Lipopeptide Production in Pseudomonas sp. Strain DSS73 Is Regulated by Components of Sugar Beet Seed Exudate via the Gac Two-Component Regulatory System

Pseudomonas sp. strain DSS73 isolated from the sugar beet rhizosphere produces the cyclic lipopeptide amphisin, which inhibits the growth of plant-pathogenic fungi. By Tn5::luxAB mutagenesis, we obtained two nonproducing mutant strains, DSS73-15C2 and DSS73-12H8. The gene interrupted by the transposon in strain DSS73-15C2 (amsY) encoded a protein with homology to peptide synthetases that was designated amphisin synthetase. DSS73-12H8 carried the transposon in a regulatory gene encoding a protein with homology to the sensor kinase GacS. Growth of strain DSS73-15C2 (amsY) was impaired during the transition to stationary phase in a minimal medium amended with an exudate of sugar beet seeds. This growth phenotype could be complemented by purified amphisin. Seed exudate further induced expression of bioluminescence from the amsY::luxAB reporter during the transition to stationary phase. This agreed with an increase in amphisin production by the DSS73 wild-type strain during early stationary phase. Amphisin synthesis in DSS73 was strictly dependent on GacS, and even induction by seed exudate depended on a functional gacS locus. Hence, a signal triggering the GacS/GacA two-component system appeared to be present in the seed exudate.     

Recruitment in Dentaria bulbifera; the roles of dispersal,habitat quality and mollusc herbivory

Abstract. We investigated the effects of dispersal limitation, diaspore density, soil chemistry, disturbance and mollusc herbivory on the abundance and distribution of the perennial forest herb Dentaria bulbifera (Brassicaceae). After experimental sowing of bulbils in originally empty patches, juveniles of Dentaria emerged in 83% of plots. The seventh year after sowing, plants still persisted and were reproducing in several plots, demonstrating that the species is dispersal‐limited. However, long‐term survival of transplants was higher at sites where Dentaria occurred naturally, and this difference increased with time after sowing. Thus, the importance of local factors may only be expressed fully several years after colonisation. Differences in soil chemistry and disturbance treatment were not associated with differences in patch suitability. Removal of molluscs, however, significantly increased recruitment, and the effects of a single molluscicide treatment persisted after four years. We conclude that dispersal is not the only limitation to the distribution of Dentaria, and that local factors, such as mollusc herbivory, are also crucial.     

Size-related deterioration of semi-natural grassland fragments in Sweden

Abstract. One of the most dramatic landscape changes during the 20th century in Sweden, like in most of Europe, has been the reduction and fragmentation of semi-natural grasslands. Using a set of remnant semi-natural grasslands, chosen to be as similar as possible, but differing in size, we have examined whether size of remnant fragments of traditionally managed semi-natural grasslands in Sweden is related to patterns of species richness and composition. We focused on edge-to-interior relationships, since we expected that a possible impact from invasive habitat generalists would be manifested in a gradient from the edge of fragments to their interior. We found no relationship between size of grassland fragments and (a) overall species richness, (b) species richness at different spatial scales, and (c) abundance of some typical invader species or species characteristic of semi-natural grasslands. However, the results indicated that larger grasslands have a comparatively larger number of species in the edges, whereas the opposite pattern was found in smaller grasslands. The similarity in species composition between the edge and the interior of the pastures also increased with grassland size. Thus, even though the overall species richness is still unaffected by reduction in grassland fragment size, the edges of smaller grasslands show signs of degradation, i.e. reduction in species richness and a decreased similarity to the grassland interior. We suggest that these kinds of effects may be early signs of fragmentation effects that in the future will result in species loss even if the present distribution of semi-natural grasslands is maintained.     

Analysis of short stature homeobox-containing gene (<Emphasis Type="Italic">SHOX</Emphasis>) and auxological phenotype in dyschondrosteosis and isolated Madelung deformity

Dyschondrosteosis (DCO; also called Léri-Weill syndrome) is a skeletal dysplasia characterised by disproportionate short stature because of mesomelic shortening of the limbs. Madelung deformity is a feature of DCO that is distinctive, variable in expressivity and frequently observed. Mutations of the SHOX (short stature homeobox-containing) gene have been previously described as causative in DCO. Isolated Madelung deformity (IMD) without the clinical characteristics of DCO has also been described in sporadic and a few familial cases but the genetic defect underlying IMD is unknown. In this study, we have examined 28 probands with DCO and seven probands with IMD for mutations in the SHOX gene by using polymorphic CA-repeat analysis, fluorescence in situ hybridisation (FISH), Southern blotting, direct sequencing and fibre-FISH analyses. This was combined with auxological examination of the probands and their family members. Evaluation of the auxological data showed a wide intra- and interfamilial phenotype variability in DCO. Out of 28 DCO probands, 22 (79%) were shown to have mutations in the SHOX gene. Sixteen unrelated DCO families had SHOX gene deletions. Four novel DCO-associated mutations were found in different families. In two additional DCO families, the previously described nonsense mutation (Arg195Stop) was detected. We conclude that mutations in the SHOX gene are the major factor in the pathogenesis of DCO. In a female proband with severe IMD and her unaffected sister, we detected an intrachromosomal duplication of the SHOX gene.     

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear Moloney leukemia virus 10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR, is generally applicable to any substitution-based inference problem in genomics.