Dynamics of Stone Habitats in Coastal Waters of the Southwestern Baltic Sea (Hohwacht Bay)

Cobbles and boulders on the seafloor are of high ecological value in their function as habitats for a variety of benthic species, contributing to biodiversity and productivity in marine environments. We investigate the origin, physical shape, and structure of habitat-forming cobbles and boulders and reflect on their dynamics in coastal environments of the southwestern Baltic Sea. Stone habitats are not limited to lag deposits and cannot be sufficiently described as static environments, as different dynamic processes lead to changes within the physical habitat structure and create new habitats in spatially disparate areas. Dynamic processes such as (a) ongoing exposure of cobbles and boulders from glacial till, (b) continuous overturning of cobbles, and (c) the migration of cobbles need to be considered. A distinction between allochthonous and autochthonous habitats is suggested. The genesis of sediment types indicates that stone habitats are restricted to their source (glacial till), but hydrodynamic processes induce a redistribution of individual cobbles, leading to the development of new coastal habitats. Thus, coastal stone habitats need to be regarded as dynamic and are changing on a large bandwidth of timescales. In general, wave-induced processes changing the physical structure of these habitats do not occur separately but rather act simultaneously, leading to a dynamic type of habitat

EndoNet: an information resource about endocrine networks

EndoNet is a new database that provides information about the components of endocrine networks and their relations. It focuses on the endocrine cell-to-cell communication and enables the analysis of intercellular regulatory pathways in humans. In the EndoNet data model, two classes of components span a bipartite directed graph. One class represents the hormones (in the broadest sense) secreted by defined donor cells. The other class consists of the acceptor or target cells expressing the corresponding hormone receptors. The identity and anatomical environment of cell types, tissues and organs is defined through references to the CYTOMER(®) ontology. With the EndoNet user interface, it is possible to query the database for hormones, receptors or tissues and to combine several items from different search rounds in one complex result set, from which a network can be reconstructed and visualized. For each entity, a detailed characteristics page is available. Some well-established endocrine pathways are offered as showcases in the form of predefined result sets. These sets can be used as a starting point for a more complex query or for obtaining a quick overview. The EndoNet database is accessible at

XML schemas for common bioinformatic data types and their application in workflow systems

<p>Abstract</p> <p>Background</p> <p>Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.</p> <p>Results</p> <p>Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at <url>http://bioschemas.sourceforge.net</url>, the BioDOM library can be obtained at <url>http://biodom.sourceforge.net</url>.</p> <p>Conclusion</p> <p>The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.</p

TRANSPATH(®): an information resource for storing and visualizing signaling pathways and their pathological aberrations

TRANSPATH(®) is a database about signal transduction events. It provides information about signaling molecules, their reactions and the pathways these reactions constitute. The representation of signaling molecules is organized in a number of orthogonal hierarchies reflecting the classification of the molecules, their species-specific or generic features, and their post-translational modifications. Reactions are similarly hierarchically organized in a three-layer architecture, differentiating between reactions that are evidenced by individual publications, generalizations of these reactions to construct species-independent ‘reference pathways’ and the ‘semantic projections’ of these pathways. A number of search and browse options allow easy access to the database contents, which can be visualized with the tool PathwayBuilder™. The module PathoSign adds data about pathologically relevant mutations in signaling components, including their genotypes and phenotypes. TRANSPATH(®) and PathoSign can be used as encyclopaedia, in the educational process, for vizualization and modeling of signal transduction networks and for the analysis of gene expression data. TRANSPATH(®) Public 6.0 is freely accessible for users from non-profit organizations under

Circular structures on the seabed: differentiating between natural and anthropogenic origins—Examples from the Southwestern Baltic sea

Hydroacoustic observations of shallow marine environments reveal a variety of seafloor structures–both of natural and anthropogenic origin. Natural processes can result in features with circular geometries on the seafloor, such as kettles, sinkholes or iceberg pits, but human activities such as dredging, dumping, or detonating explosives can also cause similar shapes. Explaining the origin of these features is difficult if there are only few observations or if competing natural and anthropogenic processes have acted in the same area. Even though the location of dredging and dumping operations and munition blasting may be well documented in many parts of the global coastal ocean today, little information might be available about human practices in the past. In this study, more than 3,000 circular features were identified in side-scan sonar (SSS) datasets covering 1,549 km2 of shallow waters in the southwestern Baltic Sea. Additional data obtained by multibeam echosounder (MBES), sub-bottom profiler (SBP), and different SSS was considered in the analysis of 205 circular features that were characterized based on their sedimentology, morphology, SSS and SBP acoustic signatures. Characteristic differences between the structures allow their classification into six classes, which provide insight into their formation mechanisms. The obtained parameters (morphology, MBES and SSS acoustic backscatter, SBP characteristics and spatial distribution) allow the classification to be applied to the entire SSS dataset, resulting in the classification of 2,903 features. The mapped circular features have diameters between 6 and 77 m and correspond to pockmarks, dumping spots and explosion craters in water depths ranging from 8 m up to 25 m. Despite this rather multi-methodological approach, the origin of some observed features still cannot be explained with certainty, leaving room for further investigations of natural processes and human impacts on the seafloor

A Novel Modular Antigen Delivery System for Immuno Targeting of Human 6-sulfo LacNAc-Positive Blood Dendritic Cells (SlanDCs)

Previously, we identified a major myeloid-derived proinflammatory subpopulation of human blood dendritic cells which we termed slanDCs (e.g. Schäkel et al. (2006) Immunity 24, 767-777). The slan epitope is an O-linked sugar modification (6-sulfo LacNAc, slan) of P-selectin glycoprotein ligand-1 (PSGL-1). As slanDCs can induce neoantigen-specific CD4+ T cells and tumor-reactive CD8+ cytotoxic T cells, they appear as promising targets for an in vivo delivery of antigens for vaccination. However, tools for delivery of antigens to slanDCs were not available until now. Moreover, it is unknown whether or not antigens delivered via the slan epitope can be taken up, properly processed and presented by slanDCs to T cells.Single chain fragment variables were prepared from presently available decavalent monoclonal anti-slan IgM antibodies but failed to bind to slanDCs. Therefore, a novel multivalent anti-slanDC scaffold was developed which consists of two components: (i) a single chain bispecific recombinant diabody (scBsDb) that is directed on the one hand to the slan epitope and on the other hand to a novel peptide epitope tag, and (ii) modular (antigen-containing) linker peptides that are flanked at both their termini with at least one peptide epitope tag. Delivery of a Tetanus Toxin-derived antigen to slanDCs via such a scBsDb/antigen scaffold allowed us to recall autologous Tetanus-specific memory T cells.In summary our data show that (i) the slan epitope can be used for delivery of antigens to this class of human-specific DCs, and (ii) antigens bound to the slan epitope can be taken up by slanDCs, processed and presented to T cells. Consequently, our novel modular scaffold system may be useful for the development of human vaccines