Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de

Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at and the GLYCOSCIENCES.de portal a

Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans

<p>Abstract</p> <p>Background</p> <p>There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance.</p> <p>Results</p> <p>The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties.</p> <p>Conclusion</p> <p>For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.</p

Structures of new acidic O-specific polysaccharides of the bacterium Proteus mirabilis serogroups O26 and O30

AbstractThe polysaccharide chains of the lipopolysaccharides of the Proteus mirabilis serogroups O26 and O30 were studied using sugar and methylation analysis and 1H and 13C NMR spectroscopy, including two-dimensional correlation spectroscopy and rotating-frame NOE spectroscopy. The polysaccharides were found to be acidic due to the presence of d-galacturonic acid and its amide with l-lysine in serogroup O26 or d-glucuronic acid in serogroup O30, and the structures of their tetrasaccharide repeating units were established. The O26-specific polysaccharide is structurally and serologically related to the O-specific polysaccharide of P. mirabilis O28, which includes amides of d-GalA with l-lysine and l-serine [Radziejewska-Lebrecht, J. et al. (1995) Eur. J. Biochem. 230, 705–712]

Новая электронная база данных по бактериальным углеводам (BCSDB)

A new free glycomic database (Bacterial Carbohydrate Structure Database) was established. It contains data on the structure, bibliography, NMR spectra, biochemical and other properties of all bacterial carbohydrates reported before 2006. The paper describes the database architecture and interface and BCSDB structure encoding language.Создана открытая структурная база данных по бактериальным углеводам. В работе освещается структура базы данных, ее интерфейс и специально разработанный язык линейной кодировки структур углеводов

Symbol Nomenclature for Graphical Representations of Glycans

ISSN:0959-665

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed