Design and evaluation of an oligonucleotide-microarray for the detection of different species of the genus Kitasatospora

An oligonucleotide-microarray method was developed for the detection of Kitasatospora species in soil samples. The 16S-23S rDNA internal transcribed spacer (ITS) sequence of these antibiotics-producing actinomycetes was applied to design short oligonucleotide probes. Two different 26-mers were synthesized, specific to each species used. Additionally, four oligonucleotide probes were designed to evaluate the system. The oligonucleotides were spotted onto slides of the ArrayTube microarray system and examined with a new silver-labeling detection technique. Prior to hybridization analysis, the 16S-23S rDNA were amplified by polymerase chain reaction both from bacterial cells and environmental samples using two actinomycetes specific primers containing a 5' biotin labeling. The type strains of eight Kitasatospora species included in this study were K. phosalacinea DSM 43860, K. setae DSM 43861, K. cochleata DSM 41652, K. cystarginea DSM 41680, K. azatica DSM 41650, K. mediocidica DSM 43929, K. paracochleata DSM 41656, and K. griseola DSM 43859. The actinomycetes-specific primers were shown to amplify the entire 16S-23S rDNA ITS region from all tested strains. More importantly, the described technique allows the detection of Kitasatospora strains from soil samples by extracting metagenomic DNA followed by a PCR amplification step. This indicates that the oligonucleotide-microarray method developed in this study is a reliable tool for the detection of Kitasatospora species in environmental samples.     

The area composita of adhering junctions connecting heart muscle cells of vertebrates. II. Colocalizations of desmosomal and fascia adhaerens molecules in the intercalated disk

Using immunofluorescence histochemistry and immunoelectron microscopy on sections through myocardiac tissues of diverse mammalian (human, cow, rat, mouse) and fish species we show that both desmosomal and fascia adhaerens proteins identified by gel electrophoresis and immunoblot occur in the area composita, the by far major type of plaque-bearing junctions of the intercalated disks (IDs) connecting cardiomyocytes. Specifically, we demonstrate that desmoplakin and the other desmosomal proteins occur in these junctions, together with N-cadherin, cadherin-11, alpha- and beta-catenin as well as vinculin, afadin and proteins p120(ctn), ARVCF, p0071, and ZO-1, suggestive of colocalization. We conclude that the predominant type of adhering junction present in IDs is a junction sui generis, termed area composita, that is characterized by an unusually high molecular complexity and an intimate association of molecules of both ensembles, the desmosomal one and the fascia adhaerens category. We discuss possible myocardium-specific, complex-forming interactions between members of the two ensembles and the relevance of our findings for the formation and functioning of the heart and for the understanding of hereditary and other cardiomyopathies. We further propose to use this highly characteristic area composita ensemble of molecules as cardiomyocyte markers for the monitoring of cardiomyogenesis, cardiomyocyte regeneration and possible cardiomyocyte differentiation from mesenchymal stem cells.     

Host-parasitoid dynamics of a generalized Thompson model

A discrete-time host-parasitoid model including host-density dependence and a generalized Thompson escape function is analyzed. This model assumes that parasitoids are egg-limited but not search-limited, and is proven to exhibit five types of dynamics: host failure in which the host goes extinct in the parasitoid's presence or absence, unconditional parasitoid failure in which the parasitoid always goes extinct while the host persists, conditional parasitoid failure in the host and the parasitoid go extinct or coexist depending on the initial host-parasitoid ratio, parasitoid driven extinction in which the parasitoid invariably drives the host to extinction, and coexistence in which the host and parasitoid coexist about a global attractor. The latter two dynamics only occur when the parasitoid's maximal rate of growth exceeds the host's maximal rate of growth. Moreover, coexistence requires parasitism events to be sufficiently aggregated. Small additive noise is proven to alter the dynamical outcomes in two ways. The addition of noise to parasitoid driven extinction results in random outbreaks of the host and parasitoid with varying intensity. Additive noise converts conditional parasitoid failure to unconditional parasitoid failure. Implications for classical biological control are discussed.     

See globally, spike locally: oscillations in a retinal model encode large visual features

We show that coherent oscillations among neighboring ganglion cells in a retinal model encode global topological properties, such as size, that cannot be deduced unambiguously from their local, time-averaged firing rates. Whereas ganglion cells may fire similar numbers of spikes in response to both small and large spots, only large spots evoke coherent high frequency oscillations, potentially allowing downstream neurons to infer global stimulus properties from their local afferents. To determine whether such information might be extracted over physiologically realistic spatial and temporal scales, we analyzed artificial spike trains whose oscillatory correlations were similar to those measured experimentally. Oscillatory power in the upper gamma band, extracted on single-trials from multi-unit spike trains, supported good to excellent size discrimination between small and large spots, with performance improving as the number of cells and/or duration of the analysis window was increased. By using Poisson distributed spikes to normalize the firing rate across stimulus conditions, we further found that coincidence detection, or synchrony, yielded substantially poorer performance on identical size discrimination tasks. To determine whether size encoding depended on contiguity independent of object shape, we examined the total oscillatory activity across the entire model retina in response to random binary images. As the ON-pixel probability crossed the percolation threshold, which marks the sudden emergence of large connected clusters, the total gamma-band activity exhibited a sharp transition, a phenomena that may be experimentally observable. Finally, a reanalysis of previously published oscillatory responses from cat ganglion cells revealed size encoding consistent with that predicted by the retinal model.     

Peptide uptake in the ectomycorrhizal fungus Hebeloma cylindrosporum: characterization of two di- and tripeptide transporters (HcPTR2A and B)

Constraints on plant growth imposed by low availability of nitrogen are a characteristic feature of ecosystems dominated by ectomycorrhizal plants. Ectomycorrhizal fungi play a key role in the N nutrition of plants, allowing their host plants to access decomposition products of dead plant and animal materials. Ectomycorrhizal plants are thus able to compensate for the low availability of inorganic N in forest ecosystems. The capacity to take up peptides, as well as the transport mechanisms involved, were analysed in the ectomycorrhizal fungus Hebeloma cylindrosporum. The present study demonstrated that H. cylindrosporum mycelium was able to take up di- and tripeptides and use them as sole N source. Two peptide transporters (HcPTR2A and B) were isolated by yeast functional complementation using an H. cylindrosporum cDNA library, and were shown to mediate dipeptide uptake. Uptake capacities and expression regulation of both genes were analysed, indicating that HcPTR2A was involved in the high-efficiency peptide uptake under conditions of limited N availability, whereas HcPTR2B was expressed constitutively.     

Dancing between the devil and deep blue sea: the stabilizing effect of enemy-free and victimless sinks

Theoretical and empirical studies have shown that enemy–victim interactions in spatially homogenous environments can exhibit diverging oscillations which result in the extinction of one or both species. For enemy–victim models with overlapping generations, we investigate the dynamical implications of spatial heterogeneity created by enemy-free sinks or victimless sinks. An enemy-free sink is a behavioral, physiological or ecological state that reduces or eliminates the victim's vulnerability to the enemy but cannot sustain the victim population. For victims that move in an ideal-free manner, we prove that the inclusion of an enemy-free sink shifts the population dynamics from diverging oscillations to stable oscillations. During these stable oscillations, the victim disperses in an oscillatory manner between the enemy-free sink and the enemy-occupied patch. Enemy-free sinks with lower mortality rates exhibit oscillations with smaller amplitudes and longer periods. A victimless sink, on the other hand, is a behavioral, physiological or ecological state in which the enemy has limited (or no) access to its victims. For enemies that move in an ideal-free manner, we prove that victimless sinks also stabilize diverging oscillations. Simulations suggest that suboptimal behavior due to information gathering or learning limitations amplify oscillations for systems with enemy-free sinks and dampen oscillations for systems with victimless sinks. These results illustrate that the coupling of a sink created by unstable enemy–victim interactions and a sink created by unsuitable environmental conditions can result in population persistence at the landscape level.