Parachlamydia acanthamoebae enters and multiplies within pneumocytes and lung fibroblasts

Parachlamydia acanthamoebae is a Chlamydia-like organism that naturally infects free-living amoebae. P. acanthamoebae is a putative emerging agent of community-acquired and inhalation pneumonia that may enter and multiply within human macrophages. However, since Parachlamydia induces their apoptosis, macrophages may not represent a perennial niche for this obligate intracellular bacterium. Therefore, we investigated whether pneumocytes and lung fibroblasts are permissive to Parachlamydia infection and might act as a replicative niche. Entry of Parachlamydia into pneumocytes (A549) and lung fibroblasts (HEL) was confirmed by confocal and electron microscopy. In A549 cells, the mean number of Parachlamydia per cell increased 7-fold from day 0 to day 7, independently of the technique used to label the bacteria. The proportion of infected A549 cells also increased over time, whereas cell viability remained unaffected by Parachlamydia infection. The sustained (3 weeks) viability of Parachlamydia when incubated in the presence of A549 cells contrasted with that observed in the absence of cells. HEL cells were also permissive to Parachlamydia infection, as we observed a 3- to 4-fold increase in the mean number of bacteria per cell. In HEL cells, Parachlamydia retained some viability for 2 weeks. These findings demonstrate that Parachlamydia is able to enter and multiply within pneumocytes and fibroblasts. The viability of both cell types was not compromised after Parachlamydia infection. We therefore conclude that these cells may remain infected for a prolonged time and may represent an intrapulmonary niche for the strictly intracellular Parachlamydia. This indirectly supports the role of Parachlamydia as an agent of pneumonia.     

A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations

MOTIVATION: The identification of signatures of positive selection can provide important insights into recent evolutionary history in human populations. Current methods mostly rely on allele frequency determination or focus on one or a small number of candidate chromosomal regions per study. With the availability of large-scale genotype data, efficient approaches for an unbiased whole genome scan are becoming necessary. METHODS: We have developed a new method, the whole genome long-range haplotype test (WGLRH), which uses genome-wide distributions to test for recent positive selection. Adapted from the long-range haplotype (LRH) test, the WGLRH test uses patterns of linkage disequilibrium (LD) to identify regions with extremely low historic recombination. Common haplotypes with significantly longer than expected ranges of LD given their frequencies are identified as putative signatures of recent positive selection. In addition, we have also determined the ancestral alleles of SNPs by genotyping chimpanzee and gorilla DNA, and have identified SNPs where the non-ancestral alleles have risen to extremely high frequencies in human populations, termed 'flipped SNPs'. Combining the haplotype test and the flipped SNPs determination, the WGLRH test serves as an unbiased genome-wide screen for regions under putative selection, and is potentially applicable to the study of other human populations. RESULTS: Using WGLRH and high-density oligonucleotide arrays interrogating 116 204 SNPs, we rapidly identified putative regions of positive selection in three populations (Asian, Caucasian, African-American), and extended these observations to a fourth population, Yoruba, with data obtained from the International HapMap consortium. We mapped significant regions to annotated genes. While some regions overlap with genes previously suggested to be under positive selection, many of the genes have not been previously implicated in natural selection and offer intriguing possibilities for further study. AVAILABILITY: the programs for the WGLRH algorithm are freely available and can be downloaded at http://www.affymetrix.com/support/supplement/WGLRH_program.zip.     

Soybean Aphid Predators in Québec and the Suitability of Aphis glycines as Prey for Three Coccinellidae

Since its invasion of North America in 2000, the soybean aphid, Aphis glycines Matsumura (Homoptera: Aphididae) has notably changed the arthropod community of the soybean agroecosystem. The objectives of this study were to characterize the foliar predatory fauna associated with A. glycines in commercial soybean fields in Québec, Canada, and to evaluate the suitability of A. glycines as prey for three coccinellid species: Harmonia axyridis Pallas, Propylea quatuordecimpunctata L. and Coleomegilla maculata lengi Timberlake (Coleoptera: Coccinellidae). Field surveys showed that several predators responded rapidly to expanding and increasing populations of the soybean aphid. Coccinellidae were the most important aphidophagous predators observed in 2002 (58.6%) and 2003 (44.8%), with mainly four native and naturalized species co-occurring with the soybean aphid throughout the growing season. Measurement of fitness parameters under laboratory conditions (survival, development time, longevity, fecundity) indicated that A. glycines is an excellent prey for the development and reproduction of all three of the coccinellid species studied. The intrinsic rate of natural increase (r_m) was highest for H. axyridis (0.238 d⁻¹), intermediate for P. quatuordecimpunctata (0.215 d⁻¹) and lowest for C. maculata (0.134 d⁻¹).     

Pneumocystis oryctolagi sp. nov., an uncultured fungus causing pneumonia in rabbits at weaning: review of current knowledge, and description of a new taxon on genotypic, phylogenetic and phenotypic bases

The genus Pneumocystis comprises noncultivable, highly diversified fungal pathogens dwelling in the lungs of mammals. The genus includes numerous host-species-specific species that are able to induce severe pneumonitis, especially in severely immunocompromised hosts. Pneumocystis organisms attach specifically to type-1 epithelial alveolar cells, showing a high level of subtle and efficient adaptation to the alveolar microenvironment. Pneumocystis species show little difference at the light microscopy level but DNA sequences of Pneumocystis from humans, other primates, rodents, rabbits, insectivores and other mammals present a host-species-related marked divergence. Consistently, selective infectivity could be proven by cross-infection experiments. Furthermore, phylogeny among primate Pneumocystis species was correlated with the phylogeny of their hosts. This observation suggested that cophylogeny could explain both the current distribution of pathogens in their hosts and the speciation. Thus, molecular, ultrastructural and biological differences among organisms from different mammals strengthen the view of multiple species existing within the genus Pneumocystis. The following species were subsequently described: Pneumocystis jirovecii in humans, Pneumocystis carinii and Pneumocystis wakefieldiae in rats, and Pneumocystis murina in mice. The present work focuses on Pneumocystis oryctolagi sp. nov. from Old-World rabbits. This new species has been described on the basis of both biological and phylogenetic species concepts.     

Lateral spacing of integrin ligands influences cell spreading and focal adhesion assembly

Cell-extracellular matrix (cell-ECM) interactions mediated by integrin receptors are essential for providing positional and environmental information necessary for many cell functions, such as proliferation, differentiation and survival. In vitro studies on cell adhesion to randomly adsorbed molecules on substrates have been limited to sub-micrometer patches, thus preventing the detailed study of structural arrangement of integrins and their ligands. In this article, we illustrate the role of the distance between integrin ligands, namely the RGD (arginine-glycine-aspartate) sequence present in ECM proteins, in the control of cell adhesion. By using substrates, which carry cyclic RGD peptides arranged in highly defined nanopatterns, we investigated the dynamics of cell spreading and the molecular composition of adhesion sites in relation to a fixed spacing between the peptides on the surface. Our novel approach for in vitro studies on cell adhesion indicates that not only the composition, but also the spatial organization of the extracellular environment is important in regulating cell-ECM interactions.