ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics

Modern and ancient amalgamated sandy meander‐belt deposits: recognition and controls on development

Amalgamated sandy meander belts and their deposits are common in modern continental and marine‐connected basins yet comprise a minor constituent of the reported fluvial rock record. This suggests that either amalgamated meander‐belts are uncommon in the rock record or that the recognition criteria are lacking to identify sandy meandering river deposits. To address this apparent discrepancy, the authors document the range and occurrence of amalgamated sandy meander belts (ASMB) from modern basins and the stratigraphic record. ASMB are widely distributed throughout both present and rock record sedimentary basins occurring in foreland, extensional, cratonic, strike‐slip and passive margin basins. They occur in all climatic settings ranging from tundra to hot deserts. Three specific occurrences of ASMB are recognised in modern basins: in the proximal to medial parts of distributive fluvial systems (DFS), as laterally‐confined belts that mainly form axial fluvial systems; and as valley‐confined meander belts that may infill bedrock, alluvial or coastal plain valleys. From the limited amount of rock record examples of ASMB that are available, it is clear that they occur in similar settings to those observed in modern basins, the recognition of which provides a framework for the further prediction and identification of ASMB in the rock record. The lack of recognition of ASMB in the rock record is considered to be due to an absence of characteristics that allow clear distinction between sandy meandering and braided fluvial deposits. Characteristics considered common to both include: multi‐storey, laterally extensive (sheet‐like) amalgamated channel belts, dominance of downstream accreting bedforms, no fining upwards grain‐size profile and little or no fine‐grained sediment and/or soil preservation. In contrast, features considered characteristic of meandering rivers such as inclined heterolithic stratification, high palaeocurrent dispersion, single storey channels and fining upwards grain‐size profiles are absent. The authors suggest that no single criterion can be used to definitively identify sandy meander belt deposits in the rock record and that a combination of systematic variations in accretion direction, palaeocurrent dispersal patterns and recognition of storey scale accretion surfaces is necessary to identify clearly this fluvial style. The common occurrence and distribution of sandy meander belts in modern sedimentary basins together with their limited recognition in the rock record suggests that their true stratigraphic distribution has yet to be determined. This has important implications for palaeogeographic reconstructions, understanding the impact of plant colonisation on fluvial planform style and predicting sandstone body dimensions and internal heterogeneity distribution within hydrocarbon reservoirs and aquifers