SciCombinator

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Journal: Bio Systems

27

The present study focused on beating synchronization, and tried to elucidate the interlayer regulatory mechanisms between the cells and clump in beating synchronization with using the stochastic simulations which realize the beating synchronizations in beating cells with low cell-cell conductance. Firstly, the fluctuation in interbeat intervals (IBIs) of beating cells encouraged the process of beating synchronization, which was identified as the stochastic resonance. Secondly, fluctuation in the synchronized IBIs of a clump decreased as the number of beating cells increased. The decrease in IBI fluctuation due to clump formation implied both a decline of the electrophysiological plasticity of each beating cell and an enhancement of the electrophysiological stability of the clump. These findings were identified as the community effects. Because IBI fluctuation and the community effect facilitated the beating stability of the cell and clump, these factors contributed to the spontaneous ordering in beating synchronization. Thirdly, the cellular layouts in clump affected the synchronized beating rhythms. The synchronized beating rhythm in clump was implicitly regulated by a complicated synergistic effect among IBI fluctuation of each beating cell, the community effect and the cellular layout. This finding was indispensable for leading an elucidation of mechanism of emergence. The stochastic simulations showed the necessity of considering the synergistic effect, to elucidate the interlayer regulatory mechanisms in biological system.

Concepts: DNA, Gene, Organism, Effect, Affect, Theodor Schwann, Stochastic

21

The quite recent (at least on the evolutionary time scale) emergence of nervous systems in complex organisms enabled the living beings to build a wide-ranging model of the external world in order to predict and evaluate the outcomes of their actions. Such a process likely represents a real coding activity, since, by proper handling of information, it generates a mapping between the external environment and internal cerebral activity patterns. The patterns of neural activity that correspond to the final maps, however, emerge from the holistic assembly of a multilevel functional organization. Nerve tissue components, indeed, appear organized in compartments, also called functional modules (FM), that contain system components and circuits of different miniaturizations not only arranged to work together either in parallel or in series but also nested within each other. At least three levels can be recognized in a functional module and it is possible to point out that such a hierarchical organization of the brain circuits could be mirrored by a corresponding hierarchical organization of biocodes. This feature can also suggest the hypothesis that the same logic could operate also at system level to integrate FM into functional brain areas and to associate areas to generate the final map used by humans to image the external world and to imagine untestable worlds.

4

Genetic correlation between mates at specific loci can greatly alter the evolutionary trajectory of a species. Genetic assortative mating has been documented in humans, but its existence beyond population stratification (shared ancestry) has been a matter of controversy. Here, we develop a method to measure assortative mating across the genome at 1,044,854 single-nucleotide polymorphisms (SNPs), controlling for population stratification and cohort-specific cryptic relatedness. Using data on 1,683 human couples from two data sources, we find evidence for both assortative and disassortative mating at specific, discernible loci throughout the entire genome. Then, using the composite of multiple signals (CMS) score, we also show that the group of SNPs exhibiting the most assortativity has been under stronger recent positive selection. Simulations using realistic inputs confirm that assortative mating might indeed affect changes in allele frequency over time. These results suggest that genetic assortative mating may be speeding up evolution in humans.

2

The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC’s optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.

2

Attachment scale is constructed from two components (anxiety and avoidance) effectively treated as providing salient measures in previous studies. Recent studies have suggested associations between sensitivities to physical warmth and anxiety scores of attachment scale. Some researchers also suggest that the degree of one’s comfort with physical proximity depends on attachment styles, attributing differences to the number of oxytocin (a neuropeptide released by physical touch) receptors. Lateral preference is an important aspect of physical proximity, coupled with the lateralization of visual, emotional, and other cognitive systems. However, there are few studies investigating the relationship between attachment scale scores and one’s lateral preferences in physical proximity. Here we surveyed the preferences of subjects regarding positional relations with their romantic partner in some daily situations, and examined the association with attachment scale score. Our results show that the existence or absence of partner correlates with different relations between attachment styles and subjects' awareness of lateral preferences. Lateral preferences in physical proximity may play an important role in attachment in adulthood.

2

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response. In this manner, animals are able to detect numerous parameters, ranging from temperature and humidity to light and sound to volatile or non-volatile chemicals. Most of these environmental cues represent a clearly defined stimulus array that can be described along a single physical parameter, such as wavelength or frequency; odorants, in contrast, cannot. The odor space encompasses an enormous and nearly infinite number of diverse stimuli that cannot be classified according to their positions along a single dimension. Hence, the olfactory system has to encode and translate the vast odor array into an accurate neural map in the brain. In this review, we will outline the relevant steps of the olfactory code and describe its progress along the olfactory pathway, i.e., from the peripheral olfactory organs to the first olfactory center in the brain and then to the higher processing areas where the odor perception takes place, enabling an organism to make odor-guided decisions. We will focus mainly on studies from the vinegar fly Drosophila melanogaster, but we will also indicate similarities to and differences from the olfactory system of other invertebrate species as well as of the vertebrate world.

Concepts: Biology, Animal, Sense, Olfactory bulb, Olfaction, Olfactory system, Drosophila melanogaster, Drosophila

2

Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptideā€¢RNA world.

Concepts: DNA, Protein, Gene, Natural selection, Molecular biology, RNA, Genetic code, Transfer RNA

2

It is well known that in contrast to the Prisoner’s Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness.

Concepts: Game theory, Evolution, Species, Sociology, Prisoner's dilemma, Evolutionarily stable strategy, Cultural assimilation, Inequity aversion

2

For their growth, dormant tumors, which lack angiogenesis may critically depend on gradients of nutrients and oxygen from the nearest blood vessel. Because for oxygen depletion the distance from the nearest blood vessel to depletion will generally be shorter than for glucose depletion, such tumors will contain anoxic living tumor cells. These cells are dangerous, because they are capable of inducing angiogenesis, which will “wake up” the tumor. Anoxic cells are dependent on anaerobic glucose breakdown for ATP generation. The local extracellular glucose concentration gradient is determined by the blood glucose concentration and by consumption by cells closer to the nearest blood vessel. The blood glucose concentration can be lowered by 20-40% during fasting. We calculated that glucose supply to the potentially hazardous anoxic cells can thereby be reduced significantly, resulting in cell death specifically of the anoxic tumor cells. We hypothesize that intermittent fasting will help to reduce the incidence of tumor relapse via reducing the number of anoxic tumor cells and tumor awakening.

Concepts: Cancer, Adenosine triphosphate, Enzyme, Glucose, Blood vessel, Electrochemistry, Cellular respiration, Blood sugar

1

How can one defend free will against determinism? Since quantum mechanics entails non-locality, it enables the co-existence of free will and determinism. Is non-locality in cognition possible, or must quantum mechanics be rejected? Here, we define free will, determinism and locality in terms of a binary relation between objects and representations, and we verify that the three concepts constitute a trilemma. We also show that non-locality in cognition is naturally found in decision making without any assumption of quantum mechanics. Three kinds of relations result from the trilemma. By using a rough set lattice technique, the three kinds of relations can be transformed into three kinds of logical structures. Type I is a naive set theoretical logic or Boolean algebra (i.e., all possible combinations of binary yes-no responses). Type II comprises all possible combinations of various multiple values, such as for the symptoms of schizophrenia. Type III is a non-local disjoint union of multiple contexts. The type III structure can show how non-locality in cognition can lead to the co-existence of free will and determinism. Loss of non-locality could play an essential role in the malfunction of the separation and integration of the self and others.