On the probability of the emergence of a protein with a particular function

Proteins with nearly the same structure and function (homologous proteins) are found in increasing numbers in phylogenetically different, even very distant taxa (e.g. hemoglobins in vertebrates, in some invertebrates, and even in certain plants). In discussing the origin of those proteins biologists hardly at all consider convergent evolution because the origin of proteins is held to be a random process, at least ultimately, since selection can work only what the random process delivers as having a minimum adaptive value. The repetition of a random process with the same result is considered to be extremely unlikely. The supposed (un)likelihood, however, is almost never determined quantitatively. This paper attempts such a quantitative determination. It appears that the probability for the random origin of a definite protein is greater than what one would expect in view of the enormous number of equally possible nucleotide sequences in the corresponding gene since what is equally possible is not always equally likely. The probability, however, of the convergent evolution of two proteins with approximately the same structure and function is too low to be plausible, even when all possible circumstances are present which seem to heighten the likelihood of such a convergence. If this is so, then the plausibility of a random evolution of two or more different but functionally related proteins seems hardly greater.     

Measurement of the adhesion of a desmid to a substrate

The paper describes a hydrodynamic method by which the adhesive strength of the mucilage produced from the apical proes of Closterium acerosum has been measured. An equation used to determine the drag force on the cells is presented, as are some measured adhesive strengths of the Closterium mucus to glass slides.     

Effects of a disease affecting a predator on the dynamics of a predator-prey system

We study the effects of a disease affecting a predator on the dynamics of a predator-prey system. We couple an SIRS model applied to the predator population, to a Lotka-Volterra model. The SIRS model describes the spread of the disease in a predator population subdivided into susceptible, infected and removed individuals. The Lotka-Volterra model describes the predator-prey interactions. We consider two time scales, a fast one for the disease and a comparatively slow one for predator-prey interactions and for predator mortality. We use the classical “aggregation method” in order to obtain a reduced equivalent model. We show that there are two possible asymptotic behaviors: either the predator population dies out and the prey tends to its carrying capacity, or the predator and prey coexist. In this latter case, the predator population tends either to a “disease-free” or to a “disease-endemic” state. Moreover, the total predator density in the disease-endemic state is greater than the predator density in the “disease-free” equilibrium (DFE).     

Stabilization of the population of a parasite on fruit by the population of a cleptoparasite

When there exist two species such that one is a parasite on fruit and the other exploits the parasitized fruits, they must compete for a limited resource with each other. The relation between Dacus cucurbitae and Atherigona orientalis is an example of such a situation. We raise a question whether the population of a parasite on fruit can be stabilized by the existence of the cleptoparasite of the parasite on fruit. The changes in their population densities are represented as a differential equation with time delayed parameters, which is deduced from the context of life histories of the two species. An index representing degree of overlapping of generations (g) is defined as an average oviposition period devided by the average preoviposition period, and the value is assumed to be the same in the two species. The stability of the system is classified by three parameters: the reproductive rate of the parasite on fruits (R), the survival probability of it through competition against the cleptoparasite (p), and the generation overlapping index (g). For small values of g, e.g. less than some 0.5, the stability is determined mainly by a product of Rp: the values larger than 1 result in no equilibrium and infinite increase of both species, the values near 0 lead to large amplitude oscillations, and the intermediate values make stable equilibria or regular small oscillations. As g takes the larger values, the stability region in the space (p, R) occupies the larger area. The model presented here is well adjusted to the fluctuating pattern of the population of D. cucurbitae on Okinawa Is., and would also be applied to analysis of both hyperparasitisms and inquilin.     

Behavioral effects of the presence of a dog in a classroom

Abstract

To test the idea that dogs have a positive influence on the social behavior of school children, one of three dogs was introduced alternately into a class at an elementary school in Vienna, attended by 24 children (mean age: 6.7 years). Most of the 14 boys and ten girls came from first-generation immigrant families. With parental consent, their behavior was videotaped for two hours every week, during “open teaching situations,” first during a one-month control period in the absence of dogs, followed by an experimental period of similar duration, when a dog was present in the classroom. Frequency and duration of all observable behaviors of individuals and their interactions were coded from these tapes. Although major individual differences were found in the children's interest in the dog and their behavioral responses, the group became socially more homogenous due to decreased behavioral extremes, such as aggressiveness and hyperactivity; also, formerly withdrawn individuals became socially more integrated. Effects were more pronounced in the boys than the girls. Even though the children spent considerable time watching and making contacting with the dog, they also paid more attention to the teacher. We conclude that the presence of a dog in a classroom could positively stimulate social cohesion in children and provide a relatively cheap and easy means of improving teaching conditions.     

Finding a needle in the virus metagenome haystack--micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire

Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral "needle" within the greater viral community "haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities.     

Desertification in the Sahel: a reinterpretation of a reinterpretation

In semiarid regions the ratio of annual net primary production to precipitation, rain-use efficiency (RUE), has been used as an index of desertification. In a recent publication ( Hein & de Ridder, 2006 ) it was proposed that an incorrect understanding of the relationship between RUE and rainfall has led to a misinterpretation of the satellite record of desertification in the African Sahel. Here, we examine this suggestion and show that, contrary to Hein and de Ridder's statement, satellite studies of Sahelian RUE have reported increases, decreases, and constant values since 1981. Furthermore, we find that data do not support their proposal that RUE increases with rainfall, even in nondegraded areas. Hence we reject their corollary, that constant RUE is prima facie evidence of desertification. The fundamental difficulty with the use of RUE for detection of desertification remains, that is the difficulty of estimation of the RUE for nondegraded land at a regional scale.     

Evidence for the classification of a crayfish pathogen as a member of the genus Coxiella

AIMS: The study aimed to provide characterization of a potential new species of Coxiella, identified following a series of outbreaks of disease in Australian native freshwater crayfish. METHODS AND RESULTS: PCR primers designed for amplification of Coxiella burnetii genes including 16S rDNA, com1 and sodB were used to amplify homologues in the Coxiella-like crayfish pathogen. Products were then cloned and sequenced. The organism demonstrated a high degree of sequence homology in the highly conserved 16S rDNA (96%) and sodB (99%) genes, as well as the Coxiella sp. specific com1 (100%) gene. Regions flanking the sodB coding sequence demonstrated homology to C. burnetii antioxidant AhpC/Tsa family protein and dihydrodipicolinate reductase gene. CONCLUSIONS: The degree of homology between the genes selected and flanking regions suggested the two organisms were sufficiently closely related to belong to the same genus. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provided evidence for a potential new species in the currently monospecific genus Coxiella, with the only described member being C. burnetii, a category B biological warfare agent.     

A test for a shift in the boundary of the geographical range of a species

One predicted impact of climate change is a poleward shift in the boundaries of species ranges. Existing methods for identifying such a boundary shift based on changes in the observed pattern of occupancy within a grid of cells are sensitive to changes in the overall rate of sightings and their latitudinal distribution that are unconnected to a boundary shift. A formal test for a boundary shift is described that allows for such changes. The test is applied to detect northward shifts in the northern boundary of the Essex skipper (Thymelicus lineola) butterfly and the European goldfinch (Carduelis carduelis) in Great Britain. A shift is detected in the latter case but not in the former. Results from a simulation study are presented showing that the test performs well.     

On the determination of the concentration over a sphere with a barrier layer

Slow synaptic potentials may occur in principle because diffusion of the neurotransmitter to the receptors on the post-junctional cell is impeded by a barrier layer. This possibility can sometimes be tested by examining the time course of responses to an agonist applied at different distances from the cell surface.     

Superslow oscillations of the indices of the state of a human-operator as a result of monotony

Infralow oscillations were studied of psychophysiological parameters appearing at one-minute wave range at different levels of human operator's nervous system in conditions of monotony. In experiments on recognition of noisy visual images presented with the frequency of 6-9 signals per hour, 22 subjects took part. The following was found: a) correlation between superslow components of pulse rate and the coefficient of brain potentials synchronization, established in 20-30 min after the beginning of the experiment; b) a tendency to deterioration of the quality of recognition at the stages of slowing down of infralow waves of the pulse rate and to its improvement at the phases of the increase of their frequency. Main results were obtained by the method which needs neither unartifact electrodes nor DC amplifiers. Possible mechanisms of stated dependences are discussed.     

Isolation of a factor, from the capsule of a granulosis virus, synergistic for a nuclear-polyhedrosis virus of the armyworm

When the capsules of a granulosis virus are fed together with the polyhedra of a nuclear-polyhedrosis virus to larvae of the armyworm, Pseudaletia unipuncta, the former enhances the infectivity of the latter virus, a synergistic interaction. The enhancement of infectivity depends upon the concentration of the polyhedra and the capsules. The factor responsible for the synergistic activity in the capsule can be dissolved in alkaline solution, separated from the virus particles by centrifugation, and further purified by Sephadex G-200 gel filtration with 4 m urea. The fraction obtained from Sephadex filtration and containing the synergistic factor can be separated into two components by disc-electrophoresis with 8 m urea. Both components possess synergistic activity. The ID₅₀ of the synergistic factor corresponds to 0.0015 OD₂₈₀. Its optimum pH is 8.5. Synergism is most evident when the factor is fed to larvae together with the polyhedra or is fed 24 hr prior to the ingestion of the polyhedra. The factor appears to be a simple or a conjugated protein of the capsule.     

Physical model of the formation of a low-temperature dense plasma during the irradiation of a target by a picosecond laser pulse

Results are presented from numerical simulations of the breakdown of a dense noble gas by the electrons of a boundary layer that forms during the irradiation of a metal target by a high-power picosecond laser pulse. It is shown that, when the electric field of the boundary layer is taken into account, the density of the seed electrons near the target surface increases substantially, so that the ionization process occurs much faster. The dependence of the time of the onset of breakdown on the electric field of the incident wave and on the concentration of gas atoms is calculated.     

On the Feasibility of a Coulomb Explosion in a Micropinch

Plasma Physics Reports - In this paper we present experimental data on the generation of ions with MeV-energy in a Z-pinch discharge in a heavy-element medium. The calculations show that the escape...