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Goker M.,German Collection of Microorganisms and Cell Cultures DSMZ | Grimm G.W.,Swedish Museum of Natural History | Auch A.F.,University of Tubingen | Aurahs R.,University of Tubingen | Kucera M.,University of Tubingen
Evolutionary Bioinformatics | Year: 2010

Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts.

Stackebrandt E.,German Collection of Microorganisms and Cell Cultures DSMZ
Trends in Microbiology | Year: 2010

Implementation of quality measures, compliance with the Convention on Biological Diversity (CBD), and adoption of latest bioinformatics tools are among the main steps to be taken by microbial culture collections in order to provide resources for the emerging area of the knowledge-based bioeconomy. These measures have to be introduced side by side with the deposition of increasingly phylogenetically and physiologically diverse microbiological organisms. However, the necessary expansion of human resources and infrastructure is moving slowly, if at all. Furthermore, considering that the vast majority of microbial isolates do not find their way into public collections, a strategy should be devised to encourage researchers to deposit a higher fraction of strains. It appears obvious that in order to make available an even broader range of diversity to users and researchers, collections will have to decide whether to diversify on a broad taxon spectrum of the hierarchic system, holding a small number of representatives per species, or to follow the route of focusing on in-depth holdings of selected groups of organisms, depending on existing taxonomic expertise. These decisions require a worldwide coordinated activity with the outcome to be made transparent to users in an emerging global network. © 2010 Elsevier Ltd.

Giesen U.,Physikalisch - Technische Bundesanstalt | Langner F.,Physikalisch - Technische Bundesanstalt | Mielke C.,Heinrich Heine University Dusseldorf | Mosconi M.,Physikalisch - Technische Bundesanstalt | Dirks W.G.,German Collection of Microorganisms and Cell Cultures DSMZ
Radiation Protection Dosimetry | Year: 2011

In an inter-disciplinary collaboration of Physikalisch-Technische Bundesanstalt (PTB), German Collection of Microorganisms and Cell Cultures (DSMZ) and Heinrich-Heine University, live-cell imaging has been established at the charged-particle microbeam facility of PTB. Candidate genes participating in DNA strand-break repair pathways such as PARP-1, MRE11, MSH2, MDC1 and p53BP1 have been modified to generate fluorescent fusion proteins. Using multi-cistronic expression vectors, stable genomic integration was achieved in HT-1080 fibroblasts. The aim of this study is to characterise and use these highly reliable cell lines for studying initial steps of DNA damage responses and kinetics of repair after microbeam irradiation with high- and low-linear energy transfer (LET) particles in living cells at physiological conditions. © The Author 2010. Published by Oxford University Press. All rights reserved.

Maletzki C.,University of Rostock | Schmidt F.,University of Rostock | Dirks W.G.,German Collection of Microorganisms and Cell Cultures DSMZ | Schmitt M.,University of Heidelberg | Linnebacher M.,University of Rostock
European Journal of Cancer | Year: 2013

Purpose Microsatellite instability (MSI) resulting from loss of functional DNA mismatch repair was recently found in various haematological disorders. In coding sequences, MSI leads to frameshift mutations (FSMs) and the production of C-terminally altered proteins which are foreign to the immune system. Here, we wondered whether these frame-shifted peptide (FSP) sequences represent tumour-specific antigens also for MSI+ leukaemia and lymphomas (L/L). Material and methods A total of 33 coding region microsatellites were examined in MSI+ L/L cell lines for the presence of FSMs. Thereafter, recognition of MSI+ cells by established FSP-specific CD8+ T cell lines was quantified using interferon (IFN)-γ enzyme-linked immunospot (ELISpot) assays. In each experiment, MSI+ L/L cell lines and T2 targets exogenously loaded with the cognate peptide (=internal control) were employed. Supplementary, lytic activity towards tumour cells was analysed by standard chromium release assay (51Cr). Results Mutational profiling of 33 coding microsatellite loci in nine MSI+ L/L cell lines revealed instability in at least nine microsatellites. In each cell line, a distinct mutational profile was observed. Only three of the 33 loci were stable. FSP-specific and human leukocyte antigen-A2 (HLA-A2)-restricted T cells specifically recognised MSI+ L/L cells endogenously expressing TGFβRII (-1), Caspase 5 (-1) and MSH3 (-1) in ELISpot assays. Moreover, specific killing of Caspase 5 (-1) and MSH3 (-1) expressing L/L cell lines was achieved in functional cytotoxicity assays. Conclusion Data presented here expand the importance of FSPs as shared and general tumour-specific antigens. Consequently, they open new avenues for specific immunotherapies not only for solid but also for MSI+ haematological malignancies. © 2013 Elsevier Ltd. All rights reserved.

Arp G.,University of Gottingen | Bissett A.,Max Planck Institute for Marine Microbiology | Bissett A.,CSIRO | Brinkmann N.,University of Gottingen | And 12 more authors.
Geological Society Special Publication | Year: 2010

To understand mechanisms of tufa biofilm calcification, selected karstwater stream stromatolites in Germany have been investigated with regard to their hydrochemistry, biofilm community, exopolymers, physicochemical microgradients, calcification pattern and lamination. In stream waters, CO2 degassing drives the increase in calcite saturation to maximum values of approximately 10-fold, independent from the initial Ca2+/alkalinity ratio. For the cyanobacteria of tufa biofilms, a culture-independent molecular approach showed that microscopy of resinembedded biofilm thin sections underestimated the actual diversity of cyanobacteria, i.e. the six cyanobacteria morphotypes were opposed to nine different lineages of the 16S rDNA phylogeny. The same morphotype may even represent two genetically distant cyanobacteria and the closest relatives of tufa biofilm cyanobacteria may be from quite different habitats. Diatom diversity was even higher in the biofilm at the studied exemplar site than that of the cyanobacteria, i.e. 13 diatom species opposed to 9 cyanobacterial lineages. The non-phototrophic prokaryotic biofilm community is clearly different from the soil-derived community of the stream waters, and largely composed of flavobacteria, firmicutes, proteobacteria and actinobacteria. The exopolymeric biofilm matrix can be divided into three structural domains by fluorescence lectin-binding analysis. Seasonal and spatial variability of these structural EPS domains is low in the investigated streams. As indicated by microsensor data, biofilm photosynthesis is the driving mechanism in tufa stromatolite formation. However, photosynthesis-induced biofilm calcification accounts for only 10-20% of the total CaCa2+ loss in the streams, and occurs in parallel to inorganic precipitation driven by CO2-degassing within the water column and on biofilm-free surfaces. Annual stromatolite laminae reflect seasonal changes in temperature and light supply. The stable carbon isotope composition of the laminae is not affected by photosynthesis-induced microgradients, but mirrors that of the bulk water body only reflecting climate fluctuations. Tufa stromatolites with their cyanobacterial-photosynthesis-related calcification fabrics form an analogue to porostromate cyanobacterial stromatolites in fossil settings high in CaCO3 mineral supersaturation but comparatively low in dissolved inorganic carbon. Here, the sum-effect of heterotrophic exopolymerdegradation and secondary Ca2+-release rather decreases calcite saturation, contrary to settings high in dissolved inorganic carbon such as soda lakes. © The Geological Society of London 2010.

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