Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence

Understanding the evolution of virulence is key to appreciating the role specific loci play in pathogenicity. Streptomyces species are generally non-pathogenic soil saprophytes, yet within their genome we can find homologues of virulence loci. One example of this is the mammalian cell entry (mce) locus, which has been characterised in Mycobacterium tuberculosis. To investigate the role in Streptomyces we deleted the mce locus and studied its impact on cell survival, morphology and interaction with other soil organisms. Disruption of the mce cluster resulted in virulence towards amoebae (Acanthamoeba polyphaga) and reduced colonization of plant (Arabidopsis) models, indicating these genes may play an important role in Streptomyces survival in the environment. Our data suggest that loss of mce in Streptomyces spp. may have profound effects on survival in a competitive soil environment, and provides insight in to the evolution and selection of these genes as virulence factors in related pathogenic organisms

Novel Two-Component Systems Implied in Antibiotic Production in Streptomyces coelicolor

The abundance of two-component systems (TCSs) in Streptomyces coelicolor A3(2) genome indicates their importance in the physiology of this soil bacteria. Currently, several TCSs have been related to antibiotic regulation, and the purpose in this study was the characterization of five TCSs, selected by sequence homology with the well-known absA1A2 system, that could also be associated with this important process. Null mutants of the five TCSs were obtained and two mutants (ΔSCO1744/1745 and ΔSCO4596/4597/4598) showed significant differences in both antibiotic production and morphological differentiation, and have been renamed as abr (antibiotic regulator). No detectable changes in antibiotic production were found in the mutants in the systems that include the ORFs SCO3638/3639, SCO3640/3641 and SCO2165/2166 in any of the culture conditions assayed. The system SCO1744/1745 (AbrA1/A2) was involved in negative regulation of antibiotic production, and acted also as a negative regulator of the morphological differentiation. By contrast, the system SCO4596/4597/4598 (AbrC1/C2/C3), composed of two histidine kinases and one response regulator, had positive effects on both morphological development and antibiotic production. Microarray analyses of the ΔabrC1/C2/C3 and wild-type transcriptomes revealed downregulation of actII-ORF4 and cdaR genes, the actinorhodin and calcium-dependent antibiotic pathway-specific regulators respectively. These results demonstrated the involvement of these new two-component systems in antibiotic production and morphological differentiation by different approaches. One is a pleiotropic negative regulator: abrA1/A2. The other one is a positive regulator composed of three elements, two histidine kinases and one response regulator: abrC1/C2/C3

Hybridization but No Evidence for Backcrossing and Introgression in a Sympatric Population of Great Reed Warblers and Clamorous Reed Warblers

Hybridization is observed frequently in birds, but often it is not known whether the hybrids are fertile and if backcrossing occurs. The breeding ranges of the great reed warbler (Acrocephalus arundinaceus) and the clamorous reed warbler (A. stentoreus) overlap in southern Kazakhstan and a previous study has documented hybridization in a sympatric population. In the present study, we first present a large set of novel microsatellite loci isolated and characterised in great reed warblers. Secondly, we evaluate whether hybridization in the sympatric breeding population has been followed by backcrossing and introgression

Introgression and rapid species turnover in sympatric damselflies

<p>Abstract</p> <p>Background</p> <p>Studying contemporary hybridization increases our understanding of introgression, adaptation and, ultimately, speciation. The sister species <it>Ischnura elegans </it>and <it>I. graellsii </it>(Odonata: Coenagrionidae) are ecologically, morphologically and genetically similar and hybridize. Recently, <it>I. elegans </it>has colonized northern Spain, creating a broad sympatric region with <it>I. graellsii</it>. Here, we review the distribution of both species in Iberia and evaluate the degree of introgression of <it>I. graellsii </it>into <it>I. elegans </it>using six microsatellite markers (442 individuals from 26 populations) and five mitochondrial genes in sympatric and allopatric localities. Furthermore, we quantify the effect of hybridization on the frequencies of the genetically controlled colour polymorphism in females of both species.</p> <p>Results</p> <p>In a principal component analysis of the microsatellite data, the first two principal components summarised almost half (41%) of the total genetic variation. The first axis revealed a clear separation of <it>I. graellsii </it>and <it>I</it>. <it>elegans </it>populations, while the second axis separated <it>I. elegans </it>populations. Admixture analyses showed extensive hybridization and introgression in <it>I. elegans </it>populations, consistent with <it>I. elegans </it>backcrosses and occasional F₁-hybrids, suggesting hybridization is on-going. More specifically, approximately 58% of the 166 Spanish <it>I. elegans </it>individuals were assigned to the <it>I. elegans </it>backcross category, whereas not a single of those individuals was assigned to the backcross with <it>I. graellsii</it>. The mitochondrial genes held little genetic variation, and the most common haplotype was shared by the two species.</p> <p>Conclusions</p> <p>The results suggest rapid species turnover in sympatric regions in favour of <it>I. elegans</it>, corroborating previous findings that <it>I. graellsii </it>suffers a mating disadvantage in sympatry with <it>I. elegans</it>. Examination of morph frequency dynamics indicates that hybridization is likely to have important implications for the maintenance of multiple female morphs, in particular during the initial period of hybridization.</p

The PPI value of open foams and its estimation using image analysis

The mean number of pores per inch (PPI value) is one of the most important geometric characteristics of cellular materials such as open or closed foams. It is defined as the number of pores (cells) along a straight test line related to the line length. Counting cells along a test line sounds very simple, but on the surface of an open foam specimen it is often hard to decide whether a cell hits the line or not. Thus, there exists no quick and safe method to estimate the PPI value from an optical image taken from the specimen's surface. In this article, we present a very efficient method of estimating the PPI value of foams from optical dark-field images of the surface of a foam sample. The method is based on the computation of the spectral density of the (two-dimensional) dark field images. It turns out that the radius of the first interference ring in the spectral density is proportional to the PPI value. The constant of proportionality can be determined from geometric models for open foams or analysis of three-dimensional images of foam samples. These techniques allow calibration of the estimation of the PPI value from the spectral density of two-dimensional dark field images

Classification of points in superpositions of Strauss and Poisson processes

Consider a realisation of a point process which is formed as a superposition of a regular point process, here a Strauss process, and some Poisson noise. The aim of the current work is to decide which of the two processes each point belongs to. We construct an MCMC algorithm which estimates the parameters of the superposition model and obtains posterior probabilities for each point of being a Strauss point. The algorithm is evaluated in a simulation study. Finally, it is applied to our motivating data set containing the locations of air bubbles, some of which are noise, in an Antarctic ice core

Estimating geometric anisotropy in spatial point patterns

Anisotropy in stationary spatial point patterns is investigated. We develop a two-stage non-parametric method for quantifying geometric anisotropy arising for example when the pattern is compressed or stretched. First, we fit ellipsoids to the pattern of pairwise difference vectors to estimate the direction of anisotropy. Then, we estimate the scale of anisotropy by identifying the back-transformation resulting in the most isotropic pattern. We demonstrate the applicability of the method mainly for regular patterns by numerical examples, and use it to improve the estimation of compression in 3D polar ice air bubble patterns

Tests for isotropy in spatial point patterns – A comparison of statistical indices

Isotropy of a point process, defined as invariance of the distribution under rotation, is often assumed in spatial statistics. Formal tests for the hypothesis of isotropy can be created by comparing directional summary statistics in different directions. In this paper, the statistical powers of tests based on a variety of summary statistics and several choices of deviance measures are compared in a simulation study. Four models for anisotropic point processes are considered covering both regular and clustered cases. We discuss the robustness of the results to changes of the tuning parameters, and highlight the strengths and limitations of the methods

Modeling of ceramic foams for filtration simulation

We present a stochastic model for the microstructure of a ceramic foam filter which is produced by coating an open polymer foam with liquid ceramic. First, we fit a random Laguerre tessellation to the polymer foam skeleton. Then, the coating is modeled using locally adaptable morphology which allows for the reproduction of the ceramic foam's locally varying strut thickness. Furthermore, we introduce methods for the estimation of the intensity and orientation distribution of the closed facets which are formed during the coating process. By computation of the permeability of the foam in different directions we show that the anisostropic behavior of the material is reproduced correctly in the model