BackgroundInternational fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.Methodology/Principal FindingsThis study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Conclusions/SignificanceBased on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

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DNA microarrays are currently in use almost exclusively as research tools for gene expression analysis and their application for the identification of organisms is still in its infancy, only documented by a few studies on mammals, bacteria, and viruses. The "Fish & Chips" project aims to demonstrate that DNA chips can be a new innovative tool for the identification of marine animals and phytoplankton. To achieve this goal, fishes, invertebrates, and phytoplankton were sampled in European seas and taxonomically classified. Fragments of their mitochondrial 16S, cyt b, and COI genes and from the nuclear 18S genes were sequenced and served as molecular markers to enable probe design for the microarrays. An on-line data base containing the sequences and all relevant information of the samples has been implemented. A first prototype of a "Fish Chip",is based on more than 400 sequences from the 16S rRNA gene belonging to 46 species. A second microarray prototype serves to identify flatfishes from the North Sea based on COIand 16S sequences from 70 individuals of 17 fish species. A "Phytoplankton Chip" is now available with probes for all microalgal classes and many toxic species, as well as a "Invertebrate Chip". The results show that this approach is feasible.

The State and University Library Bremen (SuUB) is dedicated to the digitization of its historical collections. Digitization is an important instrument for improving the accessibility of valuable information contained in fragile historical documents. It facilitates academic research and teaching and is indispensable to the digital humanities. Especially the research of digital serial publications benefits from ‘recent systematic digitization efforts, often initiated by libraries […]. More and more historical periodicals and other serial publications are now digitally available in full, i.e., all of their issues’ [Piotrowski, this volume]. The historical journal presented in this article is one of these and the final section will discuss why it can be considered a complete corpus. Usually, digitization projects produce digital images, metadata for cataloguing and web-navigation purposes and OCR full text for searching. This information is made available through the library's web portal for digital collections. However, digital humanists need high-quality full texts enriched with metadata in the appropriate format to analyse them with powerful software tools. The historical journal Die Grenzboten serves as an exemplary model to bridge the gap between digitization projects in libraries and research infrastructures. Die Grenzboten is a long running serial publication (1841 – 1922). It can be classified as a literary journal that also covered politics and arts. We demonstrate that OCR post correction and a page-wise structuring are prerequisites for the creation of a high-quality TEI version of a full text. The TEI version was created in cooperation with the Deutsches Textarchiv (DTA) at the Berlin-Brandenburg Academy of Sciences and Humanities (BBAW). A fully automated OCR post correction developed at the SuUB Bremen is freely available on GitHub. To enable scientists to work with powerful software tools the transfer of high-quality full texts to research infrastructures is a necessary step. We describe transfers of full text and the experience we have made, but still some general questions persist: What has to be done to prepare raw OCR output for this purpose in a reasonable and cost-effective manner? What quality is needed or expected? Which metadata and file formats are needed? Should there not be a closer cooperation between research infrastructures and libraries handling the digitization? OCR full texts, even post corrected, are not perfect but character recognition rates around 99% certainly provide more options than just being used as a search index. There is a vast amount of textual resources available ready to be made fully accessible for scientific research! Finally, some suggestions for scholars and the researchers working on digital serial publications are given.