Causes of global extinctions in the history of life: facts and hypotheses

Paleontologists define global extinctions on Earth as a loss of about three-quarters of plant and animal species over a relatively short period of time. At least five global extinctions are documented in the Phanerozoic fossil record (~500-million-year period): ~65, 200, 260, 380, and 440 million years ago. In addition, there is evidence of global extinctions in earlier periods of life on Earth – during the Late Cambrian (~500 million years ago) and Ediacaran periods (more than 540 million years ago). There is still no common opinion on the causes of their occurrence. The current study is a systematized review of the data on recorded extinctions of complex life forms on Earth from the moment of their occurrence during the Ediacaran period to the modern period. The review discusses possible causes for mass extinctions in the light of the influence of abiogenic factors, planetary or astronomical, and the consequences of their actions. We evaluate the pros and cons of the hypothesis on the presence of periodicity in the extinction of Phanerozoic marine biota. Strong evidence that allows us to hypothesize that additional mechanisms associated with various internal biotic factors are responsible for the emergence of extinctions in the evolution of complex life forms is discussed. Developing the idea of the internal causes of periodicity and discontinuity in evolution, we propose our own original hypothesis, according to which the bistability phenomenon underlies the complex dynamics of the biota development, which is manifested in the form of global extinctions. The bistability phenomenon arises only in ecosystems with predominant sexual reproduction. Our hypothesis suggests that even in the absence of global abiotic catastrophes, extinctions of biota would occur anyway. However, our hypothesis does not exclude the possibility that in different periods of the Earth’s history the biota was subjected to powerful external influences that had a significant impact on its further development, which is reflected in the Earth’s fossil record

ON THE EQUIVALENCE OF DELAYED ARGUMENTS AND TRANSFER EQUATIONS FOR MODELING DYNAMIC SYSTEMS

Development and improvement of mathematical methods used in modeling biological systems represents a topical issue of mathematical biology. In this paper, we considered a general form of a system of first-order delayed differential equations, traditionally used for describing the function of biological systems of different hierarchical levels. The main feature of this class of models is that some inherent processes (for example, elongation of DNA, RNA, and protein synthesis) are described in a subtle form and can be explicitly specified only through delayed arguments. In this paper, we propose an algorithm for rewriting systems with constant delayed arguments in an equivalent form that represents a system of partial differential equations with transfer equations. The algorithm is universal, since it does not impose any special conditions on the form of the right-hand parts of systems with delayed arguments. The proposed method is a multivariant algorithm. That is, based on one system of differential equations with delayed arguments, the algorithm allows writing out a number of special systems of partial differential equations, which are equivalent to the original system with delayed argument in the entire solution set. The results obtained indicate that delayed arguments and transfer equations are equivalent mathematical tools for describing all types of dynamic processes of energy and/or matter transfer in biological, chemical, and physical systems, indicating a deep-level similarity between properties of dynamic systems, regardless of their origin. At the same time, those processes that are subtle when retarded argument is used can be explicitly described in the form of transfer equations using systems of partial differential equations. This property is extremely important for the modeling of molecular genetic systems in which processes of DNA, RNA, and protein synthesis proceed at variable rates and need to be considered in certain problems, what can easily be done in models constructed using the mathematical tool of partial derivatives

A plausible mechanism for auxin patterning along the developing root

<p>Abstract</p> <p>Background</p> <p>In plant roots, auxin is critical for patterning and morphogenesis. It regulates cell elongation and division, the development and maintenance of root apical meristems, and other processes. In <it>Arabidopsis</it>, auxin distribution along the central root axis has several maxima: in the root tip, in the basal meristem and at the shoot/root junction. The distal maximum in the root tip maintains the stem cell niche. Proximal maxima may trigger lateral or adventitious root initiation.</p> <p>Results</p> <p>We propose a <it>reflected flow </it>mechanism for the formation of the auxin maximum in the root apical meristem. The mechanism is based on auxin's known activation and inhibition of expressed PIN family auxin carriers at low and high auxin levels, respectively. Simulations showed that these regulatory interactions are sufficient for self-organization of the auxin distribution pattern along the central root axis under varying conditions. The mathematical model was extended with rules for discontinuous cell dynamics so that cell divisions were also governed by auxin, and by another morphogen <it>Division Factor </it>which combines the actions of cytokinin and ethylene on cell division in the root. The positional information specified by the gradients of these two morphogens is able to explain root patterning along the central root axis.</p> <p>Conclusion</p> <p>We present here a plausible mechanism for auxin patterning along the developing root, that may provide for self-organization of the distal auxin maximum when the <it>reverse fountain </it>has not yet been formed or has been disrupted. In addition, the proximal maxima are formed under the <it>reflected flow </it>mechanism in response to periods of increasing auxin flow from the growing shoot. These events may predetermine lateral root initiation in a rhyzotactic pattern. Another outcome of the <it>reflected flow </it>mechanism - the predominance of lateral or adventitious roots in different plant species - may be based on the different efficiencies with which auxin inhibits its own transport in different species, thereby distinguishing two main types of plant root architecture: taproot vs. fibrous.</p

GeneNet in 2005

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/

ABOUT COMPUTATIONAL RESEARCH OF MATHEMATICAL MODELS OF HYPOTHETICAL GENE NETWORKS BY PARAMETER CONTINUATION

Resume Motivation: Needs in analyzing of gene networks require developments of new analysis methods of mathematical models. Results: In this article we present the research method of complicated hypothetical gene networks. The main point of this method is to present the initial model as whole of basic models whose properties was studied and to expose of area where the initial model behavior and basic models behavior are phase equivalent

GENE EXPRESSION AND mRNA SECONDARY STRUCTURES IN DIFFERENT Mycoplasma SPECIES

Evaluation of gene expression efficiency in different organisms is a vital task of modern biology. Microorganisms that feed on humans and pets are particularly interesting. In this work, bioinformatical analysis of 62 Mycoplasma strains is performed. It has been shown that translation efficiency in these organisms depends on the number of potential secondary structures in genes and does not depend on codon compositions. Several species with low concentrations of local inverted repeats in genes have been found. Phylogenetic analysis shows that this feature may be associated with their environment. High concentrations of local inverted repeats, not typical of other Mycoplasma species, have been found in the translation start regions of M. haemofelis genes

AUXIN DISTRIBUTION IN A TRANSVERSE ROOT SECTION

Plants differ in the types of the root central cylinder: diarch, triarch, tetrarch, pentarch, or polyarch. The type of the symmetry is the reflection of the relative positions of xylem and phloem bundles in a cross section of the root. The mechanisms forming different types of symmetries in the central cylinder remain poorly understood. It is assumed that vasculature differentiation is triggered and controlled by plant hormone auxin (Sachs, 1969). We have developed a model that describes auxin flow through a cell layer, imitating a cross section of the vascular cylinder in a root. We have studied the stationary distributions of auxin in the cell layer depending on the model parameters. It is shown that the nonlinear processes of auxin transport regulation are responsible for the formation of asymmetric auxin distributions, which may be interpreted as the positional information for development of the diarch structure of the vascular cylinder. However, these distributions always coexist with uniform stationary distributions, not providing positional information. It is hypothesized that the most likely factor in the formation of the final auxin distribution in a root section is an appropriate geometry of the auxin flow from the shoot to the root