Deleterious Mutations and the Origin of the Meiotic Ploidy Cycle

A population genetical model is investigated in which the organism either alternates between diploid and haploid states or lives entirely in the haploid state. The behavior of the organism is determined by the genotype at a modifier locus. At an independent locus deleterious mutations occur at a low but constant frequency. It is found that the haploid behavior is always an evolutionarily attainable stable trait, while the ploidy-cyclic behavior is an evolutionarily attainable stable trait only when a certain condition holds. This condition depends on the strength of selection, the degree of "sheltering" given by the heterozygote state, and the degree of linkage between the modifier locus and the locus under selection. The last result leads to the speculation that the eukaryotes are derived from an organism which first developed more than one chromosome before it evolved the ploidy cycle.     

A Simple Self-Maintaining Metabolic System: Robustness,Autocatalysis, Bistability

A living organism must not only organize itself from within; it must also maintain its organization in the face of changes in its environment and degradation of its components. We show here that a simple (M,R)-system consisting of three interlocking catalytic cycles, with every catalyst produced by the system itself, can both establish a non-trivial steady state and maintain this despite continuous loss of the catalysts by irreversible degradation. As long as at least one catalyst is present at a sufficient concentration in the initial state, the others can be produced and maintained. The system shows bistability, because if the amount of catalyst in the initial state is insufficient to reach the non-trivial steady state the system collapses to a trivial steady state in which all fluxes are zero. It is also robust, because if one catalyst is catastrophically lost when the system is in steady state it can recreate the same state. There are three elementary flux modes, but none of them is an enzyme-maintaining mode, the entire network being necessary to maintain the two catalysts.     

A method for demonstrating genetic principles using an imaginary organism

The use of an imaginary organism to illustrate principles of genetics is described. The organism is easily drawn, and is well suited to simple printing techniques. It has been used to show independent segregation of genes, partial dominance, linkage in both sex chromosomes and in autosomes, as well as the inheritance of an autosomal gene lethal in the homozygous state. Additional exercises for students are suggested.     

Parental epigenetic control of embryogenesis: a balance between inheritance and reprogramming?

At fertilization, fusion of two differentiated gametes forms the zygote that is capable of forming all of the varied cell lineages of an organism. It is widely thought that the acquisition of totipotency involves extensive epigenetic reprogramming of the germline state into an embryonic state. However, recent data argue that this reprogramming is incomplete and that substantial epigenetic information passes from one generation to the next. In this review we summarize the changes in chromatin states that take place during mammalian gametogenesis and examine the evidence that early mammalian embryogenesis may be affected by inheritance of epigenetic information from the parental generation.     

A mathematical model for cell differentiation,as an evolutionary and regulated process

We introduce an approach which allows one to introduce the concept of cell plasticity into models for tissue regeneration. In contrast to most of the recent models for tissue regeneration, cell differentiation is considered a gradual process, which evolves in time and which is regulated by an arbitrary number of parameters. In the current approach, cell differentiation is modelled by means of a differentiation state variable. Cells are assumed to differentiate into an arbitrary number of cell types. The differentiation path is considered as reversible, unless differentiation has fully completed. Cell differentiation is incorporated into the partial differential equations (PDEs), which model the tissue regeneration process, by means of an advection term in the differentiation state space. This allows one to consider the differentiation path of cells, which is not possible if a reaction-like term is used for differentiation. The boundary conditions, which should be specified for the general PDEs, are derived from the flux of the fully non-differentiated cells and from the irreversibility of the fully completed differentiation process. An application of the proposed model for peri-implant osseointegration is considered. Numerical results are compared with experimental data. Potential lines of further development of the present approach are proposed.     

Keep Your Options Open: An Information-Based Driving Principle for Sensorimotor Systems

The central resource processed by the sensorimotor system of an organism is information. We propose an information-based quantity that allows one to characterize the efficiency of the perception-action loop of an abstract organism model. It measures the potential of the organism to imprint information on the environment via its actuators in a way that can be recaptured by its sensors, essentially quantifying the options available and visible to the organism. Various scenarios suggest that such a quantity could identify the preferred direction of evolution or adaptation of the sensorimotor loop of organisms.     

预测转录单位基础上的原核生物启动子预测

启动子及转录单位预测对于了解基因间的功能及相互间的调节关系具有重要的作用 ,这方面的研究一直是生物信息学的一个重要方向 ,但预测的准确率一直都很有限。本文建立了在转录单位预测基础上进行原核生物启动子预测的新方法 ,首先根据基因间距离、功能关系及多基因比对结果来进行转录单位预测 ,得到了比较理想的结果 ,而且对于研究得比较透和研究得较少的基因组都适用。其后在转录单位预测结果基础上进行启动子预测则采用了隐Markov链模型 ,并在Markov链中考虑状态驻留时间。结果显示 ,该方法能有效地预测出启动子序列及其位置 ,准确率达到 70 %以上。     

A new mathematical model of the dynamics of an age cohort population

A new generalized conception of an organism is given. Based on this conception, a new mathematical model of ontogenesis of an individual and the survival of the age cohort of population was proposed. By using real data on the dynamics of the survival of the age cohort of population, the model enables one to determine the parameters characterizing the relationship man-environment in the context of survival and calculate the dynamics (from birth to death) of the model variables of the state of the organism.     

Properties of the enzymes of energy supply in the common frog under various physiological states. II. Changes in the heat resistance of adenosine triphosphatases and succinate dehydrogenase

The heat resistance of SDG, Na, K-ATPase and Mg-ATPase of the grass frog was determined in January, March and May, the number of animals examined being 30-40 in either experiment. It was found that the average level of the heat resistance of the enzymes studied shows significant, often differently directed changes, which depend on the physiological state of an organism. Negligible correlation between the thermal sensitivity of different enzymes of an organism during hibernation, completely disappear during the activity state.     

The Benefits of Mutualism: A Conceptual Framework

There are three general mechanisms by which phenotypic benefits are transferred between unrelated organisms. First, one organism may purloin benefits from another by preying on or parasitizing the other organism. Second, one organism may enjoy benefits that are incidental to or a by-product of the self-serving traits of another organism. Third, an organism may invest in another organism if that investment produces return benefits which outweigh the cost of the investment. Interactions in which both parties gain a net benefit are mutualistic. The three mechanisms by which benefits are transferred between organisms can be combined in pairs to produce six possible kinds of original or 'basal' mutualisms that can arise from an amutualistic state. A review of the literature suggests that most or all interspecific mutualism have origins in three of the six possible kinds of basal mutualism. Each of these three basal mutualisms have byproduct benefits flowing in at least one direction. The transfer of by-product benefits and investment are common to both intra- and interspecific mutualisms, so that some interspecific mutualisms have intraspecific analogs. A basal mutualism may evolve to the point where each party invests in the other, sometimes obscuring the nature of the original interaction along the way. Two prominent models for the evolution of mutualism do not include by-product benefits: Roughgarden's model for the evolution of the damsel-fish anemone mutualism and the 'Tit-for-Tat' model of reciprocity. Using the conceptual framework presented here, including in particular by-product benefits, I have shown how it is possible to construct more parsimonious alternatives to both models.     

Spin-labeling studies on the lipids of psychrophilic, psychrotrophic, and mesophilic clostridia.

Spin-labeling studies were conducted to elucidate the viscosity and phase transition temperatures of lipids isolated from psychrophilic, psychrotrophic, and mesophilic clostridia. Electron spin resonance spectroscopy indicated that the lipids, for all the growth temperatures tested, were in a fluid state and from 13 to 24 C higher than the corresponding lipid transition temperatures. When the organisms were grown at different temperatures, a psychrotropic and two mesophilic clostridia were shown to be able to adjust their lipid-phase transition temperature to the growth temperature. A psychrophilic Clostridium strain, when grown at different temperatures, synthesized lipids that had the same phase transition temperature. It is suggested that this lack of growth temperature-inducible regulation of lipid-phase transition temperature may be a molecular determinant for the psychrophily of this organism. It is proposed that the growth temperature range of an organism is dependent upon the ability of the organism to regulate its lipid fluidity within a specific range.     

Pilus expression in Neisseria gonorrhoeae involves chromosomal rearrangement

The Neisseria gonorrhoeae pilus protein is one of the major antigenic determinants on the cell's surface. It is comprised of identical subunits of approximately 18 kd and plays a role in the infectivity and virulence of the organism. We have cloned the gene encoding a gonococcal pilus protein into Escherichia coli, and, using one of these clones as a probe in hybridization studies, we have shown that conversion of the pilus positive to pilus negative state in N. gonorrhoeae involves chromosomal rearrangement. Although the pilus protein is produced by E. coli, it does not appear to be assembled on the surface of the cell in native form.     

Carboxylation of phosphoenolpyruvate by extracts of Neisseria gonorrhoeae.

The enzymatic carboxylation of phosphoenolpyruvate by cell-free extracts of Neisseria gonorrhoeae was examined and determined to be similar to the reaction catalyzed by phosphoenolpyruvate carboxylase (PEPC). This was shown by the irreversibility of the reaction and nucleotide independency. The enzyme was found to have some characteristics different from the other bacterial PEPCs reported. The enzyme showed catalytic activity in the presence of cobalt ions as well as magnesium and manganese ions, was not inhibited by succinate in fresh extracts, and displayed a low Michaelis constant for bicarbonate (0.27 mM), as compared with other PEPCs. The significance of this low Michaelis constant is discussed with respect to the growth of the organism and the importance of this enzyme to protein and nucleic acid synthesis.     

Reproductive suppression in female primates: A review

Reproductive performance is the currency of evolution. All things being equal, an organism should reproduce as often as possible. The puzzling questions in evolutionary biology, therefore, are not how and why an organism does reproduce, but rather how and why an organism does not reproduce. It is difficult to understand why any individual, particularly a female, might forestall reproduction when one of the biggest limitations for female mammalian reproduction is time (that is, reproductive lifespan). 1 The answer, now widely cited throughout behavioral ecology is quite simple: Reproductive suppression can be an adaptive strategy. 2     

Spontaneous Reaction Silencing in Metabolic Optimization

Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood. Here we predict computationally and analytically that any organism evolving to maximize growth rate, ATP production, or any other linear function of metabolic fluxes tends to significantly reduce the number of active metabolic reactions compared to typical nonoptimal states. The reduced number appears to be constant across the microbial species studied and just slightly larger than the minimum number required for the organism to grow at all. We show that this massive spontaneous reaction silencing is triggered by the irreversibility of a large fraction of the metabolic reactions and propagates through the network as a cascade of inactivity. Our results help explain existing experimental data on intracellular flux measurements and the usage of latent pathways, shedding new light on microbial evolution, robustness, and versatility for the execution of specific biochemical tasks. In particular, the identification of optimal reaction activity provides rigorous ground for an intriguing knockout-based method recently proposed for the synthetic recovery of metabolic function.     

Towards physical dynamic tolerance: an approach to resolve the conflict between free will and physical determinism

This paper attempts to resolve the conflict between free will and determinism. The problem is approached by demonstrating that: (a) some well-established experimental observations indicate that irreversibility persists at the molecular level, (b) microscopic reversibility is not fully compatible with macroscopic irreversibility, (c) an overall consistency can be maintained if microscopic reversibility is regarded only as an excellent approximation, whereas microscopic irreversibility together with chaos can account for macroscopic reversibility, and (d) endogenous noise serves a vital function of nerve excitation. Thus, the mean of position and momentum specified by a non-deterministic law of motion gives the law its superficially deterministic behavior and predictability, whereas its dispersion grants dynamic tolerance and irreversibility. Therefore, causality is preserved while a limited degree of freedom allows for the exercise of free will. However, it is argued that free will can never be proven or disproven by a conventional behavioral experiment.     

Effect of heavy water on metabolism of a symbiotic organism

The metabolism of the symbiotic organism medusomycete (tea fungus) and the influence of D2O on its development was studied by high-resolution NMR methods using isotopically enriched (by 13C and 2H) metabolites. The results demonstrate that D2O influences the selective utilization of certain protonated substrates during the formation of triose phosphates. It was found that protonated isotopomers derived from the first glucose fragment C1-C2-C3 are predominantly utilized. This explains why the metabolism slows down by a factor of 2 to 3 if D2O concentration in the medium increases. It was also shown that approximately 10% of the organisms are in the state of dynamic extracellular endosymbiosis. This state is characterized by the ability to exchange the metabolic products through close intercellular contacts. As a result of the metabolic exchange, a multicellular organism is formed, with metabolic elements localized in different partners. A distinguishing feature of this organism is the ability to accumulate the internal resources of carbon, thus making it better adapted to the unfavorable environment.     

Use of body-water content to assess the physiological state of roach Rutilus rutilus L. in natural conditions

It is shown that in natural conditions roach have two levels of water content in their organisms during their annual cycle which reflect different physiological states of the fish. During the feeding period, the body-water content is maintained at a low level of 72.6 ± 0.05%, determining the physiological state related to the growth of fishes. In winter, spring, and postspawning periods, the water content in the roach organism is high, 75 ± 0.06%, which reflects the physiological state of survival during periods of the year unfavorable for growth. The water content in the organism of fish is a convenient integrated parameter for assessing the general physiological state of fish in natural conditions.     

Comparative analysis of cell replacement in hibernators.

1. Cell renewal in hibernators undergoes seasonal rhythm independent of the hibernation state. 2. We propose that seasonal depression of cell renewal in tissues of hibernators is caused by seasonal involution of thymus in these animals. 3. The latter is known to be involved in the control of cell proliferation. 4. The state of hibernation per se has also an effect on cellular proliferation. 5. It induces the block of cells in the permitotic phase. It is suggested that the blockage of cells in renewing tissues of hibernators under natural deep hypothermia throughout a period of torpidity represents the adaptive reaction of the organism.