conclusions obtained by analysis of the chain of biochemical reactions describing LTP can be generalized to other chains of interactions or for creating the logical elements for biological computers.

Long since, people tried to solve the mystery of the way that led to the appearance and propagation of living entities. However, no harmonious understanding of this mystery existed, because neither the scientifically grounded source minerals nor the ambient conditions were proposed and because it was groundlessly taken that the process of living matter origination is endothermal. The Life Origination Hydrate Theory (LOH-Theory) first suggests the chemical way capable of leading from the specified abundant natural minerals to origination of multitudes of multitudes of simplest living entities and gives an original explanation for the phenomena of chirality and racemization delay. The LOH-Theory covers the period up to origination of the genetic code. The LOH-Theory is grounded on the following three discoveries based on the available information and on the results of our experimental works performed using original instrumentation and computer simulations. (1) There is the only one triad of natural minerals applicable for exothermal thermodynamically possible chemical syntheses of simplest living-matter components. (2) N-base, ribose, and phosphdiester radicals and nucleic acids as whole are size-compatible with structural gas-hydrate cavities. (3) The gas-hydrate structure arises around amido-groups in cooled undisturbed systems consisting of water and highly-concentrated functional polymers with amido-groups.The natural conditions and historic periods favorable for simplest living matter origination are revealed. The LOH-Theory is supported by results of observations, biophysical and biochemical experiments, and wide application of original three-dimensional and two-dimensional computer simulations of biochemical structures within gas-hydrate matrix. The instrumentation and procedures for experimental verification of the LOH-Theory are suggested. If future experiments are successful, they, possibly, could be the first step on the way to industrial synthesis of food from minerals, i.e., to execution of the work that is performed by plants.

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