Granzyme a, a stealth killer in the mitochondrion

The induction of caspase-independent cell death by killer lymphocytes involves the serine protease granzyme A (GzmA). In this issue, Martinvalet et al. (2008) show that GzmA penetrates the mitochondrial matrix without perturbing normal mitochondrial functions. In the mitochondrial matrix, GzmA cleaves NDUFS3 (a component of the electron transport chain) leading to production of reactive oxygen species and ultimately to cell death.     

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.     

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.     

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.     

Living inside a sponge skeleton: the association of a sponge,a macroalga and a diatom

The relationships between sponges and macroalgae have been poorly investigated, especially in temperate waters. This work describes the consortium between the dictyoceratid sponge Dysidea pallescens and the red alga Acrochaetium spongicola permeating spongin fibres in the Mediterranean Sea; moreover, this is the first report of a diatom, Amphora pediculus, living also inside the spongin skeleton. The annual trend of the total algal biomass did not vary over time in relation to the temperature, irradiance and incorporation of foreign bodies. Our analyses, conducted by light and electron microscopy, suggest that both the macroalga and the diatom invade the skeleton of the sponge from the external environment, and that the benthic diatom, epiphyte of the macroalga, is passively carried inside the fibres through the growth of Acrochaetium spongicola. All the examined samples of D. pallescens showed that the macroalga permeated at least some fibres, while the presence of the diatom was occasional. The superficial layer of the sponge, thin and reticulate, likely allows the passage of the light and ensures the algal survival inside the sponge tissue. The high occurrence of the association with A. spongicola, together with the morphological adaptations of the sponge favouring the algal life, suggest that the relationship is mutualistic. The possible benefits for the involved partners are hypothesized. The taxonomy and ecology of endozoic Acrochaetiales are controversial due to the reduced size of thalli, the absence of peculiar diagnostic characters and unknown reproductive structures. Therefore, detailed studies on the relationships between the algae and their hosts will provide helpful information for the algal identification.     

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).     

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.     

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.     

Solving the autism puzzle a few pieces at a time

In this issue, a pair of studies (Levy et al. and Sanders et al.) identify several de novo copy-number variants that together account for 5%-8% of cases of simplex autism spectrum disorders. These studies suggest that several hundreds of loci are likely to contribute to the complex genetic heterogeneity of this group of disorders. An accompanying study in this issue (Gilman et al.), presents network analysis implicating these CNVs in neural processes related to synapse development, axon targeting, and neuron motility.     

Disentangling the dynamic core: a research program for a neurodynamics at the large-scale

My purpose in this paper is to sketch a research direction based on Francisco Varela's pioneering work in neurodynamics (see also Rudrauf et al. 2003, in this issue). Very early on he argued that the internal coherence of every mental-cognitive state lies in the global self-organization of the brain activities at the large-scale, constituting a fundamental pole of integration called here a "dynamic core". Recent neuroimaging evidence appears to broadly support this hypothesis and suggests that a global brain dynamics emerges at the large scale level from the cooperative interactions among widely distributed neuronal populations. Despite a growing body of evidence supporting this view, our understanding of these large-scale brain processes remains hampered by the lack of a theoretical language for expressing these complex behaviors in dynamical terms. In this paper, I propose a rough cartography of a comprehensive approach that offers a conceptual and mathematical framework to analyze spatio-temporal large-scale brain phenomena. I emphasize how these nonlinear methods can be applied, what property might be inferred from neuronal signals, and where one might productively proceed for the future. This paper is dedicated, with respect and affection, to the memory of Francisco Varela.     

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...     

Are the Basques a single and a unique population?

Different analyses of genetic polymorphisms performed on the Basque population have suggested a possible heterogeneity of the Basques and a singularity of their genetic characteristics. In this paper, both aspects are analyzed by means of the genetic study of seven polymorphic systems--ACP, ADA, AK, ESD, PGD, GC, and HP--in 854 autochthonous individuals from the province of Vizcaya. The individuals were classified as being from the regions of Arratia, Guernica, Durango, Uribe, Marquina, Lea, and Bilbao, on the basis of the birthplaces of their four grandparents. Analyses for heterogeneity of the gene frequencies distribution suggest that there is a moderate genetic heterogeneity, probably produced by centuries of geographical and administrative isolation of these regions. The comparison with caucasoid populations, performed using the principal components analysis and Cavalli-Sforza and Edwards arc distance, indicates that the subpopulations of the province of Vizcaya have experienced little genetic exchange with other caucasoids and that the distribution of their genetic frequencies differentiates them from other populations.     

Dynamics of a model for the variability of the interspike intervals in a retinal neuron

Recently, a model has been proposed to explain the statistics of the variability of interspike intervals of ganglion cells in the retina of goldfish under steady-state stimulation. In this note, it is shown that the dynamical behaviour of the model, both under steady-state and dynamical stimuli, is characterized by input-invariance of the output random process after a time transformation. This allows to study the signalprocessing properties of the model, and to test its applicability by a more complete experimental analysis.