Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil.

A bacterial strain named IGB-41(T) was isolated from a soil sample from an ant hill near Stuttgart, Germany. The strain was Gram-negative, rod-shaped, motile and facultatively anaerobic. Phylogenetic analysis based on 16S rRNA grouped the strain IGB-41(T) within the class Betaproteobacteria into the family Neisseriaceae together with Silvimonas amylolytica NBRC 103189(T), Silvimonas iriomotensis NBRC 103188(T) and Silvimonas terrae KM-45(T) as the closest relatives with sequence similarities of 96.7, 96.6 and 96.1 %, respectively. The G+C content of the genomic DNA was determined to be 61.5 mol% and quinone analysis revealed Q-8 as the only detectable quinone. Major cellular fatty acids were identified as C(16 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) and C(18 : 1)ω7c . Strain IGB-41(T) was unique in harbouring phosphoaminolipids, aminolipids and glycoaminolipids when compared with Silvimonas amylolytica NBRC 103189(T) in polar lipid analysis. On the basis of the physiological, phenotypic and genotypic characteristics of strain IGB-41(T), we suggest that the novel strain should be assigned to a new genus Amantichitinum and novel species Amantichitinum ursilacus. The type species of the genus Amantichitinum is Amantichitinum ursilacus and the type strain is IGB-41(T) (=DSM 23761(T) =CIP 110167(T)).

Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.

Since its development, microarray technology has evolved to a standard method in the biotechnological and medical field with a broad range of applications. Nevertheless, the underlying mechanism of the hybridization process of PCR-products to microarray capture probes is still not completely understood, and several observed phenomena cannot be explained with current models. We investigated the influence of several parameters on the hybridization reaction and identified ssDNA to play a major role in the process. An increase of the ssDNA content in a hybridization reaction strongly enhanced resulting signal intensities. A strong influence could also be observed when unlabeled ssDNA was added to the hybridization reaction. A reduction of the ssDNA content resulted in a massive decrease of the hybridization efficiency. According to these data, we developed a novel model for the hybridization mechanism. This model is based on the assumption that single stranded DNA is necessary as catalyst to induce the hybridization of dsDNA. The developed hybridization model is capable of giving explanations for several yet unresolved questions regarding the functionality of microarrays. Our findings not only deepen the understanding of the hybridization process, but also have immediate practical use in data interpretation and the development of new microarrays.