A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution

There are two fundamental axioms of surface metabolism theory: (i) pyrite formation from H2S and FeS is proposed as a source of energy for life, and (ii) archaic reductive citric acid cycle is put into the center of a metabolic network. However, the concept fails to indicate how sulfide oxidation ought to be coupled to processes driven by free energy change occurring during pyrite production, and secondly, how reductive citric acid cycle ought to be supplied with row material(s). Recently, the non-enzymatic methylglyoxalase pathway has been recommended as the anaplerotic route for the reductive citric acid cycle. In this paper a mechanism is proposed by which the oxidation of lactate, the essential step of the anaplerotic path, becomes possible and a coupling system between sulfide oxidation and endergonic reaction(s) is also presented. Oxidoreduction for other redox pairs is discussed too. It is concluded that the S(o)/H2S system may have been the clue to energy production at the early stage of evolution, as hydrogen sulfide produced by the metabolic network may have functioned as a coupling molecule between endergonic and exergonic reactions.     

The energetics of the reductive citric acid cycle in the pyrite-pulled surface metabolism in the early stage of evolution

The chemoautotrophic theory concerning the origin of life postulates that a central role is played in the prebiotic chemical machinery by a reductive citric acid cycle operating without enzymes. The crucial point in this scenario is the formation of pyrite from hydrogen sulfide and ferrous sulfide, a reaction suggested to be linked to endergonic reactions, making them exergonic. This mechanism is believed to provide the driving force for the cycle to operate as a carbon dioxide fixation network. The present paper criticizes the thermodynamic calculations and their presentation in the original version of the archaic reductive citric acid cycle [W?chtersh?user, 1990. Evolution of the first metabolic cycles. Proc. Natl Acad. Sci. USA 87, 200-204.]. The most significant differences between the W?chtersh?user hypothesis and the present proposal: W?chtersh?user did not consider individual reactions in his calculations. A particularly questionable feature is the involvement of seven molecules of pyrite which does not emerge as a direct consequence of the chemical reactions presented in the archaic reductive citric acid cycle. The involvement of a considerable number of sulfur-containing organic intermediates as building blocks is also disputed. In the new scheme of the cycle proposed here, less free energy is liberated than hypothesized by W?chtersh?user, but it has the advantages that the free energy changes for the individual reactions can be calculated, the number of pyrite molecules involved in the cycle is reduced, and fewer sulfur-containing intermediates are required for the cycle to operate. In combination with a plausible route for the anaplerotic reactions [Kalapos, 1997a. Possible evolutionary role of methylglyoxalase pathway: anaplerotic route for reductive citric acid cycle of surface metabolists. J. Theor. Biol. 188, 201-206.], this new presentation of the cycle assigns a special meaning to hydrogen sulfide formation in the early stage of biochemical evolution.     

A theoretical approach to cluster formation in biological membranes

A theoretical analysis of cluster formation within the lipid matrix of biological membranes is presented. Various models are analysed: (a) one-dimensional monolayer, (b) two-dimensional monolayer and (c) one dimensional bilayer. Furthermore, lipid-protein interactions are considered. The model is based on differential equations for the probabilities a_i and b₁ which characterize the occupation of the lattice site i by the lipids A and B, respectively. These differential equations are an approximation of the Master-equation. Steady states as well as time-dependent variations are analysed. Depending on the interaction energies of the two lipids, different stationary lipid distributions are obtained, including clusters of lipids A or B and alternating structures. The distributions may be dynamically stable or unstable. It is shown that phase transitions within the lipid matrix may be induced by alteration of the composition of the membrane, by changing the interaction energies of the lipids, by variation of the temperature or by lipid-protein interactions. The transitions between different stationary distributions are studied by use of bifurcation diagrams. The analysis of time-dependent states reveals that unstable structures of the membrane may be important for certain time periods. Consideration of the lipid bilayer leads to a great number of possible distributions, which may be symmetric or asymmetric with respect to the outer and inner leaflets of the membrane.     

A theoretical approach to the large-scale evolution of multicellularity and cell differentiation

In contrast to Darwinian evolution in which organisms have been selected by the instantaneous judgment of advantage or disadvantage for a mutated gene, the large-scale evolution of multicellular organisms by drastic changes in their genomes to produce new genes is theoretically formulated on the basis of the new concept of ‘biological activity’. The ‘biological activity’ of an organism is a macroscopic quantity determined by its whole genome and the environment, consisting of three terms; the energy acquired from the outside, the energy stored in the form of bio-molecules, and the systematization of multicellularity as well as of organizing genes and their products. The acquired energy minus stored energy is lost as heat, and the entropy production by the heat must compensate for the entropy reduction owing to the systematization in the organism. Under the boundary determined by this thermodynamic law, the organisms, which experienced gene duplication to produce new genes for multicellularity and cell differentiation, first decline to be minor members in a population by the increase in the energy to be stored and by the advanced systematization of cell differentiation. If the acquired energy is raised by the cooperative action of newly differentiated cells with the pre-existing types of cells, however, the ‘biological activity’ of this new style of organism can be recovered. The new style of organism generated through this evolutionary process does not necessarily expel the old style of organism to extinction but can coexist by choosing different material and energy resources. Moreover, this theory of large-scale evolution not only explains the punctuated mode of evolution indicated by paleontology but also reproduces the divergence of body plans observed in Triploblastica and Tracheophyta.     

A game theoretical approach to the evolution of structured communication codes

Structured meaning-signal mappings, i.e., mappings that preserve neighborhood relationships by associating similar signals with similar meanings, are advantageous in an environment where signals are corrupted by noise and sub-optimal meaning inferences are rewarded as well. The evolution of these mappings, however, cannot be explained within a traditional language evolutionary game scenario in which individuals meet randomly because the evolutionary dynamics is trapped in local maxima that do not reflect the structure of the meaning and signal spaces. Here we use a simple game theoretical model to show analytically that when individuals adopting the same communication code meet more frequently than individuals using different codes—a result of the spatial organization of the population—then advantageous linguistic innovations can spread and take over the population. In addition, we report results of simulations in which an individual can communicate only with its K nearest neighbors and show that the probability that the lineage of a mutant that uses a more efficient communication code becomes fixed decreases exponentially with increasing K. These findings support the mother tongue hypothesis that human language evolved as a communication system used among kin, especially between mothers and offspring.     

A virus-like molecule in the early stage of encoded molecular evolution

The recent advances of the evolutionary molecular engineering revealed the effectiveness of bonding strategy for assignment of the phenotype to its genotype, which non-enveloped viruses such as simple bacteriophages adopt. On the other hand, cellular organisms adopt another kind of the strategy, namely the compartmentalzation of both genotype and phenotype molecules in a single compartment enclosed with a cell membrane. The simplest strategy is that adopted by ribozymes in the RNA world. A single molecule carries both genotype and its phenotype. Based on the definition of “virus”-type and “cell”-type of the assignment strategy, we propose a virus-early/cell-late model of the history of life.     

A theoretical approach of S. I. Malyshev to the evolution of behavior

In his book The Genesis of Hymenoptera and Phases of Their Evolution, S.I. Malyshev not only examined the evolution of the behavior of Hymenoptera but also implicitly presented an original theoretical approach to the evolution of species-specific behavior in general. This article suggests a reconstruction of this theoretical approach. The phases of evolution of the Hymenoptera singled out by Malyshev do not conform to specific taxa. They are regular phases of evolution of behavior as a integral functional system. In the same way, Malyshev develops his hypothesis of the origin of ants and bees, distinguishing transitional behavior phases from the solitary life of the Hymenoptera to the social organization of bees and ants.     

Systems biological approach to investigate the lack of familial link between Down's Syndrome & Neural Tube Disorders

Systems Biology involves the study of the interactions of biological systems and ultimately their functions. Down''s syndrome (DS) is one of the most common genetic disorders which are caused by complete, or occasionally partial, triplication of chromosome 21, characterized by cognitive and language dysfunction coupled with sensory and neuromotor deficits. Neural Tube Disorders (NTDs) are a group of congenital malformations of the central nervous system and neighboring structures related to defective neural tube closure during the first trimester of pregnancy usually occurring between days 18-29 of gestation. Several studies in the past have provided considerable evidence that abnormal folate and methyl metabolism are associated with onset of DS & NTDs. There is a possible common etiological pathway for both NTDs and Down''s syndrome. But, various research studies over the years have indicated very little evidence for familial link between the two disorders. Our research aimed at the gene expression profiling of microarray datasets pertaining to the two disorders to identify genes whose expression levels are significantly altered in these conditions. The genes which were 1.5 fold unregulated and having a p-value <0.05 were filtered out and gene interaction network were constructed for both NTDs and DS. The top ranked dense clique for both the disorders were recognized and over representation analysis was carried out for each of the constituent genes. The comprehensive manual analysis of these genes yields a hypothetical understanding of the lack of familial link between DS and NTDs. There were no genes involved with folic acid present in the dense cliques. Only – CBL, EGFR genes were commonly present, which makes the allelic variants of these genes – good candidates for future studies regarding the familial link between DS and NTDs.

Abbreviations

NTD - Neural Tube Disorders, DS - Down''s Syndrome, MTHFR - Methylenetetrahydrofolate reductase, MTRR– 5 - methyltetrahydrofolate-homocysteine methyltransferase reductase.     

A link between mitochondrial gene expression and life stage morphologies in Trypanosoma cruzi

The protozoan Trypanosoma cruzi has a complicated dual-host life cycle, and starvation can trigger transition from the replicating insect stage to the mammalian-infectious nonreplicating insect stage (epimastigote to trypomastigote differentiation). Abundance of some mature RNAs derived from its mitochondrial genome increase during culture starvation of T. cruzi for unknown reasons. Here, we examine T. cruzi mitochondrial gene expression in the mammalian intracellular replicating life stage (amastigote), and uncover implications of starvation-induced changes in gene expression. Mitochondrial RNA levels in general were found to be lowest in actively replicating amastigotes. We discovered that mitochondrial respiration decreases during starvation in insect stage cells, despite the previously observed increases in mitochondrial mRNAs encoding electron transport chain (ETC) components. Surprisingly, T. cruzi epimastigotes in replete medium grow at normal rates when we genetically compromised their ability to perform insertion/deletion editing and thereby generate mature forms of some mitochondrial mRNAs. However, these cells, when starved, were impeded in the epimastigote to trypomastigote transition. Further, they experience a short-flagella phenotype that may also be linked to differentiation. We hypothesize a scenario where levels of mature RNA species or editing in the single T. cruzi mitochondrion are linked to differentiation by a yet-unknown signaling mechanism.     

On the theoretical and experimental modeling of initial stages of metabolism formation in prebiotic systems

A concept of the initial stages of chemical prebiotic evolution, which eliminates a number of difficulties in the problem of the origin of life and permits experimental verification, is proposed. According to this concept, a predecessor of living beings has to be sufficiently simple to allow its self-assembly during a geologically short time period. In addition, the predecessor has to possess autocatalytic properties, and an ability for further complication (evolution). A possible scenario of the initial steps of the origin of life in nature and inside an experimental facility is considered. In the scope of the scenario the model of a multivariant oligomeric autocatalyst coupled with phase-separated particles is described. Results of computational simulations of possible initial steps in chemical evolution are presented. The estimates obtained show that the emergence of autocatalytic oligomeric phase-separated systems is possible at reasonable values of kinetics parameters of involved chemical reactions in a small-scale flow reactor.     

A critical stage in the formation of acid mine drainage: Colonization of pyrite by Acidithiobacillus ferrooxidans under pH-neutral conditions

A dominant Acidithiobacillus ferrooxidans ssp. was isolated from the supergene copper deposit in Morenci, Arizona, USA. Washed bacterial suspensions (10⁸ MPN per treatment), in pH‐neutral buffer, were inoculated onto pyrite cubes for 24 h. Heterogeneous bacterial absorption onto the pyrite removed approximately 90% of the viable bacteria from the inoculum. At T = 0, the bacteria were observed primarily in regions enriched in phosphorus. Over 30 days, the bacterial population on the pyrite cubes increased from 1.3 × 10⁷ to 2.9 × 10⁸ bacteria cm^?2. During this growth stage, low levels of thiobacilli (228 ± 167 MPN mL^?1) were also recovered from the fluid phase; however, this population decreased to zero within 30 days. Growth on pyrite occurred as micrometre‐scale planar microcolonies, a biofilm, coating the mineral surfaces. These microcolonies possessed viable thiobacilli, even after 4 months at ‘circumneutral pH’. Imaging the pyrite cubes using SEM‐EDS and scanning force microscopy demonstrated that the thiobacilli grew as iron oxy‐hydroxide‐cemented cells, leading to the formation of mineralized microcolonies. Removing the iron oxy‐hydroxides with oxalic acid did not dislodge the bacteria, demonstrating that the secondary minerals were not responsible for ‘gluing’ the bacteria to the pyrite surface. Removing organic material, i.e. the cells, by an oxygen plasma treatment revealed the presence of corrosion pits the size and shape of bacteria. Because of the inherent geochemical constraints on pyrite oxidation at neutral pH, the colonization of pyrite under circumneutral pH conditions must be facilitated by the development of an acidic nanoenvironment between the bacteria and the pyrite mineral surface.     

A study of C-reactive protein,lipid metabolism and peripheral blood to identify a link between periodontitis and cardiovascular disease

Periodontitis is characterized by systemic inflammatory host responses that may contribute to a higher risk for cardiovascular disease. We hypothesized that periodontitis may be associated with altered C-reactive protein levels, serum levels of lipids and peripheral blood counts, and that these characteristics may serve as markers for a link between periodontitis and cardiovascular disease. Sixty subjects, 25–60 years old, were divided into three groups of 20 subjects each. Group 1, age and sex matched healthy controls; group 2, patients diagnosed with chronic periodontitis; group 3, patients diagnosed with acute periodontal lesions including periodontal abscess and pericoronal abscesses. Serum C-reactive protein levels, lipid levels and peripheral blood counts were obtained for all three groups. Significant increases in C-reactive protein and serum lipid levels, and altered peripheral blood counts were observed between the experimental groups; these factors were correlated with chronic periodontitis and cardiovascular disease. These simple, economical clinical measurements can be used to assess periodontal tissue damage and may be useful for predicting risk of cardiovascular disease in these subjects.     

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi

The filamentous ascomycete genus Neurospora encompasses taxa with a wide range of reproductive modes. Sexual reproduction in this genus can be divided into three major modes; heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-compatibility). In addition to the sexual pathway, most of the heterothallic taxa propagate with morphologically distinct, vegetative dissemination propagules (macroconidia), while this feature is undetected in the majority of the homothallic taxa. In this study, we used sequence information of seven nuclear gene loci from 43 taxa (295 of the possible 301 locus-by-taxon combinations) to create a phylogeny of Neurospora. The results suggest that transitions in reproductive mode have occurred at multiple times within this group of fungi. Although a homothallic ancestor would imply fewer switches in reproductive mode, we argue that the ancestor of Neurospora was likely heterothallic and that homothallism has evolved independently at least six times in the evolutionary history of the genus. Furthermore, the two pseudohomothallic taxa of Neurospora (N. tetrasperma and N. tetraspora) represent two independent origins of pseudohomothallism. Likelihood ratio tests of substitution rates among branches in the phylogeny indicate that reproductive mode is an important factor driving genome evolution in Neurospora. First, an increased level of non-synonymous/synonymous substitutions in branches delineating homothallic taxa was found, suggesting a reduced efficiency of purifying selection in these taxa. Furthermore, elevated nucleotide substitution rates were found in heterothallic, conidia-producing, lineages as compared to the homothallic non-conidiating lineages. The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration.     

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.     

A simple theoretical approach to the band gaps of conjugated polymers

Engineering the band gap of a conjugated polymer is an effective way to improve the performance of the corresponding photoelectric device. In this study, a repeating unit of a conjugated polymer is reduced to a phenylene, a vinylene/ethynylene or a combination of them according to the characteristics of the atoms and the bonds. And the trends of the band gaps of polyphenylene, polyvinylene/polyethynylene, their substituted derivatives and alternating copolymers are given by using Hückel molecular orbital method with the parameters for the electron-withdrawing powers and the strengths of the bonding interactions of atoms. The approximation for complex structures and the trends of simple structures make it very convenient to analyse and predict the band gap of a conjugated polymer qualitatively.     

Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression

Two-component signal transduction, consisting of sensor kinases and response regulators, is the predominant signalling mechanism in bacteria. This signalling system originated in prokaryotes and has spread throughout the eukaryotic domain of life through endosymbiotic, lateral gene transfer from the bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplasmic, bioenergetic organelles—chloroplasts and mitochondria. Until recently, it was thought that two-component systems inherited from an ancestral cyanobacterial symbiont are no longer present in chloroplasts. Recent research now shows that two-component systems have survived in chloroplasts as products of both chloroplast and nuclear genes. Comparative genomic analysis of photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast two-component systems. The components and the systems they comprise have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. Sequence and functional characteristics of chloroplast two-component systems point to their fundamental role in linking photosynthesis with gene expression. We propose that two-component systems provide a coupling between photosynthesis and gene expression that serves to retain genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian inheritance of plastid-associated characters. We discuss the role of this coupling in the chronobiology of cells and in the dialogue between nuclear and cytoplasmic genetic systems.