Microarray-based comparison of genetic differences between strains of Streptomyces turgidiscabies with focus on the pathogenicity island

The areas of the pathogenicity island (PAI) designated as 'colonization region' (CR) and 'toxicogenic region' (TR) [Lerat et al. (2009) Mol. Plant Pathol. 10, 579-585] contain genes required for virulence and phytoxin production, respectively, in Streptomyces spp. causing common scab on potatoes. The PAI was tested for genetic variability by microarray analysis in strains of S. turgidiscabies isolated from potatoes in Finland. The data revealed four types of PAI based on divergent CR and TR which occurred in different combinations. Only one PAI type was highly similar to S. scabies (strains 87.22 and ATTC49173). Using probes designed for the predicted genes of S. scabies, two gene clusters in S. scabies appeared to be similar to most strains of S. turgidiscabies and contained PAI genes corresponding to CR and TR. They were located approximately 5 Mb apart in the S. scabies genome, as compared with only 0.3 Mb in S. turgidiscabies Car8. Data from comparative genomic hybridization with probes designed for S. scabies genes and for the PAI of S. turgidiscabies were compared by multilocus cluster analysis, which revealed two strains of S. turgidiscabies that were very closely related at the whole-genome level, but contained distinctly different PAIs. The type strain of S. reticuliscabiei (DSM41804; synonymous to S. turgidiscabies) was clustered with S. turgidiscabies. Taken together, the data indicate wide genetic variability of PAIs among strains of S. turgidiscabies, and demonstrate that PAI is made up of a mosaic of regions which may undergo independent evolution.     

Double labelling immunohistochemical characterization of autonomic sympathetic neurons innervating the sow retractor clitoridis muscle

Retrograde neuronal tracing and immunohistochemical methods were used to define the neurochemical content of sympathetic neurons projecting to the sow retractor clitoridis muscle (RCM). Differently from the other smooth muscles of genital organs, the RCM is an isolated muscle that is tonically contracted in the rest phase and relaxed in the active phase. This peculiarity makes it an interesting experimental model. The fluorescent tracer fast blue was injected into the RCM of three 50 kg subjects. After a one-week survival period, the ipsilateral paravertebral ganglion S1, that in a preliminary study showed the greatest number of cells projecting to the muscle, was collected from each animal. The co-existence of tyrosine hydroxylase with choline acetyltransferase, neuronal nitric oxide synthase, calcitonin gene-related peptide, leu-enkephalin, neuropeptide Y, substance P and vasoactive intestinal polypeptide was studied under a fluorescent microscope on cryostat sections. Tyrosine hydroxylase was present in about 58% of the neurons projecting to the muscle and was found to be co-localized with each of the other tested substances. Within fast blue-labelled cells negative to the adrenergic marker, small populations of neurons singularly containing each of the other enzymatic markers or peptides were also observed. The present study documents the complexity of the neurochemical interactions that regulate the activity of the smooth myocytes of the RCM and their vascular components.     

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.     

Time–frequency warping of spectrograms applied to bird sound analyses

A new method is introduced which tolerates distortions between spectrogram patterns in template matching. Cross-correlation provides a fast method to calculate similarities but it is sensitive to durational and spectral fluctuations. Dynamic time warping tolerates durational differences but requires that frequency components match. An extension to dynamic time warping is introduced where frequency is warped in addition to time. This allows for a detailed analysis to find the similarities and differences between the sound units to be compared. The method was applied to analyses of owl and Bengalese finch vocalizations.     

Involvement of two-component system CBO0366/CBO0365 in the cold shock response and growth of group I (proteolytic) Clostridium botulinum ATCC 3502 at low temperatures

The role of the two-component system (TCS) CBO0366/CBO0365 in the cold shock response and growth of the mesophilic Clostridium botulinum ATCC 3502 at 15°C was demonstrated by induced expression of the TCS genes upon cold shock and impaired growth of the TCS mutants at 15°C.