Strong differentiation within Diplocarpon rosae strains based on microsatellite markers and greenhouse-based inoculation protocol on Rosa

The haploid ascomycete Diplocarpon rosae is the causal agent of black spot disease on roses, a widespread and devastating disease in the outdoor landscape. In this study, we established a Eurasian collection of 77 monoconidial strains of D. rosae: 50 strains collected on cultivated roses in Europe and Asia, and 27 strains on wild roses in Kazakhstan. To provide tools to describe its biology and to study its genetic diversity, we sequenced two strains of D. rosae using Illumina paired-end technology. The genome sizes of these two strains were estimated at 31.1 and 35.2 Mb, which are two times smaller than the genome size of the unique strain previously published. A BUSCO analysis confirmed a genome duplication of the strain previously sequenced and partial gene duplication of strains analysed in this study. Using the two genome sequences, 27 polymorphic microsatellite markers were identified. Polymorphism analysis of the 77 strains revealed a strong genetic differentiation between strains from cultivated and wild roses, and a lower diversity within the fungal population from cultivated roses compared to the population from wild roses. Pathogenicity of 10 strains was evaluated on 9 rose cultivars inoculated in the greenhouse. Disease scoring allowed the classification of strains into three groups and the characterization of resistance of rose cultivars. Good correlation observed between resistance scoring in greenhouse conditions and in the field indicates that pathogenicity assays in controlled conditions could be very useful in the near future to rapidly characterize the resistance of new rose varieties to black spot disease.     

Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka

Avian pathogenic Escherichia coli (APEC) causes economically significant infections in poultry. The genetic diversity of APEC and phylogenetic relationships within and between APEC and other pathogenic E. coli are not yet well understood. We used multilocus sequence typing (MLST), PCR-based phylogrouping and virulence genotyping to analyse 75 avian E. coli strains, including 55 isolated from outbreaks of colisepticaemia and 20 from healthy chickens. Isolates were collected from 42 commercial layer and broiler chicken farms in Sri Lanka. MLST identified 61 sequence types (ST) with 44 being novel. The most frequent ST, ST48, was represented by only six isolates followed by ST117 with four isolates. Phylogenetic clusters based on MLST sequences were mostly comparable to phylogrouping by PCR and MLST further differentiated phylogroups B1 and D into two subgroups. Genotyping of 16 APEC associated virulence genes found that 27 of the clinical isolates and one isolate from a healthy chicken belonged to highly virulent genotype according to previously established classification schemes. We found that a combination of four genes, ompT, hlyF, iroN and papC, gave a comparable prediction to that of using five and nine genes by other studies. Four STs (ST10, ST48, ST117 and ST2016) contained APEC isolates from this study and human UPEC isolates reported by others, suggesting that these STs are potentially zoonotic. Our results enhanced the understanding of APEC population structure and virulence association.     

C-cadherin ectodomain structure and implications for cell adhesion mechanisms

Cadherins are transmembrane proteins that mediate adhesion between cells in the solid tissues of animals. Here we present the 3.1 angstrom resolution crystal structure of the whole, functional extracellular domain from C-cadherin, a representative "classical" cadherin. The structure suggests a molecular mechanism for adhesion between cells by classical cadherins, and it provides a new framework for understanding both cis (same cell) and trans (juxtaposed cell) cadherin interactions. The trans adhesive interface is a twofold symmetric interaction defined by a conserved tryptophan side chain at the membrane-distal end of a cadherin molecule from one cell, which inserts into a hydrophobic pocket at the membrane-distal end of a cadherin molecule from the opposing cell.     

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

Mechanical unfolding trajectories for single molecules of the Tetrahymena thermophila ribozyme display eight intermediates corresponding to discrete kinetic barriers that oppose mechanical unfolding with lifetimes of seconds and rupture forces between 10 and 30 piconewtons. Barriers are magnesium dependent and correspond to known intra- and interdomain interactions. Several barrier structures are "brittle," breakage requiring high forces but small (1 to 3 nanometers) deformations. Barrier crossing is stochastic, leading to variable unfolding paths. The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication.     

Species diversity and seasonal abundance of Collembola in turfgrass ecosystems of North America

In North America, lawns are the most widely used plantings in urban areas. However, despite the ubiquity and ecological roles of turfgrass soil arthropods, many aspects of their composition and diversity have been neglected. We investigated assemblages of Collembola and their seasonal fluctuations in a newly established lawn and a 10-year old lawn located in Québec City, Canada. Collembola were sampled every month from May to October in 2003 and 2004 by extracting individuals from soil cores using a modified Berlese funnel. A total of 21 species representing 17 genera and nine families were identified. Four species are new records for the province of Quebec: Brachystomella parvula, Mesaphorura simplex, Isotomodes productus, and Sphaeridia pumilis. Turfgrass supports mainly three cosmopolitan species from the Isotomidae family, which represent 73.5% of all Collembola collected during the survey: Parisotoma notabilis, Isotoma viridis, and Cryptopygus thermophilus. Collembola were twice more abundant at the newly established site, but there were minor differences in species diversity between sites and years. No clear patterns of seasonal relative abundance were observed for the whole Collembola populations, as well as for the three dominant species. Turfgrass ecosystem provides a suitable habitat for epedaphic and hemiedaphic Collembola, such as the Isotomidae, most likely because turfgrass mowing and natural leaf, stem and root replacement produces large amounts of decaying organic matter.     

The SAHGA model to calculate the Spatial Ammoniacal Heterogeneity at the soil surface after fertiliser Granule Application

After dissolution of fertiliser granules, a high nitrogen concentration is recovered in the immediate vicinity of granules, which may enhance damaging processes like nitrite accumulation or ammonia volatilisation. Based on the diffusion equations of Cranck, the granule-soil microsite was modelled to obtain the actual fertilised surface plot and the effective rate of N application on this surface. Parameterisation of the diffusion coefficient of solutes consisted of a temperature and soil texture correction. The model was tested against an experimental data set obtained from soil incubations at two soil water contents (21.2% m³ m^–3 and 28.3% m³ m^–3) and two temperatures (4°C and 25°C) by comparing NH₄⁺ recovery at various distances from the granules. The simulated radius of the granule-soil microsite was more affected by the water content than by the temperature. The model is very accurate because 95–100% of total NH₄⁺ applied was recovered in the modelled surface depending on the experimental conditions (temperature and water content). The model was simple enough to be easily integrated into larger models dealing with surface-applied granule fertilisers.     

Genetic differentiation among Ecuadorian Theobroma cacao L. accessions using DNA and morphological analyses

The quality of Ecuadorian cacao is presently threatened by the introduction of hybrid material. An estimation of genetic diversity in Ecuador is required in order to avoid the loss of fine flavored cocoa. Genetic variability amongst 60 Ecuadorian genotypes of Theobroma cacao has been evaluated using molecular and phenotypic markers. The two distance matrices derived from the molecular and phenotypic data were found to be correlated (R² = 0.5). Dynamic clustering analyses classified the genotypes in two or three groups depending on the markers used. The genotypes coming from Sebasti{àn Arteaga (SA) and Balao Chico (BCH) plantations appeared related to each other suggesting a common genetic origin. They also may be considered as a distinct group with high RFLP homozygosity. The EETP (Estací}on Experimental Tropical Pichilingue of Ecuador) collection was comprised of more variable genotypes possessing variable heterozygosity levels. The low heterozygous genotypes may be genetically related to SA and BCH trees, whereas the higher heterozygous genotypes may have resulted from hybridizations between original Nacional material of Ecuador and genotypes imported from Trinidad at the beginning of the century. Thus genetic introgression may have occurred giving rise to a range of variation between Nacional and hybrid forms. This revised version was published online in July 2006 with corrections to the Cover Date.     

CT is helpful for the detection and presurgical planning of lung perforation in dogs with spontaneous pneumothorax induced by grass awn migration: 22 cases

Spontaneous pneumothorax induced by grass awns accounts for 5% of spontaneous pneumothorax and 22.5% of thoracic grass awn cases. Previous studies report limited interest of CT for spontaneous pneumothorax. Aims of this retrospective case series were to describe CT features of this condition and determine if CT features can efficiently localize the perforation site. Dogs that had a spontaneous pneumothorax, CT examination, thoracic surgery, and confirmed lung perforation due to a grass awn were included. Computed tomography studies were reviewed and compared to the surgical findings.  In 19 of 22 (86.4%) dogs, the pneumothorax or its recurrence were ipsilateral to the perforation site. The perforation site was identified in 21 of 22 (95.5%) dogs and involved the caudal lobes in 20 of 22 (90.9%) cases. The lateralization and the involved lung lobe corresponded to surgical findings in 21 of 22(95.5%) dogs. The perforation site was characterized as a soft tissue attenuating focus lying against an extensive pleural thickening in 21 of 22(95.5%) dogs. An adjacent defect in the visceral pleura was seen in 13 of 22(59.1%) dogs. A grass awn was seen in 11 of 22(50%) dogs.  The pneumothorax distribution and grass awn position consistently indicated the perforation side in this sample of dogs. The comparison with surgical findings suggests CT might be helpful for future presurgical planning of this etiology for pneumothorax.     

Droplet infiltration and organic matter composition of intact crack and biopore surfaces from clay‐illuvial horizons

The organic matter (OM) in biopore walls and aggregate coatings may be important for sorption of reactive solutes and water as well as for solute mass exchange between the soil matrix and the preferential flow (PF) domains in structured soil. Structural surfaces are coated by illuvial clay‐organic material and by OM of different origin, e.g., earthworm casts and root residues. The objectives were to verify the effect of OM on wettability and infiltration of intact structural surfaces in clay‐illuvial horizons (Bt) of Luvisols and to investigate the relevance of the mm‐scale distribution of OM composition on the water and solute transfer. Intact aggregate surfaces and biopore walls were prepared from Bt horizons of Luvisols developed from Loess and glacial till. The mm‐scale spatial distribution of OM composition was scanned using diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The ratio between alkyl and carboxyl functional groups in OM was used as potential wettability index (PWI) of the OM. The infiltration dynamics of water and ethanol droplets were determined measuring contact angles (CA) and water drop penetration times (WDPT). At intact surfaces of earthworm burrows and coated cracks of the Loess‐Bt, the potential wettability of the OM was significantly reduced compared to the uncoated matrix. These data corresponded to increased WDPT, indicating a mm‐scaled sub‐critical water repellency. The relation was highly linear for earthworm burrows and crack coatings from the Loess‐Bt with WDPT > 2.5 s. Other surfaces of the Loess‐Bt and most surfaces of the till‐derived Bt were not found to be repellent. At these surfaces, no relations between the potential wettability of the OM and the actual wettability of the surface were found. The results suggest that water absorption at intact surface structures, i.e., mass exchange between PF paths and soil matrix, can be locally affected by a mm‐scale OM distribution if OM is of increased content and is enriched in alkyl functional groups. For such surfaces, the relation between potential and actual wettability provides the possibility to evaluate the mm‐scale spatial distribution of wettability and sorption and mass exchange from DRIFT spectroscopic scanning.